Systematic analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum L． leaves
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Rheum Palmatum
TISSUE(S): Leaf
SUBMITTER: 
Xianliang Ma
LAB HEAD: Jinzhe Du
PROVIDER: PXD026307 | Pride | 2021-05-29
REPOSITORIES: Pride
Similar Datasets
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
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.
2021-06-10 | PXD020790 | Pride
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
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.
2021-09-09 | PXD020819 | Pride
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 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.
2022-09-20 | PXD036505 | Pride
Project description:Aspergillus fumigatus is the main culprit of invasive aspergillosis, which has a high mortality rate in immunocompromised patients. 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 A. fumigatus. 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 A. fumigatus. We identified 3494 Khib-modified proteins with 18091 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 amino acids and nucleocytoplasmic transport – of which the ribosome pathway is the most affected pathway. When compared with other reported Khib eukaryotes, both Khib-modified sites and Khib-modified proteins also remained the highest. It proves that this modification is of great importance in A. fumigatus. At the same time, several enzymes in the fungal ergosterol synthesis pathway are modified with Khib. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and the process of fungal resistance. Findings in this study may provide new insights for studying PTM-associated mechanisms in fungal development and antifungal drug development.
2024-01-26 | PXD041490 | Pride
Project description:Lysine 2-hydroxyisobutyrylation (Khib) is an evolutionary conserved and widespread protein posttranslational modification (PTM) that has diverse cellular functions. Recently, it has been demonstrated that Khib can be regulated by p300 and Tip60. Although the specific Khib substrates mediated by p300 has been revealed, how Tip60 regulates diverse cellular processes through the Khib pathway and the different roles between Tip60 and p300 towards regulating Khib remains largely unknown, which hinders our understanding of the mechanisms by which this modification exerts its biological functions. Here we report the first Khib proteome mediated by Tip60. A total of 2999 unique Khib sites on 956 proteins were identified. Among them, 397 Khib sites from 322 proteins presented only in Tip60 overexpressing cells and 10 Khib sites increased greater than 2-fold in response of Tip60 overexpression, indicating that Tip60 significantly affected global Khib . Surprisingly, only 5 of the 407 Tip60-targeted Khib sites overlapping with the 149 known p300-targeted Khib sites, indicating that Tip60 and p300 have different substrate preference for Khib. In addition, the Khib substrates regulated by Tip60 are deeply involved in processes such as mRNA translation and protein co-folding, and some are associated with diseases such as Parkinson. Together, this study reveals the Khib substrates in response to Tip60, which elucidates the role of Tip60 in regulating various cellular processes through Khib pathway, and provides new insights into functional mechanism of Tip60.
2022-02-22 | PXD029297 | Pride
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
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
Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation in eukaryotes, but its prevalence and genomic function in higher plants remain unclear. Using mass spectrometry, we identified histone lysine 2-hydroxyisobutyrylation in Arabidopsis
2021-06-09 | PXD018017 | Pride