Crotonylome analysis of liver samples for normal and MASLD mice models
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus Rattus
SUBMITTER: 
Zhongtao Zhang
PROVIDER: PXD065361 | iProX | Tue Jun 24 00:00:00 BST 2025
REPOSITORIES: iProX
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Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. Here, we performed a global crotonylome analysis of rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were predicted to be associated with chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. Furthermore, to assess the relevance between histone Kcr and the genome, we performed a genomic localization analysis of histone Kcr by ChIP-seq analysis. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in genes, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedling. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
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Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. In addition, a genomic localization analysis of histone Kcr by ChIP-seq was performed to assess the relevance between histone Kcr and the genome. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in gene body, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedlings. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
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Project description: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.
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Project description:We generated a global crotonylome analysis of the leaves in Pinellia ternata. We found 4509 crotonylated sites on 1757 proteins totally, and three specific amino acids surrounding crotonylation sites were identified in Pinellia ternata: KcrF, K***Y**Kcr and Kcr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participate in the carbohydrate metabolism pathway, were modified also by lysine crotonylation.
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Project description:Lysine crotonylation (Kcr), a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kcr are unknown in B. cinerea or any other plant fungal pathogens. Here, we comprehensively evaluated the crotonylation proteome of B. cinerea and identified 3967 Kcr sites in 1041 proteins, of which contained in 9 types of modification motifs. Our results show that although the crotonylation were largely conserved, different organisms contained distinct crotonylated proteins with unique functions. Bioinformatic analysis demonstrated that the majority of crotonylated proteins were distributed in cytoplasm (35%), mitochondria (26%) and nucleus (22%). The identified proteins were found to be involved in various metabolic and cellular processes, such as cytoplasmic translation and structural constituent of ribosome. Particularly, 26 crotonylated proteins participated in the pathogenicity of B. cinerea, suggesting a significant role for Kcr in this process. Protein interaction network analysis demonstrated that a mass of protein interactions are regulated by crotonylation. These data represent the first report of the crotonylome of B. cinerea and provide a good foundation for further explorations of the role of Kcr in plant fungal pathogens.
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