PXD001473

PXD001473 is an original dataset announced via ProteomeXchange.

Title	Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis
Description	Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 minutes and 12 hours. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. A total of 1,104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signalings, such as auxin and ABA signalings. Comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested BR signaling not only induces gene expression, but also change protein activation by phosphorylation via various kinases. Through a large-scale dynamic profile of phosphoproteome coupling bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified from our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.
HostingRepository	PRIDE
AnnounceDate	2016-08-10
AnnouncementXML	Submission_2016-08-10_07:14:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Li-Ling Lin
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-10 03:56:54	ID requested
⏵ 1	2016-08-10 07:14:05	announced

Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC, Juan HF, Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics, 16(1):533(2015) [pubmed]

curator keyword: Biological

submitter keyword: Brassinosteroid, Phosphorylation, Arabidopsis

Hsueh-Fen Juan
contact affiliation	Department of Life Science, National Taiwan University
contact email	yukijuan@ntu.edu.tw
lab head
Li-Ling Lin
contact affiliation	ntu
contact email	li.ling0306@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001473
     1. Label: PRIDE project
     2. Name: Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis