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 Glycine max

ABSTRACT: 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 leaf, 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 soybean 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 soybeanleaf.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Triticum Aestivum (wheat)

TISSUE(S): Leaf

SUBMITTER: Xianliang Ma

LAB HEAD: Geng Li

PROVIDER: PXD036505 | Pride | 2022-09-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	QE-HFX-Khib-1.raw	Raw
	QE-HFX-Khib-2.raw	Raw
	QE-HFX-_Khib-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

Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

2021-09-09 | PXD020819 | 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

Proteome analysis of lysine 2-hydroxyisobutyrylation in the peripheral blood of systemic lupus erythematosus patients

Project description:Systemic lupus erythematosus (SLE) is a complex autoimmune disease that affects multiple organs. Protein lysine modifications play important roles in gene regulation, transcription, metabolism and other biological processes. The lysine 2-hydroxyisobutyrylation(Khib) histone mark has recently been discovered as a novel protein modification. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of Khib peptides, we identified 156 upregulated proteins(fold change>1.5),124 downregulated proteins(fold change<1/1.5), including 220 Khib sites that were upregulated and 187 Khib sites that were downregulated. Our data demonstrate that proteins with Khib sites were localized in the cytoplasm. Functional enrichment analysis revealed that proteins with Khib sites are broadly involved in a wide range of biological processes, cellular components and molecular functions. The 03010 Ribosome pathways may exert important influence on the SLE pathogenic mechanism, according to a KEGG analysis. The functional analysis of Khib is of value for important future investigations of SLE pathogenesis.

2023-03-10 | PXD015351 | 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

Proteomic analysis of lysine 2-hydroxyisobutyryl in SLE reveals protein modification alteration in Complement and coagulation cascades and Platelet activation pathways

Project description:Post-translational modifications (PTMs) are considered to be an important factor in the pathogenesis of SLE. Lysine 2-hydroxyisobutyryl (Khib), as an emerging post-translational modification of proteins, is involved in some important biological metabolic activities. We compared the Khib levels of SLE patients and healthy controls based on liquid chromatography-tandem mass spectrometry, and then performed proteomic analysis. The results showed that Khib in SLE patients was up-regulated at 865 sites of 416 proteins and down-regulated at 630 sites of 349 proteins. The site abundance, distribution and function of Khib protein were further analyzed. Bioinformatics analysis showed that complement, coagulation cascade and platelet activation in immune-related pathways were significantly enriched, indicating that the differential modification proteins between them might affect SLE.

2023-10-24 | PXD040218 | Pride

Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of C. albicans. We identified 1438 Khib-modified proteins with 6659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.

2021-01-15 | PXD023013 | Pride

Proteomic analyses of lysine 2-hydroxyisobutyrylation in Fusarium graminearum in response to tebuconazole and carbendazim

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.

2022-04-04 | PXD022499 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum

Project description: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.

2021-03-29 | PXD024730 | 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