Large-Scale Analysis of Protein Crotonylation Reveals Its Diverse Functions in Pinellia ternate
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Homo Sapiens (human) Pinellia Ternata
TISSUE(S): Leaf
SUBMITTER: 
Xianliang Ma
LAB HEAD: Weiwei Guo
PROVIDER: PXD033142 | Pride | 2022-07-31
REPOSITORIES: Pride
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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.
2022-04-13 | PXD033154 | Pride
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.
2020-09-07 | PXD019358 | Pride
Project description:In Homo sapiens, Streptococcus agalactiae is a common colonizer of the rectovaginal tract and a fundamental cause of neonatal and non-pregnant adults infectious diseases. It also causes infectious disease in fish which compromises food safety as well as possesses a zoonotic risk. Lysine crotonylation (Kcr) is a type of histone post-translational modifications discovered in 2011. Kcr dynamics are involved in active gene promoters and potential enhancers in yeast and mammalian. However, lysine crotonylation in S. agalactiae has not yet been studied. In the present study, we conducted the first proteome-wide profiling of Kcr in S. agalactiae and identified 241 Kcr sites on 675 proteins, representing the Kcr event in S. agalactiae. Bioinformatics analysis showed that 164 sequences were matched to a total of six definitively conserved motifs, and many of them were significantly enriched in metabolic processes, cellular process, and single-organism processes. Moreover, we found four crotonylation modified proteins predicted as quorum sensing system and virulence factors, which indicate the important role of PTM on bacterial QS system and virulence. These data represent the first report of a global crotonylation proteome and provide a promising starting point for further functional research of crotonylation in bacterial virulence in S. agalactiae.
2021-12-30 | PXD026445 | Pride
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.
2018-09-20 | PXD010376 | Pride
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.
2019-05-09 | PXD011610 | Pride
Project description:Lysine crotonylation of histone proteins is a newly identified post-translational modification with diversified cellular functions. However, there’s few reports on lysine crotonylation of non-histone proteins in fruit plant cells. By using high-resolution LC-MS coupled with highly sensitive specific immune-affinity antibody analysis, a whole crotonylation proteome analysis of Dendrobium huoshanese was performed. In total, 1,591 proteins with 4,725 lysine crotonylation sites were found, among them eleven conserved motifs have been identified. Bioinformatic analysis linked crotonylated proteins to multiple metabolic pathways, including secondary metabolites biosynthesis, transport and catabolism; energy production and conversion; carbohydrate transport and metabolism; and translation, ribosomal structure and biogenesis.
2021-11-29 | PXD028293 | Pride
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.
2018-07-23 | PXD008716 | Pride
Project description:LC-MS/MS was used to carry out the analysis of the crotonylome in C. albicans (Candida albicans) comprehensively in our study. Generally, 5242 specific crotonylated sites of 1584 crotonylated proteins were detected among 9038 proteins in C. albicans. The crotonylome involved in the regulation of metabolism through the bioinformatics analysis. Moreover, the crotonylated proteins related to biosynthesis and carbon metabolism were prevalence phenomenon. Moreover, a universal rule were found in crotonylated motifs: D/E were found in the position (+1, +2 or +3) and K/R were found in the position (+5 or +6) of the residue; A/E/F/G/P/W/Y were found in the -1 position and A/K/R were found in the position (-5, -6, -7 or -8) of the residue. As far as we know, crotonylated histone sites that screened in C. albicans of this study have not been reported before. Furthermore, a variety of connections in PPI (protein-protein interaction network) of ribosome, oxidative phosphorylation, nucleus and proteasome were modified by acetylation, succinylation and crotonylation. Sir2 inhibitor AK-1 was able to promote histone lysine crotonylation and non-histone lysine crotonylation.
2021-01-08 | PXD018848 | Pride
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.
2023-03-10 | PXD012966 | Pride
Project description:Histone lysine crotonylation (Kcr) is a newly discovered protein post-translational modification (PTM), which was detected from yeast to humans and is mainly related with active transcription. With the development of proteomics technologies, high abundance of non-histone proteins modified by Kcr was also found recently. Here, we first report that lysine Kcr also occurs on cytoplasmic and mitochondrial proteins in common wheat (Triticum aestivum L.). We identified 4,696 Lys-acetylated sites on 1,726 proteins which involved in a wide variety of biological processes, such as chromatin-associated processes, Calvin-Benson cycle, glycolysis, protein metabolism and transport, which representing the largest dataset of lysine acylation proteome reported in the plant kingdom. Interestingly, 98 proteins were involved in multiple processes of photosynthesis, suggesting an important role of lysine Kcr in processes. In addition, 21 potentially specific Kcr motifs in wheat were detected. The protein interaction network analysis revealed that diverse interactions are modulated by protein Kcr. The overlap between Kcr and acetylation (Kac) indicated that they may coordinately regulate the function of some proteins in common wheat. Futhermore, comparative analysis indicated that lysine Kcr is conserved between common wheat and Nicotiana tabacum. Taken together, this study provided the first global survey of Kcr in wheat, making a promising starting point for further functional analysis of Kcr in plants.
2023-07-20 | PXD008483 | Pride