Dataset Information

The Role of CDYL-Regulated Crotonylation of RPA1 in Homologous Recombination-Mediated DNA Repair

ABSTRACT: Lysine crotonylation (Kcr) is a recently-identified protein short-chain acylation. We have previously reported that chromodomain Y-like transcription corepressor CDYL acts as a crotonyl-CoA hydratase and negatively regulates histone Kcr. However, the global crotonylome of CDYL-regulated Kcr on non-histone substrates remains unclear. Using proteome-wide quantitative Kcr analysis, we identified 14,311 Kcr sites across 3,734 proteins in HeLa cells, providing by far the largest crotonylome data set from a single study. Upon depletion of CDYL, 1,141 Kcr sites from 759 proteins were increased by more than 1.5 fold, and 933 Kcr sites from 528 proteins were decreased by more than 0.67 fold. Upregulated crotonylome alterations upon CDYL depletion include components from diverse cellular pathways such as RNA splicing, DNA replication, and amino acid metabolism. Specifically, CDYL regulates K88 and K379 of crotonylation on RPA1, which affects its binding to other DNA repair factors including BLM, DNA2L, RAD50 and WRN. We showed evidence that CDYL-mediated RPA1 crotonylation is critical for the homologous recombination (HR) repair of camptothecin (CPT)-induced DNA damage. Together, our results provide a broad lysine crotonylome in response to CDYL and shed new light on the role of RPA1 Kcr in DNA repair, implicating functional importance of Kcr on non-histone substrates in diverse cellular processes.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Whole Body

SUBMITTER: xiaonan fu

LAB HEAD: Jing Liang

PROVIDER: PXD013616 | Pride | 2020-04-02

REPOSITORIES: Pride

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Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair.

Yu Huajing H Bu Chen C Liu Yuncheng Y Gong Tianyu T Liu Xiaoping X Liu Shumeng S Peng Xiaojun X Zhang Wenting W Peng Yani Y Yang Jianguo J He Lin L Zhang Yu Y Yi Xia X Yang Xiaohan X Sun Luyang L Shang Yongfeng Y Cheng Zhongyi Z Liang Jing J

Science advances 20200313 11

Previously, we reported that chromodomain Y-like (CDYL) acts as a crotonyl-coenzyme A hydratase and negatively regulates histone crotonylation (Kcr). However, the global CDYL-regulated crotonylome remains unclear. Here, we report a large-scale proteomics analysis for protein Kcr. We identify 14,311 Kcr sites across 3734 proteins in HeLa cells, providing by far the largest crotonylome dataset. We show that depletion of CDYL alters crotonylome landscape affecting diverse cellular pathways. Specifi ...[more]

PMID: 32201722

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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.

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Dataset Information

The Role of CDYL-Regulated Crotonylation of RPA1 in Homologous Recombination-Mediated DNA Repair

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Publications

Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair.

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