PXD046531

PXD046531 is an original dataset announced via ProteomeXchange.

Title	Does protein-bound methionine sulfoxide provides a proteomic basis for ageing in beech seeds?
Description	Beech trees produce seeds irregularly, necessitating the storage of these seeds for forestation. Despite the acquisition of desiccation tolerance during development, beech seeds lose viability during long-term storage faster than orthodox-type seeds. Seeds stored for short (3 years) and long (20 years) periods under optimal conditions were compared. Aged seeds characterized with germination capacity reduced to 30% displayed increased membrane damage, manifested as electrolyte leakage and lipid peroxidation levels. Analyses have been based on embryonic axes containing higher levels of reactive oxygen species (ROS) and higher levels of protein-bound methionine sulfoxide (MetO) in aged seeds. Using gel-free shotgun proteomics, 3,949 proteins were identified and 2,442 were reliably quantified to indicate 25 proteins with upregulated abundance and 35 with downregulated abundance in beech seeds under long-term storage compared to those under short-term storage. Functional analyses based on gene ontology annotations revealed that nucleic acid binding activity (biological process), hydrolases (molecular function), ribosome organization or biogenesis and transmembrane transport (cellular processes), and ATP synthesis (pathway) were affected in aged seeds. To verify whether MetO the oxidative posttranslational modification of proteins reversed via the action of methionine sulfoxide reductase (Msr) enzymes is involved in ageing of beech seeds we identified 316 and reliably quantified 226 MetO-containing proteins, among which 9 and 19 exhibited significantly up- and downregulated MetO levels, respectively, in beech seeds under long-term storage. Several Msr isoforms were identified and recognized as MsrA1-like, MsrA4, MsrB5 and MsrB5-like in beech seeds. Only MsrA1-like displayed decreased abundance in aged seeds. We demonstrated that the loss of membrane integrity reflected in elevated abundance of membrane proteins had higher impact on seed ageing progress rather than MetO/Msr system.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:42:07.754.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046531
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sara Dufour
SpeciesList	scientific name: Fagus sylvatica; NCBI TaxID: 28930;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-31 06:34:20	ID requested
1	2024-05-23 00:58:11	announced
⏵ 2	2024-10-22 06:42:08	announced	2024-10-22: Updated project metadata.

10.6019/PXD046531;

Kalemba EM, Gevaert K, Impens F, Dufour S, Czerwoniec A, The association of protein-bound methionine sulfoxide with proteomic basis for aging in beech seeds. BMC Plant Biol, 24(1):377(2024) [pubmed]

10.1186/s12870-024-05085-6;

submitter keyword: longevity, methionine sulfoxide reductase, oxidative stress,Fagus sylvatica, seed storage

Ewa Marzena Kalemba
contact affiliation	Institute of Dendrology Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
contact email	kalemba@man.poznan.pl
lab head
Sara Dufour
contact affiliation	VIB-UGent
contact email	sara.dufour@vib-ugent.be
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/2024/05/PXD046531

PRIDE project URI

• PRIDE
  1. PXD046531
     1. Label: PRIDE project
     2. Name: Does protein-bound methionine sulfoxide provides a proteomic basis for ageing in beech seeds?