PXD039588

PXD039588 is an original dataset announced via ProteomeXchange.

Title	Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds
Description	Rice is a major component of the human diet and feeds more than 50 million people across the globe. Therefore, efforts are being made to improve the nutritional quality of rice seeds in order to make a super-rice cultivar rich in antioxidants and vitamins. We previously developed two rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that were highly rich in antioxidants and exhibited high levels of radical scavenging activities. However, the molecular mechanism underlying the color development and accumulation of different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi, and Super-jami seeds and compared with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes (ANOVA, Benjamini-Hochberg FDR ≤ 0.01, fold change ≥ 1.5). Functional annotation of the differentially modulated proteins led to the identification of a phytoene desaturase (PDS3) that was highly enriched in the red seeds and was decreased in the black seeds as compared to the control white seeds. PDS3 is involved in the conversion of phytoene to ζ-carotene which may be responsible for the accumulation of red color in red seeds. Moreover, black seeds seem to accumulate higher levels of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. In addition, proteins associated with lignin and tocopherol biosynthesis were found to be highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:03:35.171.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD039588
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sun Tae Kim
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-20 03:35:07	ID requested
1	2023-09-20 22:28:40	announced
2	2023-11-14 09:05:26	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:03:36	announced	2024-10-22: Updated project metadata.

10.1002/pmic.202300035;

Gupta R, Min CW, Jung JY, Ham TH, Jeon JS, Cho LH, Kwon SW, Kim ST, Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds. Proteomics, 23(12):e2300035(2023) [pubmed]

10.6019/PXD039588;

submitter keyword: pigmented seeds, proteomics, seeds,Rice

Sun Tae Kim
contact affiliation	Pusan National University, Miryang, South Korea
contact email	stkim5505@gmail.com
lab head
Sun Tae Kim
contact affiliation	Pusan National University
contact email	stkim5505@gmail.com
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/2023/09/PXD039588

PRIDE project URI

• PRIDE
  1. PXD039588
     1. Label: PRIDE project
     2. Name: Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds