iSucc-PseAAC:基于集成机器学习的赖氨酸琥珀酰化修饰位点预测

赖氨酸琥珀酰化是一种新型的翻译后修饰,在蛋白质调节和细胞功能控制中发挥重要作用,所以准确识别蛋白质中的琥珀酰化位点是有必要的。传统的实验耗费物力和财力。通过计算方法预测是近段时间以来提出的一种高效的预测方法。本研究中,我们开发了一种新的预测方法iSucc-PseAAC,它是通过使用多种分类算法结合不同的特征提取方法。最终发现,基于耦合序列(PseAAC)特征提取下,使用支持向量机分类效果是最好的,并结合集成学习解决了数据不平衡问题。与现有方法预测效果对比,iSucc-PseAAC在区分赖氨酸琥珀酰化位点方面,更具有意义和实用性。     

琥珀酰化修饰参与癌症的研究进展

琥珀酰化是一种新型的翻译后修饰(post-translational modifications, PTM),是在琥珀酰辅酶A的介导下将一个负电荷四碳琥珀酰基转移到赖氨酸残基伯胺上的过程。近年来研究发现,琥珀酰化参与多种疾病的发生发展,尤其是可通过酶调节或者非酶方式参与癌症的发生发展。本文对相关调控机制(包括对代谢途径、组蛋白、肿瘤微环境、氧化还原稳态、DNA损伤及血管生成的调控)进行综述,从修饰组学角度探讨了癌症的发病机制,以期为推进癌症的预防治疗提供参考。     

综述与专论：运动与蛋白质酰化修饰的研究进展

除蛋白质乙酰化修饰外，近年来不同类型的酰化修饰被陆续发现。组蛋白赖氨酸的酰化修饰，影响转录作用于表观调节；非组蛋白的酰化修饰，广泛参与细胞分子生物学调控。研究表明，运动一方面调节物质代谢，改变体内代谢小分子水平，为酰化修饰提供丰富的供体；另一方面，运动时剧烈的氧化还原反应和激酶活性的变化，还能改变去酰化酶如sirtuins家族的表达与活性，调控酰化/去酰化修饰的动态平衡，影响生理和病理过程。运动对蛋白质酰化修饰的调节是运动改善代谢、促进健康和防治慢病的新机制。     

组蛋白赖氨酸酰化新修饰研究进展

蛋白质的翻译后修饰是细胞生命活动的基本形式之一,对蛋白质生物功能的发挥具有极为重要的影响,包括细胞的生长、分化、代谢等生命过程。赖氨酸酰化修饰是重要研究内容之一,其广泛参与细胞分化、细胞代谢等重要生理活动,成为生命科学领域研究热点。随着生物质谱的扫描速度、灵敏度、分辨率的不断提高,近几年来许多新的赖氨酸酰化修饰被研究者鉴定。该文总结了琥珀酰化、巴豆酰化、丙二酰化、戊二酰化、2-羟基异丁酰化、β-羟基丁酰化等新型赖氨酸酰化修饰的发现确证、修饰调控酶、底物鉴定和生理病理功能等方面的最新研究进展。     

非组蛋白巴豆酰化修饰的生物学功能研究进展

赖氨酸巴豆酰化是一种新近发现的蛋白质翻译后修饰类型,在基因表达、细胞代谢及疾病治疗等许多病理生理过程中都具有重要的调节意义,可能是潜在的药物新靶标。目前研究多关注于组蛋白巴豆酰化修饰,而非组蛋白巴豆酰化修饰的研究逐渐被重视。本文简要介绍非组蛋白巴豆酰化修饰的生物学功能及其在疾病中的作用,将有助于了解非组蛋白巴豆酰化修饰的功能和机制。     

蛋白质亚磺酰化修饰及其在生理和病理过程中的作用

细胞正常生理或病理过程中均伴随着活性氧(ROS)和活性氮(RNS)的产生，引起蛋白质半胱氨酸发生氧化翻译后修饰。亚磺酰化是氧化翻译后修饰中的一种，指ROS将蛋白质的巯基氧化成亚磺酰基(R-SOH)的过程，广泛存在于多种物种中。亚磺酰化修饰蛋白质的捕获、富集和修饰位点的确定目前仍极具挑战性。半胱氨酸亚磺酰化的检测方法主要包括基于转录因子Yap1和基于小分子化合物dimedone或bicyclo[6.1.0]nonyne的分子探针。在此基础上，研究人员通过偶联生物素等标签分子又设计出了更多便于富集亚磺酰化蛋白质的衍生物探针。将亚磺酰化蛋白质捕获和富集后，与LC-MS/MS等质谱分析技术联用，则可确定发生亚磺酰化修饰的半胱氨酸位点。近几年的研究表明，细胞信号通路中的许多蛋白质或酶都会发生亚磺酰化修饰，调控蛋白质功能、稳定性或催化活性，从而引起下游信号通路或代谢过程的变化，进而影响机体生理或病理状态。随着对蛋白质亚磺酰化修饰的深入研究，越来越多疾病的发生发展新机制被发现，靶向该修饰有望为疾病治疗提供新的策略。本文从蛋白质氧化修饰的过程和亚磺酰化修饰检测的方法入手进行阐述，总结了近几年亚磺酰化修...     

蛋白质的棕榈酰化修饰

棕榈酰化修饰是蛋白质翻译后脂质修饰的重要形式,是调控蛋白质的转运、稳定、定位和功能的重要机制,同时,棕榈酰化修饰还参与多种细胞生物学进程,与许多疾病的发生发展密切相关。本文主要就蛋白质棕榈酰化及其修饰酶与蛋白质功能、相关疾病的关系做一综述。     

蛋白质棕榈酰化修饰及其研究方法

蛋白质棕榈酰化是蛋白质翻译后脂质共价修饰的一种重要形式,对象主要是胞质蛋白质,对蛋白质功能产生多重影响。近年来由于相关新技术引入,对蛋白质棕榈酰化主要修饰酶及其对靶蛋白功能调节方面的研究已渐成为新热点。本文主要对近几年来蛋白质棕榈酰化修饰及其研究方法作了综述。     

植物细胞中蛋白脂酰化修饰的生物学功能

蛋白脂肪酰化修饰是蛋白翻译修饰的重要形式,在细胞信号转导、生长发育和代谢等过程中发挥着重要的作用。N-肉豆蔻酰化和S-酰化是脂肪酰化修饰的两种主要形式,长链的脂肪酸被共价结合到蛋白质上,使蛋白结构发生变化,从而影响细胞的一系列生理作用。近年来,相比于真菌和动物细胞中蛋白脂肪酰化修饰的功能研究而言,植物蛋白质脂酰化修饰及其生物学功能的研究相对较少,且两者并不完全相同,引起了研究人员的广泛关注。研究发现,植物蛋白质N-肉豆蔻酰化和S-酰化修饰过程中分别需要相对应的豆蔻酰基转移酶和S-酰基转移酶来催化,通过对两种转移酶缺失的突变体的研究发现,这两种酰基转移酶的活性与植物种子萌发、花期长短及表型正常化有关;N-肉豆蔻酰化和S-酰化蛋白通过疏水性的酰基键插入膜上相应的位置,进行膜锚定;参与调控植物生长、信号转导及免疫应答等过程。综述了近年来N-肉豆蔻酰化和S-酰化在植物细胞生物学功能中的研究进展,并对植物G蛋白偶联受体(GPCRs)脂质修饰在感知细菌信号分子N-酰基高丝氨酸内脂(AHLs)过程中的作用进行了讨论,旨在为采用遗传干预技术提高农作物生产、优质及抗逆提供理论指导。     

组蛋白的生物素酰化修饰

组蛋白修饰对基因表达的表观遗传学调控起着重要作用。组蛋白生物素酰化修饰是近年来新发现的一种组蛋白修饰,具有重要的生物学功能。有证据表明组蛋白生物素酰化在细胞增殖、DNA修复、维持基因组稳定等方面发挥作用。组蛋白的生物素酰化修饰是由羧化全酶合成酶与组蛋白直接相互作用的结果。本文主要介绍了组蛋白生物素酰化发现的过程,并对近年来在组蛋白生物素酰化催化机制和组蛋白生物素酰化功能方面的研究进展进行了综述,最后对组蛋白生物素酰化研究领域存在的问题进行了探讨。     

Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum)

Post-translational modification of proteins through lysine succinylation plays important regulatory roles in living cells. Lysine succinylation was recently identified as a novel post-translational modification in Escherichia coli, yeast, Toxoplasma gondii, HeLa cells, and mouse liver. Interestingly, only a few sites of lysine succinylation have been detected in plants to date. In this study, we identified 347 sites of lysine succinylation in 202 proteins in tomato by using high-resolution mass spectrometry. Succinylated proteins are implicated in the regulation of diverse metabolic processes, including chloroplast and mitochondrial metabolism. Bioinformatic analysis showed that succinylated proteins are evolutionarily conserved and involved in various cellular functions such as metabolism and epigenetic regulation. Moreover, succinylated proteins exhibit diverse subcellular localizations. We also defined six types of definitively conserved succinylation motifs. These results provide the first in-depth analysis of the lysine succinylome and novel insights into the role of succinylation in tomato, thereby elucidating lysine succinylation in the context of cellular physiology and metabolite biosynthesis in plants.     

A Qualitative Proteome-Wide Lysine Succinylation Profiling of Tea Revealed its Involvement in Primary Metabolism

Lysine succinylation of proteins has potential impacts on protein structure and function, which occurs on post-translation level. However, the information about the 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 a qualitative analysis to globally identify the lysine succinylation of proteins using high accuracy nano LC-MS/MS combined with affinity purification. As a result, a total of 142 lysine succinylation sites were identified on 86 proteins in tea leaves. The identified succinylated proteins were involved in various biological processes and a large proportion of the succinylation sites were presented on proteins in the primary metabolism, including glyoxylate and dicarboxylate metabolism, TCA cycle and glycine, serine and threonine metabolism. Moreover, 10 new succinylation sites were detected on histones in tea leaves. The results suggest that succinylated proteins in tea plants might play critical regulatory roles in biological processes, especially in the primary metabolism. This study not only comprehensively analyzed the lysine succinylome in tea plants, but also provided valuable information for further investigating the functions of lysine succinylation in tea plants.     

The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids

Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of acyl group donors. Lysine succinylation has a profound effect on the corresponding site within the protein, as it dramatically changes the charge of the residue. In eukaryotes, it predominantly affects mitochondrial proteins because the donor of succinate, succinyl-CoA, is primarily generated in the tricarboxylic acid cycle. Although numerous succinylated mitochondrial proteins have been identified in Saccharomyces cerevisiae, a more detailed characterization of the yeast mitochondrial succinylome is still lacking. Here, we performed a proteomic MS analysis of purified yeast mitochondria and detected 314 succinylated mitochondrial proteins with 1763 novel succinylation sites. The mitochondrial nucleoid, a complex of mitochondrial DNA and mitochondrial proteins, is one of the structures whose protein components are affected by succinylation. We found that Abf2p, the principal component of mitochondrial nucleoids responsible for compacting mitochondrial DNA in S. cerevisiae, can be succinylated in vivo on at least thirteen lysine residues. Abf2p succinylation in vitro inhibits its DNA-binding activity and reduces its sensitivity to digestion by the ATP-dependent ScLon protease. We conclude that changes in the metabolic state of a cell resulting in an increase in the concentration of tricarboxylic acid intermediates may affect mitochondrial functions.     

Identification of lysine succinylation as a new post-translational modification

Of the 20 ribosomally coded amino acid residues, lysine is the most frequently post-translationally modified, which has important functional and regulatory consequences. Here we report the identification and verification of a previously unreported form of protein post-translational modification (PTM): lysine succinylation. The succinyllysine residue was initially identified by mass spectrometry and protein sequence alignment. The identified succinyllysine peptides derived from in vivo proteins were verified by western blot analysis, in vivo labeling with isotopic succinate, MS/MS and HPLC coelution of their synthetic counterparts. We further show that lysine succinylation is evolutionarily conserved and that this PTM responds to different physiological conditions. Our study also implies that succinyl-CoA might be a cofactor for lysine succinylation. Given the apparent high abundance of lysine succinylation and the significant structural changes induced by this PTM, it is expected that lysine succinylation has important cellular functions.     

Succinylome Analysis Reveals the Involvement of Lysine Succinylation in the Extreme Resistance of Deinococcus radiodurans

Increasing evidence shows that the succinylation of lysine residues mainly regulates enzymes involved in the carbon metabolism pathway, in both prokaryotic and eukaryotic cells. Deinococcus radiodurans is one of the most radioresistant organisms on earth and is famous for its robust resistance. A major goal in the current study of protein succinylation is to explore its function in D. radiodurans. High‐resolution LC–MS/MS is used for qualitative proteomics to perform a global succinylation analysis of D. radiodurans and 492 succinylation sites in 270 proteins are identified. These proteins are involved in a variety of biological processes and pathways. It is found that the enzymes involved in nucleic acid binding/processing are enriched in D. radiodurans compared with their previously reported levels in other bacteria. The mutagenesis studies confirm that succinylation regulates the enzymatic activities of species‐specific proteins PprI and DdrB, which belong to the radiation–desiccation response regulon. Together, these results provide insight into the role of lysine succinylation in the extreme resistance of D. radiodurans.     

Quantitative Global Proteome and Lysine Succinylome Analyses Reveal the Effects of Energy Metabolism in Renal Cell Carcinoma

In light of the increasing incidence of renal cell carcinoma (RCC), its molecular mechanisms have been comprehensively explored in numerous recent studies. However, few studies focus on the influence of multi‐factor interactions during the occurrence and development of RCC. This study aims to investigate the quantitative global proteome and the changes in lysine succinylation in related proteins, seeking to facilitate a better understanding of the molecular mechanisms underlying RCC. LC‐MS/MS combined with bioinformatics analysis are used to quantitatively detect the perspectives at the global protein level. IP and WB analysis were conducted to further verify the alternations of related proteins and lysine succinylation. A total of 3,217 proteins and 1,238 lysine succinylation sites are quantified in RCC tissues, and 668 differentially expressed proteins and 161 differentially expressed lysine succinylation sites are identified. Besides, expressions of PGK1 and PKM2 at protein and lysine, succinylation levels are significantly altered in RCC tissues. Bioinformatics analysis indicates that the glycolysis pathway is a potential mechanism of RCC progression and lysine succinylation may plays a potential role in energy metabolism. These results can provide a new direction for exploring the molecular mechanism of RCC tumorigenesis.     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

低氧与铁代谢相关蛋白

氧和铁这两种元素对生命活动十分重要. 低氧诱导因子(hypoxia-inducible factors, HIFs)作为转录因子,参与一系列靶基因的表达调控以适应低氧. 铁参与 DNA合成、氧气运输、代谢反应等多种细胞活动,过量游离铁会通过Haber-Weiss或 Fenton反应产生毒性自由基. 细胞通过与铁吸收、存储和利用有关的多种铁代谢相 关蛋白之间的协同作用来维持铁稳态. 与铁稳态相关的一些基因是HIFs的靶基因或 者间接受低氧调控,包括转铁蛋白、转铁蛋白受体、二价金属转运体1、铁调素、膜 铁转运蛋白、血浆铜蓝蛋白、铁蛋白等,而胞内铁浓度的改变能影响HIFs的表达. 本文就低氧与铁代谢相关蛋白的关系,尤其是低氧对铁代谢相关蛋白的调节作一综 述.     

Succinylated Octopamine Ascarosides and a New Pathway of Biogenic Amine Metabolism in Caenorhabditis elegans

The ascarosides, small-molecule signals derived from combinatorial assembly of primary metabolism-derived building blocks, play a central role in Caenorhabditis elegans biology and regulate many aspects of development and behavior in this model organism as well as in other nematodes. Using HPLC-MS/MS-based targeted metabolomics, we identified novel ascarosides incorporating a side chain derived from succinylation of the neurotransmitter octopamine. These compounds, named osas#2, osas#9, and osas#10, are produced predominantly by L1 larvae, where they serve as part of a dispersal signal, whereas these ascarosides are largely absent from the metabolomes of other life stages. Investigating the biogenesis of these octopamine-derived ascarosides, we found that succinylation represents a previously unrecognized pathway of biogenic amine metabolism. At physiological concentrations, the neurotransmitters serotonin, dopamine, and octopamine are converted to a large extent into the corresponding succinates, in addition to the previously described acetates. Chemically, bimodal deactivation of biogenic amines via acetylation and succinylation parallels posttranslational modification of proteins via acetylation and succinylation of l-lysine. Our results reveal a small-molecule connection between neurotransmitter signaling and interorganismal regulation of behavior and suggest that ascaroside biosynthesis is based in part on co-option of degradative biochemical pathways.