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Mass spectrometry identification of PPARγ methylation sites

ABSTRACT: Purified recombinant PPARγ-Flag and PRMT4-His were used for in vitro methyltransferase assay.We separated purified methylated PPARγ proteins by SDS-PAGE, visualized them by staining with Coomassie blue, protein lanes were cut into pieces about 1 mm3, and followed further destained.

ORGANISM(S): Homo Sapiens

SUBMITTER: Kai Huang

PROVIDER: PXD034929 | iProX | Mon Jun 27 00:00:00 BST 2022

REPOSITORIES: iProX

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PRMT4 Facilitates White Adipose Tissue Browning and Thermogenesis by Methylating PPARγ.

Zhong Yi Y Wang Yilong Y Li Xiaoguang X Qin Haojie H Yan Shu S Rao Caijun C Fan Di D Liu Duqiu D Deng Fei F Miao Yanli Y Yang Ling L Huang Kai K Huang Kai K

Diabetes 20230801 8

Obesity is a global health threat, and the induction of white adipose tissue (WAT) browning presents a promising therapeutic method for it. Recent publications revealed the essential role of protein arginine methyltransferase 4 (PRMT4) in lipid metabolism and adipogenesis, but its involvement in WAT browning has not been investigated. Our initial studies found that the expression of PRMT4 in adipocytes was upregulated in cold-induced WAT browning but downregulated in obesity. Besides, PRMT4 over ...[more]

PMID: 37216643

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Project description:Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the SAM-auxotrophic Saccharomyces cerevisiae based on the online multidimensional μHPLC/MS/MS technology. We identified 117 methylated proteins, containing 182 methylation events associated with 174 methylation sites. About 90% of these methylation events were previously unknown. Our results indicated, 1) over 6% of the yeast proteome are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys >> Arg > Asp > Glu ≈ Gln ≈ Asp > His > Cys, 3) the methylation state on nitrogen center is largely exclusive, and 4) the methylated proteins are located mainly in nucleus/ribosome associated with translation/transcription and DNA/RNA processing. Our dataset is the most comprehensive methylproteome known-to-date of all living organisms, and should significantly contribute to the field of protein methylation and related research.

2020-01-27 | PXD000606 | Pride

TBK1 methylation site identification

Project description:Identification of TBK1 methylated residues by recombinant SETD4 protein

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NEDDylation promotes nuclear protein aggregation and protects the Ubiquitin Proteasome System upon proteotoxic stress

Project description:SILAC quantitative mass spectrometry analysis on protein aggregates induced upon heat shock. Two separate performed analysis: A) control siRNA cells (light) with siRNA NEDD8 cells (heavy) and B) control cells (light) with MLN4924 treated cells (heavy). In all conditions cells were heat shocked at 43oC before cell mixing and aggregate isolation. Samples were solubilised in 2xSDS Laemmli buffer, 50ug of protein were run for 15min on 4-12% precast NuPAGE and coomassie blue stained. Lanes were cut in 2 gel pieces before in gel trypsin digestion and mass spectrometry analysis.

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Transcriptome analysis of CARNMT1 knockout tissue

Project description:Histidine (His) residues are methylated in various proteins, but their roles and regulation mechanisms remain unknown. Here, we showed that CARNMT1, a known His methyltransferase of dipeptide carnosine (βAla-His), is the major protein His N-position-specific methyltransferase. ProSeAM labeling and proteomic analysis revealed that 52 His sites in 20 proteins underwent CARNMT1-mediated methylation. The consensus methylation site for CARNMT1 was identified as Cx(F/Y)xH, which is a C3H zinc finger (C3H-ZF) motif. CARNMT1-deficient and catalytically-inactive mutant mice showed embryonic lethality. Among the CARNMT1-target C3H-ZF proteins, RNA degradation mediated by Roquin and TTP was affected by CARNMT1 and its enzymatic activity. Furthermore, splicing factor, U2AF1’s 3’-splice site recognition was perturbed and pre-mRNA alternative splicing (AS) was also affected by CARNMT1 deficiency. These findings indicate that CARNMT1-mediated protein His methylation, which is essential for embryogenesis, plays roles in diverse aspects of RNA metabolism by targeting C3H-ZF-type RNA-binding proteins and modulating their functions, including pre-mRNA AS and regulation of mRNA degradation.

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