Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum

ABSTRACT: Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring post-translational modification. The system Khib identification at proteomics level has been performed in various species and tissues to characterize the role of Khib in biological activities. However, the study of Khib in plant species is relatively less. In the present study, the first plant root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat with antibody immunoprecipitation affinity, high resolution mass spectrometry-based proteomics and bioinformatics analysis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Rheum Palmatum

TISSUE(S): Leaf

SUBMITTER: Xianliang Ma

LAB HEAD: Jinzhe Du

PROVIDER: PXD024730 | Pride | 2021-03-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DH-IP-1.raw	Raw
	DH-IP-2.raw	Raw
	DH-IP-3.raw	Raw
	txt.zip	Other

Items per page:

1 - 4 of 4

Similar Datasets

Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf

2021-06-10 | PXD020790 | Pride

Systematic analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum L． leaves

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered posttranslational modification (PTM). Its structure characterization and function illustration have been reported in some species. However, the study of Khib in plant species is still relatively limited.Rheum palmatum L. is a global important plant. In this study, the first wheat global Khib analysis was performed with leave tissues; with the purpose of uncover the possible biological and physiological role of Khib in Rheum palmatum L.growth and development. Antibody based affinity enrichment technique was used to capture the modified peptides and high resolution mass spectrometry combining bioinformatics was applied to detect and decipher the Khib sites and proteins.

2021-05-29 | PXD026307 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

2021-09-09 | PXD020819 | Pride

Global PTM Mapping for Lysine 2-hydroxyisobutyrylation in one Oryza Sativa Japonica sample

Project description:By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine 2-hydroxyisobutyrlome analysis was performed in Oryza Sativa. Altogether, 9916 lysine 2-hydroxyisobutyrylation sites in 2512 protein groups were identified. Intensive bioinformatic analysis was then carried out to annotate those lysine 2-hydroxyisobutyrylated targets, including protein annotation, functional classification, functional enrichment, functional enrichment-based cluster analysis, etc. Based on the results, further studies following the large-scale lysine 2-hydroxyisobutyrylome analysis were suggested.

2018-10-26 | PXD005986 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in Glycine max

2022-09-20 | PXD036505 | Pride

Proteome-wide analyses reveal the diverse functions of lysine 2-hydroxyisobutyrylation in Oryza sativa

Project 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.

2021-09-09 | PXD018778 | Pride

Landscape of the Regulatory Elements for Lysine 2-Hydroxyisobutyrylation Pathway

Project description:This project reported a comprehensive global lysine 2-hydroxyisobutyrylome that provided a dataset of 6548 reliable lysine 2-hydroxyisobutyrylation (Khib) sites on 1725 proteins in HeLa cells. This dataset represents the first Khib proteome in mammalian cell to date, and illustrates a broad landscape of the Khib pathway.

2017-12-06 | PXD005414 | Pride

Khib proteome in response to p300 KO

Project description:We used quantitative proteomics to characterize the p300-regulated lysine 2-hydroxyisobutyrylome in wild type (WT) and p300 knockout (KO) cells.

2018-07-11 | PXD008525 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring PTM, which is firstly discovered in histone. The system Khib detection at proteomics level has been performed in various species and tissues for the function and role characterization of Khib in biological activities. However, the Khib study in plant species is relatively less and the plant root, one of the critical plant organ, haven’t been studied. In the present study, the first root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat specie with antibody immunoprecipitation affinity and high resolution mass spectrometry-based proteomics. Bioinformatics analyses including function classification, subcellular location predication, gene ontology enrichment and pathway enrichment were conducted to demonstrate the roles of these Khib sites and proteins in wheat root. In total, 6328 Khib sites corresponding to 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution while cytoplasm was the primary subcellular compartment where Khib protein located. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways potentially were affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also the hotspots where protein Khib occurred. Our work illustrated the potential regulation role of Khib in wheat leaf physiology and biology, which could be used as a useful reference for Khib studies in plant leaf.

2021-06-08 | PXD020788 | Pride

Lysine 2-hydroxyisobutyrylatome profiling reveals extensive lysine 2-hydroxyisobutyrylation in common wheat

Project description:In this work, we first analyzed wheat (Triticum aestivum L.) lysine Khib sites by mass spectrometry. A total of 3,348 lysine modification sites from 1,047 proteins were identified in wheat seedlings. The identified Kcr proteins were discovered to be widespread. Bioinformatic data indicated these Kcr proteins involved in diverse biology and metabolic processes. Our data indicated that Khib is as dynamic as Kac and Khib changes in response to the deacetylase inhibitors Trichostatin A (TSA) and nicotinamide (NAM). We tested histone Khib and deacylation activities of several wheat HATs and HDACs using wheat Krnose EMS mutants. Finally, we confirmed lysine Khib on K206 of PGK was a regulatory modification using mustagenesis experiments and found that de-Khib impaired protein interactions of PGK. Our data demonstrate that the regulatory scope of lysine Khib is broad and comparable with that of other major PTMs. Wheat histone Khib are dynamically regulated by environmental cues and are likely to be removed by different mechanisms.

2022-12-31 | PXD012666 | Pride