PXD017085

PXD017085 is an original dataset announced via ProteomeXchange.

Title	Application of TurboID-mediated proximity labeling and phosphoproteomics for mapping a GSK3 kinase signaling network in Arabidopsis
Description	Transient protein-protein interactions (PPIs), such as those between posttranslational modifying enzymes and their substrates, play key roles in cellular regulation, but are difficult to identify. Here we demonstrate the application of enzyme-catalyzed proximity labeling (PL), using the engineered promiscuous biotin ligase TurboID, as a sensitive method for characterizing PPIs in signaling networks. We show that TurboID fused with the GSK3-like kinase BIN2 or a PP2A phosphatase biotinylate their known substrate, the BZR1 transcription factor, with high specifically and efficiency. We optimized the protocol of biotin labeling and affinity purification in transgenic Arabidopsis expressing a BIN2-TurboID fusion protein. Subsequent quantitative mass spectrometry (MS) analysis identified about three hundred proteins biotinylated by BIN2-TurboID more efficiently than the YFP-TurboID control. These include a significant subset of previously proven BIN2 interactors and a large number of new BIN2 interactors that uncover a broad BIN2 signaling network. Our study illustrates that PL-MS using TurboID is a powerful tool for mapping signaling networks in plants, and reveals broad roles of this GSK3-like kinase in cellular signaling and regulation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:46:25.895.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chuan-Chih Hsu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	biotinylated residue; phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-14 01:31:50	ID requested
1	2023-05-10 09:51:50	announced
⏵ 2	2023-11-14 08:46:27	announced	2023-11-14: Updated project metadata.

Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY, Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. Plant Cell, 35(3):975-993(2023) [pubmed]

submitter keyword: proximity labeling, TurboID, mass spectrometry, protein interactome, protein-protein interaction, GSK3 kinase, phosphoproteomics, plant, biotinylation

Zhi-Yong Wang
contact affiliation	Carnegie Institution for Science
contact email	zwang@carnegiescience.edu
lab head
Chuan-Chih Hsu
contact affiliation	Academia Sinica
contact email	without1102@gmail.com
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/2023/05/PXD017085

PRIDE project URI

• PRIDE
  1. PXD017085
     1. Label: PRIDE project
     2. Name: Application of TurboID-mediated proximity labeling and phosphoproteomics for mapping a GSK3 kinase signaling network in Arabidopsis