Table_4_Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis.XLSX

BackgroundLysine succinylation is a newly identified posttranslational modification (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 S. epidermidis proteins has not been investigated.ObjectivesThe purpose of this study was to investigate the physiological and pathological processes of S. epidermidis at the level of PTM. Moreover, by analyzing previous succinylome datasets in various organisms, we tried to provide an in-depth understanding of lysine succinylation.MethodsUsing antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of S. epidermidis (ATCC 12228). Then, bioinformatics analysis was performed, including Gene Ontology (GO), KEGG enrichment, motif characterization, secondary structure, protein–protein interaction, and BLAST analysis.ResultsA total of 1557 succinylated lysine sites in 649 proteins were identified in S. epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes accounted for the most. 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.ConclusionWe performed the first comprehensive profile of succinylation in S. 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 (Data are available via ProteomeXchange with identifier PXD022866).

背景赖氨酸琥珀酰化作为一种新近发现的翻译后修饰（PTM），其存在范围广泛，从原核生物至真核生物均有涉及，并参与多种细胞过程，特别是在代谢过程中。表皮葡萄球菌作为一种皮肤共生菌，因其附着于医疗设备并形成生物膜而成为病原体，尤其在免疫抑制患者和新生儿中受到广泛关注。然而，赖氨酸琥珀酰化在表皮葡萄球菌蛋白中的意义尚未得到深入研究。目标本研究旨在从PTM层面探讨表皮葡萄球菌的生理和病理过程。此外，通过分析不同生物体中的先前琥珀酰化组数据集，我们试图对赖氨酸琥珀酰化有更深入的理解。方法利用抗体亲和富集结合LC-MS/MS分析，我们检测了表皮葡萄球菌（ATCC 12228）的琥珀酰化组。随后，进行了生物信息学分析，包括基因本体（GO）、KEGG富集、基序特征化、二级结构、蛋白质-蛋白质相互作用和BLAST分析。结果在表皮葡萄球菌（ATCC 12228）中鉴定出1557个琥珀酰化赖氨酸位点，分布于649种蛋白中。在这些琥珀酰化蛋白中，GO注释显示与代谢过程相关的蛋白所占比例最高。KEGG通路特征化表明，与糖酵解/糖异生和柠檬酸循环（TCA循环）通路相关的蛋白更易发生琥珀酰化。此外，鉴定出13个保守基序。保守基序KsuD在模型原核生物和真核生物中均有所保守。具有此基序的琥珀酰化蛋白在糖酵解/糖异生通路中高度富集。在群体感应系统中的关键酶S-核糖基同型半胱氨酸合酶中，鉴定出一个琥珀酰化位点（K144），这表明琥珀酰化可能在细菌过程中发挥调节作用。此外，通过BLAST分析预测表皮葡萄球菌中存在15种琥珀酰转移酶和18种脱琥珀酰化酶（擦除酶）。结论我们首次对表皮葡萄球菌的琥珀酰化进行了全面分析，阐述了琥珀酰化可能在能量代谢、QS系统及其他细菌行为中发挥的重要作用。本研究可能成为探究表皮葡萄球菌定植、致病性和感染潜在机制的基石，并为琥珀酰化对代谢过程可能产生的调控效应提供新的见解（数据可通过ProteomeXchange使用标识符PXD022866获取）。