PXD047713

PXD047713 is an original dataset announced via ProteomeXchange.

Title	Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase–Client (KiC) assay
Description	Plants are remarkable in their ability to adapt to changing environments, with receptor-like kinases (RLKs) playing a pivotal role in perceiving and transmitting environmental cues into cellular responses. Despite extensive research on RLKs from the plant kingdom, the function and activity (i.e., their substrates or “clients”) of many kinases remain uncharted. To validate a novel client prediction workflow and learn more about an important RLK, this study focuses on P2K1 (DORN1), which acts as a key receptor for extracellular ATP (eATP), playing a crucial role in plant stress resistance and immunity. We designed a Kinase-Client (KiC) assay library of 225 synthetic peptides, incorporating previously identified phosphorylation sites and novel predictions from a deep-learning phosphorylation site prediction model (MUsite) and a trained hidden Markov model (HMM) . Screening the library against purified P2K1, we identified 46 putative substrates, including 34 novel clients, 27 of which may be novel peptides, not previously identified experimentally. Gene Ontology (GO) analysis among phosphopeptide candidates revealed proteins associated with important biological processes in metabolism, structure development, and response to stress, as well as molecular functions of kinase activity, catalytic activity, and transferase activity. We offer efficient selection criteria for further in vivo experiments to confirm these discoveries. This approach not only expands our knowledge of P2K1's substrates and functions but also highlights effective prediction algorithms for identifying additional potential substrates. Overall, the results further support use of the KiC assay as a valuable tool in unraveling the complexities of plant phosphorylation and provide a foundation for predicting the phosphorylation landscape of plant species based on peptide library results.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:34:26.921.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gabriel Lemes Jorge
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	phosphorylated residue; monohydroxylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-11 07:52:43	ID requested
1	2024-03-25 10:19:38	announced
⏵ 2	2024-10-22 06:34:27	announced	2024-10-22: Updated project metadata.

10.3389/FPLS.2024.1372361;

submitter keyword: phosphopeptides, P2K1, in vitro screening,protein kinase, deep learning

Jay J. Thelen
contact affiliation	Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
contact email	thelenj@missouri.edu
lab head
Gabriel Lemes Jorge
contact affiliation	University of Missouri
contact email	glj2d5@umsystem.edu
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/2024/03/PXD047713

PRIDE project URI

• PRIDE
  1. PXD047713
     1. Label: PRIDE project
     2. Name: Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase–Client (KiC) assay