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A Qualitative Proteome-wide Lysine Succinylation Profiling of Tea Revealed Its Involvement in Primary Metabolism

ABSTRACT: Background: Lysine succinylation of proteins has potential impacts on protein structure and function, which occurred on post-translation level. However, the information about the lysine succinylation of proteins in tea plants is limited. In the present study, the significant signal of succinylation in tea plants was found by western blot. Subsequently, we performed qualitative analyses to globally identify lysine succinylation substrates by using high accuracy nano LC-MS/MS combined with affinity purification. Results: As a result, a total of 142 lysine succinylation sites were identified in 86 proteins. The identified succinylated proteins are involved in various biological processes and a large proportion of the succinylation sites are present on proteins in the primary metabolism pathway, including glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle and glycine, serine and threonine metabolism. Moreover, 10 new succinylated sites on histones were detected in tea plants either. Conclusions: These results suggested that succinylated proteins in tea plants might play critical regulatory roles in biological processes, especially in the primary metabolism. This study not only globally analysed the functional annotation of lysine succinylation in tea plants, but also provided valuable information for further investigating the functions of lysine succinylation in tea plants.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Camellia Sinensis

TISSUE(S): Seedling

SUBMITTER: lihuan Qin

LAB HEAD: Zhaotang Ding

PROVIDER: PXD011717 | Pride | 2022-02-23

REPOSITORIES: Pride

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Project description:Background Hypothyroidism is a common disease, and its molecular mechanism still needs further investigation. Succinylation, as a newly identified protein posttranslational modification, is found to be involved in various metabolisms and cellular processes. In the present study, we performed quantitative analysis of the lysine succinylome in the thyroid of rats with hypothyroxinemia. Methods Hypothyroxinemia was induced in rats through the administration of a high-fat diet and then the thyroid tissues were taken out for further analysis. Affinity enrichment and liquid chromatography-tandem mass spectrometry techniques were applied for the quantitative proteome and succinylome analyses, respectively. Bioinformatic analyses were performed to decipher the differentially expressed proteins and succinylated sites, including the gene ontology (GO) annotation-based classification, Wolfpsort-based subcellular localization prediction, Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional pathway enrichment, and conserved domains of protein and succinylation sites prediction. Finally, the mitochondrial oxygen consumption rates of human normal thyroid epithelial cells were measured to further verify the role of lysine succinylation in vitro. Results Overall, 3869 proteins were identified, among which 129 differentially expressed proteins were quantified. Downregulated expressed proteins were enriched in the thyroid hormone synthesis and thyroid hormone signaling pathways and were mainly localized to the mitochondria and ATPase complex. In addition, 685 lysine succinylation sites on 250 proteins were identified, of which 172 lysine succinylation sites on 104 proteins were obvious changed (7 upregulated on 5 proteins and 165 downregulated on 99 proteins). Decreased succinylated proteins were involved in diverse metabolic pathways and biological processes, including the tricarboxylic acid cycle (TCA cycle), cellular respiration, energy derivation by oxidation of organic compounds and aerobic respiration. Moreover, these decreased succinylated proteins were primarily localized to the mitochondria. Finally, OCRs related to basal respiration, ATP production and maximal respiration were markedly blunted in the normal thyroid epithelial cells treated with palmitic acid (all p < 0.05), and the changes were reversed when the cells were treated with palmitic acid and desuccinylase inhibitor together (all p < 0.05). Conclusions The thyroid differentially expressed proteins and changed succinylation levels played a potential role in the mitochondria-mediated energy metabolism in the HFD-induced hypothyroxinemia rat model.

Project description:Background: Lysine succinylation is a newly identified PTM, which exists widely from prokaryotes to eukaryotes and participates in various cellular processes, especially in the metabolic processes. Staphylococcus epidermidis is a commensal bacterium in the skin, which attracts more attention as a pathogen, especially in immunocompromised patients and neonates by attaching to medical devices and forming biofilms. However, the significance of lysine succinylation in proteins of Staphylococcus epidermidis has not been investigated. Materials and methods: Using antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of Staphylococcus epidermidis (ATCC®12228™). Then, bioinformatics analysis was performed, including Gene Ontology, KEGG enrichment, motif characterization, secondary structure, protein-protein interaction, and BLAST analysis. Results: A total of 1557 succinylated lysine sites in 649 proteins were identified in Staphylococcus epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes and binding activity accounted for the most based on the analysis of biological process and molecular function, respectively. KEGG pathway characterization indicated that proteins associated with the glycolysis/ gluconeogenesis, and citrate cycle (TCA cycle) pathway were more likely to be succinylated. Moreover, 13 conserved motifs were identified. The specific motif KsuD was conserved in model prokaryotes and eukaryotes. Succinylated proteins with this motif were highly enriched in the glycolysis/gluconeogenesis pathway. One succinylation site(K144) was identified in S-ribosylhomocysteine lyase, a key enzyme in the quorum sensing system, indicating the regulatory role succinylation may play in bacterial processes. Furthermore, 15 succinyltransferases and 18 desuccinylases(erasers) were predicted in S.epidermidis by BLAST analysis. Conclusions: We performed the first comprehensive profile of succinylation in Staphylococcus epidermidis and illustrated the significant role succinylation may play in energy metabolism, QS system, and other bacterial behaviors. This study may be a fundamental basis to investigate the underlying mechanisms of colonization, virulence, and infection of S. epidermidis, as well as provide a new insight into regulatory effects succinylation may lay on metabolic processes.

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A Qualitative Proteome-wide Lysine Succinylation Profiling of Tea Revealed Its Involvement in Primary Metabolism

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