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Landscape of the Regulatory Elements for Lysine 2-Hydroxyisobutyrylation Pathway

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: He Huang

LAB HEAD: Yingming Zhao

PROVIDER: PXD005414 | Pride | 2017-12-06

REPOSITORIES: Pride

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Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway.

Huang He H Luo Zhouqing Z Qi Shankang S Huang Jing J Xu Peng P Wang Xiuxuan X Gao Li L Li Fangyi F Wang Jian J Zhao Wenhui W Gu Wei W Chen Zhucheng Z Dai Lunzhi L Dai Junbiao J Zhao Yingming Y

Cell research 20171201 1

Short-chain fatty acids and their corresponding acyl-CoAs sit at the crossroads of metabolic pathways and play important roles in diverse cellular processes. They are also precursors for protein post-translational lysine acylation modifications. A noteworthy example is the newly identified lysine 2-hydroxyisobutyrylation (K<sub>hib</sub>) that is derived from 2-hydroxyisobutyrate and 2-hydroxyisobutyryl-CoA. Histone K<sub>hib</sub> has been shown to be associated with active gene expression in s ...[more]

PMID: 29192674

Similar Datasets

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

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

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

Quantitative Proteomics Reveals the role of Lysine 2-hydroxyisobutyrylation Pathway mediated by Tip60

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

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

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

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

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.

2021-06-10 | PXD020790 | Pride

human pancreatic cancer LC-MS/MS

Project description:selecte tissues from seven patients with pancreatic cancer and then investigated the Khib modification in them by using proteomics technology.

2022-12-02 | PXD029817 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in Glycine max

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