PXD058130

PXD058130 is an original dataset announced via ProteomeXchange.

Title	Proteomics- and metabolomics-based analysis of the regulation of germination in Norway maple and sycamore embryonic axes
Description	Norway maple and sycamore belong to the Acer genus and produce desiccation-tolerant and desiccation-sensitive seeds, respectively. We investigated the seed germination process at the imbibed and germinated stages using metabolomic and proteomic approaches to determine why sycamore seeds germinate earlier and are more successful at establishing seedlings than Norway maple seeds under controlled conditions. Embryonic axes and embryonic axes with protruded radicles were analyzed at the imbibed and germinated stages, respectively. Among the 212 identified metabolites, 44 and 67 differentially abundant metabolites were found at the imbibed and germinated stages, respectively, in both Acer species. Higher levels of amines, growth and defense stimulants, including B vitamins, were found in sycamore. We identified 611 and 447 proteins specific to the imbibed and germinated stages, respectively, in addition to groups of proteins expressed at different levels. Functional analysis of significantly regulated proteins revealed that proteins with catalytic and binding activity were enriched during germination, and proteins possibly implicated in nitrogen metabolism and metabolite interconversion enzymes were the predominant classes. Proteins associated with the control of plant growth regulation and seed defense were observed in both species at both germination stages. Sycamore proteins possibly involved in abscisic acid signal transduction pathway, stress tolerance and alleviation, ion binding and oxygenase activities appeared to accompany germination in sycamore. We identified peptides containing methionine (Met) oxidized to methionine sulfoxide (MetO), and functional analyses of proteins with significantly regulated MetO sites revealed that translation, plant growth and development, and metabolism of nitrogen compounds were the main processes under Met/MetO redox control. We propose that higher levels of storage proteins and amines together with higher levels of B vitamins supported more efficient nitrogen utilization in sycamore, resulting in faster seedling growth. In conclusion, omic signatures identified in sycamore seem to predispose germinated sycamore seeds to better postgerminative growth.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_05:01:27.769.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD058130
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sara Dufour
SpeciesList	scientific name: Fagus sylvatica; NCBI TaxID: 28930; scientific name: Acer; NCBI TaxID: 4022;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-21 03:58:40	ID requested
⏵ 1	2025-05-07 05:01:28	announced

10.6019/PXD058130;

10.1093/treephys/tpaf003;

Kalemba EM, Dufour S, Gevaert K, Impens F, Meimoun P, Proteomics- and metabolomics-based analysis of the regulation of germination in Norway maple and sycamore embryonic axes. Tree Physiol, 45(2):(2025) [pubmed]

submitter keyword: seed physiology,Acer platanoides, vitamin B., metabolite profiling, redox status, Acer pseudoplatanus, methionine sulfoxide, posttranslational modification

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/2025/05/PXD058130

PRIDE project URI

• PRIDE
  1. PXD058130
     1. Label: PRIDE project
     2. Name: Proteomics- and metabolomics-based analysis of the regulation of germination in Norway maple and sycamore embryonic axes