PXD007979-1

PXD007979 is an original dataset announced via ProteomeXchange.

Title	Comparative Qualitative Phosphoproteomics Analysis Identifies Shared Phosphorylation Motifs and Associated Biological Processes in Flowering Plants
Description	In this work we carried out a comparative bioinformatics analysis of pre-existing phosphoproteomics data in the public domain: PXD000033 and PXD000421 (Arabidopsis. thaliana) and PXD002222 and PXD000923 (O. sativa; rice). The aim of the analysis was to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. From data set re-analysis, we identified 6,537 phosphopeptides from 3,189 phosphoproteins in Arabidopsis and 2,307 phosphopeptides from 1,613 phosphoproteins in rice. The relative abundance ratio of serine, threonine, and tyrosine phosphorylation sites in rice and Arabidopsis were highly similar: 88.3: 11.4: 0.4 and 86.7: 12.8: 0.5, respectively. In addition, tyrosine phosphorylation shows features different from those of the serine and threonine phosphopeptides and was found to be more frequent in doubly-phosphorylated peptides in Arabidopsis. We identified protein sequence motifs in the two species to explore the similarities, finding nineteen pS motifs and two pT motifs that are shared in rice and Arabidopsis; among them are five novel motifs that have not previously been described in both species. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high conservation of these pathways. We also identified shared patterns of crosstalk between phosphoserines with motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid, in both species indicating this is an evolutionary conserved signaling mechanism in flowering plants.
HostingRepository	PRIDE
AnnounceDate	2018-04-13
AnnouncementXML	Submission_2018-04-13_03:55:14.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007979
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Da Qi
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Rice(O. sativa); NCBI TaxID: 4530;
ModificationList	iTRAQ4plex; Phospho; Methylthio; Deamidated; Oxidation; Acetyl; Carbamidomethyl
Instrument	LTQ Orbitrap Velos; TripleTOF 5600; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-17 05:43:55	ID requested
⏵ 1	2018-04-13 03:55:15	announced
2	2024-10-22 04:16:15	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Phosphoproteomics, Rice, Arabidopsis, Plants, Quanlitative

Andrew R Jones
contact affiliation	Institue of Integrative Biology, University of Liverpool
contact email	andrew.jones@liverpool.ac.uk
lab head
Da Qi
contact affiliation	University of Liverpool
contact email	ddq@liv.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007979
     1. Label: PRIDE project
     2. Name: Comparative Qualitative Phosphoproteomics Analysis Identifies Shared Phosphorylation Motifs and Associated Biological Processes in Flowering Plants