PXD032820

PXD032820 is an original dataset announced via ProteomeXchange.

Title	A high confidence Physcomitrium patens plasmodesmata proteome
Description	Cells of multicellular organisms exchange nutrients, building blocks and information. In animals this exchange happens via gap junctions, in plants via plasmodesmata (PD). PD have striking properties with a large range of molecules from ions, to metabolites and synthetic dyes, RNA and proteins up to 40 kDa being translocated, ranging. PD are hard to characterize due to deep embedding into cell walls and presence of several membranes. Previous studies of the protein composition of PD of angiosperms identified large lists of proteins, few were validated. Here, we developed a probabilistic scoring approach in iteration with systematic localization on a large scale to define a high-confidence PD proteome of Physcomitrium patens. Conservation of targeting allowed us to validate 100s of proteins in tobacco. We developed a PD Score based on protein enrichment during PD preparation and significantly enriched protein features of known PD proteins from literature. PD scoring was iteratively improved by extensive validation of PD candidate protein localizations. As a result we establish a high confidence PD proteome from Physcomitrium patens comprising close to 300 proteins which together with the bona fide PD proteins from literature are made available in the public PDDB database. Conservation in localization strengthens the reliability of plant proteome and provides a basis for exploring the evolution of this important organelle. Glycolyl hydrolase family 17 proteins are presented as example of an abundant PD protein family with representatives across an evolutionary scale.
HostingRepository	PRIDE
AnnounceDate	2024-01-19
AnnouncementXML	Submission_2024-01-18_20:21:07.521.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lin Xi
SpeciesList	scientific name: Physcomitrella patens subsp. patens (Moss); NCBI TaxID: 3218;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-26 14:15:21	ID requested
⏵ 1	2024-01-18 20:21:08	announced

10.1111/nph.18730;

Gombos S, Miras M, Howe V, Xi L, Pottier M, Kazemein Jasemi NS, Schladt M, Ejike JO, Neumann U, H, ä, nsch S, Kuttig F, Zhang Z, Dickmanns M, Xu P, Stefan T, Baumeister W, Frommer WB, Simon R, Schulze WX, A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution. New Phytol, 238(2):637-653(2023) [pubmed]

submitter keyword: plasmodesmata,Physcomitrium patens, proteome

Waltraud X. Schulze
contact affiliation	Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
contact email	wschulze@uni-hohenheim.de
lab head
Lin Xi
contact affiliation	University of Hohenheim
contact email	lin.xi.260@uni-hohenheim.de
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/2024/01/PXD032820

PRIDE project URI

• PRIDE
  1. PXD032820
     1. Label: PRIDE project
     2. Name: A high confidence Physcomitrium patens plasmodesmata proteome