PXD060844

PXD060844 is an original dataset announced via ProteomeXchange.

Title	STREAMLINE PROTOCOL FOR ARABIDOPSIS APOPLASTIC FLUID ISOLATION ENABLES A DETAILED PROTEOMIC VIEW OF THE EXTRACELLULAR SPACE SURROUNDING PLANT CELLS
Description	The apoplastic space surrounding plant cells, encompassing the cell well matrix, extracellular spaces and xylem, is the least understood compartment within plant tissues due to its lack of limiting membranes and its unavoidable damage upon tissue homogenization. Using a streamlined vacuum-infiltration/centrifugation protocol to enrich for the Arabidopsis apoplastic fluid (APF) combined with in-depth tandem mass spectrometry, we provide an improved view of its proteome that includes over 1,500 proteins possibly assigned to this compartment with minimized cytosolic contamination. Included are large and varied collections of hydrolytic activities devoted to cell wall metabolism, oxido-reductase reactions, cell-cell signaling, proteolysis, and pathogen protection via basal defense pathways. While numerous apoplast proteins were predicted to house N-terminal signal peptide sequences to direct extracellular secretion, a number did not, suggesting wide-spread use of non-classical export route(s). Among APF constituents are numerous pathogenesis-related proteins, glycosidases, subtilisin-type serine and aspartyl proteases, and the complement of subunits that assembles the core particle of the 26S proteasome. When this APF proteome is compared with those based on prior isolation methods, a consensus collection of 338 polypeptides emerges that offers a comprehensive view of the core APF proteome that manages the cell wall and interfaces with the environment.
HostingRepository	PRIDE
AnnounceDate	2025-03-28
AnnouncementXML	Submission_2025-03-28_13:36:13.763.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD060844
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kuo-En Chen
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-15 06:22:51	ID requested
⏵ 1	2025-03-28 13:36:14	announced

10.6019/PXD060844;

submitter keyword: apoplast,APF, mass spectrometary, proteomic, apoplastic fluid

Richard D. Vierstra
contact affiliation	Department of Biology, Washington University in St. Louis
contact email	rdvierstra@wustl.edu
lab head
Kuo-En Chen
contact affiliation	Department of Biology, Washington University in St. Louis
contact email	kuo-en@wustl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060844
     1. Label: PRIDE project
     2. Name: STREAMLINE PROTOCOL FOR ARABIDOPSIS APOPLASTIC FLUID ISOLATION ENABLES A DETAILED PROTEOMIC VIEW OF THE EXTRACELLULAR SPACE SURROUNDING PLANT CELLS