PXD039588 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2023-09-21 |
AnnouncementXML | Submission_2023-09-20_22:28:39.800.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD039588 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Sun TaeKim |
SpeciesList | scientific name: Oryza sativa (Rice); NCBI TaxID: 4530; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF |
Dataset History
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. |
Publication List
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; |
Keyword List
submitter keyword: pigmented seeds, proteomics, seeds,Rice |
Contact List
Sun TaeKim |
contact affiliation | Pusan National University, Miryang, South Korea |
contact email | stkim5505@gmail.com |
lab head | |
Sun TaeKim |
contact affiliation | Pusan National University |
contact email | stkim5505@gmail.com |
dataset submitter | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039588
- Label: PRIDE project
- Name: Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds