PXD002254

PXD002254 is an original dataset announced via ProteomeXchange.

Title	Using proteomics to understand seed development in Phaseolus vulgaris L.: developing resources to modulate seed quality traits
Description	Common bean (Phaseolus vulgaris L.) is the most consumed grain legume in developing countries in Latin America and Sub-Saharan Africa1. Like other legumes, common bean seeds are rich in protein, carbohydrates, fibers and other health-promoting phenolic compounds thus being vital for food security and income source for local small farmers2. Seed quality traits depend on accumulation of various storage molecules during the seed development (SD) process and influenced by the genotype and adaptive changes to environment3. Concerning common bean, there is still a lack of a deeper molecular knowledge of SD that is hampering the development of new biotech approaches for seed trait modulation and could timely address challenges of agriculture or industry. Our present work aims to unravel the molecular mechanisms underlying SD using a proteomic approach. To achieve this goal, we characterized SD in terms biomass, seed length and weight in the genotype SER16, one of the most promissory drought-resistant release of the CIAT-CGIAR. Seed samples were collected at the 4 main SD stages: Late-Embryogenesis (10 days after anthesis, d.a.a.), Early (20 d.a.a.) and Late Maturation (30 d.a.a.) and Desiccation (40 d.a.a.). The analysis of bean proteome was conducted using a gel-free proteomic analysis (LC-MS/MS) under the scope of EU-FP7-PRIME-XS project. A total of 410 unique proteins were differentially expressed throughout the 4 major seed development stages, in which most of the identified proteins belong in the ‘protein metabolism’ (31,98%) functional category, that includes synthesis, regulation, folding. Other functional categories are represented such as carbohydrate and lipid metabolism (11,26%) and stress/defense and redox metabolism (11,04%). We identified 93 proteins were unique to the first (10-20 d.a.a.), 22 to the second (20-30 d.a.a.) and 40 to the last (30-40 d.a.a.) phase transition, reflecting the major biological processes occurring at this specific seed developmental stage. This study will contribute to reveal key metabolic pathways and mechanisms with potential role in modulating common bean seed development and quality traits.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:24:50.700.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jamila Bouraada
SpeciesList	scientific name: Phaseolus vulgaris (Kidney bean) (French bean); NCBI TaxID: 3885;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-05-29 07:20:29	ID requested
1	2018-01-05 01:38:23	announced
⏵ 2	2024-10-22 04:24:59	announced	2024-10-22: Updated project metadata.

10.1016/j.dib.2015.07.037;

Trapp J, Almunia C, Gaillard JC, Pible O, Chaumot A, Geffard O, Armengaud J, Data for comparative proteomics of ovaries from five non-model, crustacean amphipods. Data Brief, 5():1-6(2015) [pubmed]

ProteomeXchange project tag: PRIME-XS Project

curator keyword: Biological

submitter keyword: seed trait modulation, metabolic pathways, seed quality,seed development, label-free

Maarten Altelaar
contact affiliation	Biomolecular Mass Spectrometry and Proteomics
contact email	m.altelaar@uu.nl
lab head
Jamila Bouraada
contact affiliation	Utrecht University
contact email	j.bouraada@uu.nl
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/2018/01/PXD002254

PRIDE project URI

• PRIDE
  1. PXD002254
     1. Label: PRIDE project
     2. Name: Using proteomics to understand seed development in Phaseolus vulgaris L.: developing resources to modulate seed quality traits