PXD036806

PXD036806 is an original dataset announced via ProteomeXchange.

Title	Application of proteomic characterization reveals protein accumulation mechanisms in embryo, endosperm, and bran of weedy rice varieties
Description	Rice grains are rich in starch but are deficient in proteins containing essential amino acids such as lysine and threonine. Therefore, efforts have been made to improve the nutritional value of rice by overexpressing the genes involved in lysine biosynthesis and/or suppression of lysine catabolism that led to the increased protein content in rice grains. Despite the economic and nutritional benefits rice, the protein accumulation mechanisms are largely elusive. Therefore, to explore the comprehensive proteome profiles, three different parts of rice grains including embryo, endosperm, bran were harvested from weedy rice cultivars (cv. Dharial) and its EMS mutant (DM) having 9.3 and 14.8% of protein content in rice grains, respectively. Here, we utilized a label-free quantitative proteomic analysis and this approach led to the identification of total 5,821 proteins. Of these, 322, 723, and 550 proteins revealed significant differences in their abundance in rice embryo, endosperm, and bran, respectively. Functional classification of identified proteins revealed that enrichment of proteins associated with nitrogen compound biosynthesis and transport, intracellular transport, localization, protein/amino acid synthesis, and photosynthesis, among others were observed in endosperm and bran of high protein mutant rice cultivar. Taken together, the current study uncovers the proteome changes and highlight the various functions of metabolic pathways associated with protein accumulation in rice.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:24.438.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sun Tae Kim
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 13:48:43	ID requested
1	2023-09-20 23:00:39	announced
⏵ 2	2023-11-14 09:05:29	announced	2023-11-14: Updated project metadata.

Min CW, Gupta R, Jung JY, Rakwal R, Kang JW, Cho JH, Jeon JS, Kim ST, Comparative Proteome-wide Characterization of Three Different Tissues of High-Protein Mutant and Wild Type Unravels Protein Accumulation Mechanisms in Rice Seeds. J Agric Food Chem, 71(32):12357-12367(2023) [pubmed]

submitter keyword: Weedy rice, Intracellular transport, EMS mutant

Proteomics, High-protein content, Label-free analysis

Sun Tae Kim
contact affiliation	Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
contact email	stkim5505@gmail.com
lab head
Sun Tae Kim
contact affiliation	Pusan National University
contact email	stkim5505@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD036806
     1. Label: PRIDE project
     2. Name: Application of proteomic characterization reveals protein accumulation mechanisms in embryo, endosperm, and bran of weedy rice varieties