Dataset Information

A proteomic analysis of lysine crotonylation in systemic lupus erythematosus patients

ABSTRACT: Posttranslational modification (PTM) refers to the process of the covalent processing of translated proteins, as well as the activities and functions of proteins, and it is involved in almost all cellular pathways and processes. Lysine crotonylation (Kcr) is a recently identified PTM and plays a key role in regulating various biological processes. In the present study, we performed a crotonylation proteome analysis in both Systemic lupus erythematosus(SLE) and normal control (NC) subjects using high resolution LC-MS/MS. We identified a total of 1109 lysine modification sites distributed on 347 proteins, including 417 crotonylated sites that were upregulated and 275 that were downregulated. By intensive bioinformatic analysis, our data proved that subcellular locations of crotonylated proteins include the cytoplasm, mitochondria, nucleus and extracellular regions. Kcr was related to multiple metabolism pathways, such as the focal adhesion, PI3K-Akt signaling, salmonella infection, cell cycle, hypertrophic cardiomyopathy (HCM), neurotrophin signaling, natural killer cell-mediated cytotoxicity, malaria, Hippo signaling and legionellosis pathways, while downregulated Kcr proteins were related to carbon metabolism, biosynthesis of amino acids, glutathione metabolism, complement and coagulation cascades and the pentose phosphate pathway. Several Kcr proteins related to focal adhesion have also been discussed. Enrichment analysis using Gene Ontology (GO) revealed that the Kcr proteins were enriched in the platelet alpha granule lumen, actin filament binding and platelet degranulation classes. Protein domain enrichment analysis revealed that the 14-3-3, immunoglobulin-like fold, EF-hand and Ca-insensitive domains were enriched in Kcr proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: xiaomei li

LAB HEAD: Yong Dai

PROVIDER: PXD012966 | Pride | 2023-03-10

REPOSITORIES: Pride

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			Action	DRS
	7128TPCR_1.raw	Raw
	txt.zip	Other

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Publications

Proteomics analysis of lysine crotonylation and 2-hydroxyisobutyrylation reveals significant features of systemic lupus erythematosus.

Xie Ting T Dong Jingjing J Zhou Xianqing X Tang Donge D Li Dandan D Chen Jiejing J Chen Yumei Y Xu Huixuan H Xue Wen W Liu Dongzhou D Hong Xiaoping X Tang Fang F Yin Lianghong L Dai Yong Y

Clinical rheumatology 20220808 12

<h4>Introduction/objectives</h4>To seek significant features of systemic lupus erythematosus (SLE) by utilizing bioinformatics analysis.<h4>Method</h4>Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify lysine crotonylation (Kcr) and lysine 2-hydroxyisobutyrylation (Khib) in peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematosus (SLE) patients and normal controls.<h4>Results</h4>Seventy-six differentially modified proteins (DMPs) dually modified by ...[more]

PMID: 35941338

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Project description:Background: Lysine crotonylation (Kcr), as a novel evolutionarily conserved type of PTM, is ubiquitous and essential in cell biology. However, its functions in tea plant, an important beverage crop, are largely unknown. Our study firstly attempted to describe Kcr proteins in tea leaves under NH4+ deficiency/resupply, and provided significant insights into exploring the physiological role of Kcr in plants for N utilization. Results: We performed the global analysis of crotonylome in tea plants under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 kcr sites on 971 proteins were identified, of which contained in 15 types of Kcr motifs. Most of Kcr proteins were located in chloroplast and cytoplasm. 120 and 151 Kcr proteins were significantly changed at 3 hours and 3days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed Kcr proteins participated in diverse biological processes such as photosynthesis, carbon fixation and amino acid metabolism, suggesting Kcr plays important roles in these processes. Interestingly, a large number of enzymes were crotonylated, and the activity and Kcr level of these enzymes changed significantly after NH4+ resupply, indicating a potential function of Kcr in the regulation of enzyme activities. Moreover, the protein-protein interaction analysis revealed that the diverse interactions of identified Kcr proteins mainly involved in photosynthesis, carbon fixation, amino acid metabolism and ribosome. Conclusions: The results suggested that lysine crotonylated proteins might play regulating roles in metabolic process in tea leaves under NH4+ deficiency/resupply. The critical regulatory roles mainly involved in diverse aspects of primary metabolic processes, especially in photosynthesis, carbon fixation and amino acid metabolism. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine crotonylation in tea plants.