PXD018778

PXD018778 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide analyses reveal the diverse functions of lysine 2-hydroxyisobutyrylation in Oryza sativa
Description	Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. In this study, using LC-MS/MS qualitative proteomic strategies, we identified 4,163 Khib sites on 1,596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalks of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms. In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:27:19.776.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhiyun Gong
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-24 01:18:41	ID requested
1	2021-09-08 18:39:56	announced
⏵ 2	2024-10-22 05:27:27	announced	2024-10-22: Updated project metadata.

10.1186/s12284-020-00389-1;

Xue C, Qiao Z, Chen X, Cao P, Liu K, Liu S, Ye L, Gong Z, Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa. Rice (N Y), 13(1):34(2020) [pubmed]

submitter keyword: Oryza sativa

lysine 2-hydroxyisobutyrylation;photosynthesis;histone acylation

Zhiyun Gong
contact affiliation	Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
contact email	zygong@yzu.edu.cn
lab head
Zhiyun Gong
contact affiliation	Agricultural College of Yangzhou University
contact email	zygong@yzu.edu.cn
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/2021/09/PXD018778

PRIDE project URI

• PRIDE
  1. PXD018778
     1. Label: PRIDE project
     2. Name: Proteome-wide analyses reveal the diverse functions of lysine 2-hydroxyisobutyrylation in Oryza sativa