Formation of Nepsilon-(succinyl)lysine in vivo: a novel marker for docosahexaenoic acid-derived protein modification

SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm

Protein succinylation is a novel type of post-translational modification in recent decade years. It played an important role in biological structure and functions verified by experiments. However, it is time consuming and laborious for the wet experimental identification of succinylation sites. Traditional technology cannot adapt to the rapid growth of the biological sequence data sets. In this study, a new computational method named SuccSPred2.0 was proposed to identify succinylation sites in the protein sequences based on multifeature fusion and maximal information coefficient (MIC) method. SuccSPred2.0 was implemented based on a two-step strategy. At first, high-dimension features were reduced by linear discriminant analysis to prevent overfitting. Subsequently, MIC method was employed to select the important features binding classifiers to predict succinylation sites. From the compared experiments on 10-fold cross-validation and independent test data sets, SuccSPred2.0 obtained promising improvements. Comparative experiments showed that SuccSPred2.0 was superior to previous tools in identifying succinylation sites in the given proteins.

pSuc-FFSEA: Predicting Lysine Succinylation Sites in Proteins Based on Feature Fusion and Stacking Ensemble Algorithm

Being a new type of widespread protein post-translational modifications discovered in recent years, succinylation plays a key role in protein conformational regulation and cellular function regulation. Numerous studies have shown that succinylation modifications are closely associated with the development of many diseases. In order to gain insight into the mechanism of succinylation, it is vital to identify lysine succinylation sites. However, experimental identification of succinylation sites is time-consuming and laborious, and traditional identification tools are unable to meet the rapid growth of datasets. Therefore, to solve this problem, we developed a new predictor named pSuc-FFSEA, which can predict succinylation sites in protein sequences by feature fusion and stacking ensemble algorithm. Specifically, the sequence information and physicochemical properties were first extracted using EBGW, One-Hot, continuous bag-of-words, chaos game representation, and AAF_DWT. Following that, feature selection was performed, which applied LASSO to select the optimal subset of features for the classifier, and then, stacking ensemble classifier was designed using two-layer stacking ensemble, selecting three classifiers, SVM, broad learning system and LightGBM classifier, as the base classifiers of the first layer, using logistic regression classifier as the meta classifier of the second layer. In order to further improve the model prediction accuracy and reduce the computational effort, bayesian optimization algorithm and grid search algorithm were utilized to optimize the hyperparameters of the classifier. Finally, the results of rigorous 10-fold cross-validation indicated our predictor showed excellent robustness and performed better than the previous prediction tools, which achieved an average prediction accuracy of 0.7773 ± 0.0120. Besides, for the convenience of the most experimental scientists, a user-friendly and comprehensive web-server for pSuc-FFSEA has been established at https://bio.cangmang.xyz/pSuc-FFSEA, by which one can easily obtain the expected data and results without going through the complicated mathematics.

Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond

Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.

Histone succinylation and its function on the nucleosome

Protein post‐translational modifications (PTMs) of histones are ubiquitous regulatory mechanisms involved in many biological processes, including replication, transcription, DNA damage repair and ontogenesis. Recently, many short‐chain acylation histone modifications have been identified by mass spectrometry (MS). Lysine succinylation (Ksuc or Ksucc) is a newly identified histone PTM that changes the chemical environment of histones and is similar to other acylation modifications; lysine succinylation appears to accumulate at transcriptional start sites and to correlate with gene expression. Although numerous studies are ongoing, there is a lack of reviews on the Ksuc of histones. Here, we review lysine succinylation sites on histones, including the chemical characteristics and the mechanism by which lysine succinylation influences nucleosomal structure, chromatin dynamics and several diseases and then discuss lysine succinylation regulation to identify theoretical and experimental proof of Ksuc on histones and in diseases to inspire further research into histone lysine succinylation as a target of disease treatment in the future.

The growing landscape of succinylation links metabolism and heart disease

Post-translational modification of proteins is an important biochemical process that occurs at the protein level. Succinylation is a newly discovered post-translational modification with the hallmark of a significant chemical and structural change. Succinylation has many similarities with other modifications, but succinylation may lead to more functional changes. Although the physiological significance of succinylation has not been well characterized, the lysine succinylation modification shows great potentials during disease processes. The discovery of SIRT5 has made great progress in exploring the role of succinylation in energy metabolism, heart disease and tumorigenesis. In this review, we focus on the discovery of succinylation in organisms and mechanism of succinylation. We are also concerned with the metabolic reactions and heart diseases associated with succinylation.

Compartmentalised acyl-CoA metabolism and roles in chromatin regulation

BACKGROUND

Many metabolites serve as important signalling molecules to adjust cellular activities and functions based on nutrient availability. Links between acetyl-CoA metabolism, histone lysine acetylation, and gene expression have been documented and studied over the past decade. In recent years, several additional acyl modifications to histone lysine residues have been identified, which depend on acyl-coenzyme A thioesters (acyl-CoAs) as acyl donors. Acyl-CoAs are intermediates of multiple distinct metabolic pathways, and substantial evidence has emerged that histone acylation is metabolically sensitive. Nevertheless, the metabolic sources of acyl-CoAs used for chromatin modification in most cases remain poorly understood. Elucidating how these diverse chemical modifications are coupled to and regulated by cellular metabolism is important in deciphering their functional significance.

SCOPE OF REVIEW

In this article, we review the metabolic pathways that produce acyl-CoAs, as well as emerging evidence for functional roles of diverse acyl-CoAs in chromatin regulation. Because acetyl-CoA has been extensively reviewed elsewhere, we will focus on four other acyl-CoA metabolites integral to major metabolic pathways that are also known to modify histones: succinyl-CoA, propionyl-CoA, crotonoyl-CoA, and butyryl-CoA. We also briefly mention several other acyl-CoA species, which present opportunities for further research; malonyl-CoA, glutaryl-CoA, 3-hydroxybutyryl-CoA, 2-hydroxyisobutyryl-CoA, and lactyl-CoA. Each acyl-CoA species has distinct roles in metabolism, indicating the potential to report shifts in the metabolic status of the cell. For each metabolite, we consider the metabolic pathways in which it participates and the nutrient sources from which it is derived, the compartmentalisation of its metabolism, and the factors reported to influence its abundance and potential nuclear availability. We also highlight reported biological functions of these metabolically-linked acylation marks. Finally, we aim to illuminate key questions in acyl-CoA metabolism as they relate to the control of chromatin modification.

MAJOR CONCLUSIONS

A majority of acyl-CoA species are annotated to mitochondrial metabolic processes. Since acyl-CoAs are not known to be directly transported across mitochondrial membranes, they must be synthesized outside of mitochondria and potentially within the nucleus to participate in chromatin regulation. Thus, subcellular metabolic compartmentalisation likely plays a key role in the regulation of histone acylation. Metabolite tracing in combination with targeting of relevant enzymes and transporters will help to map the metabolic pathways that connect acyl-CoA metabolism to chromatin modification. The specific function of each acyl-CoA may be determined in part by biochemical properties that affect its propensity for enzymatic versus non-enzymatic protein modification, as well as the various enzymes that can add, remove and bind each modification. Further, competitive and inhibitory effects of different acyl-CoA species on these enzymes make determining the relative abundance of acyl-CoA species in specific contexts important to understand the regulation of chromatin acylation. An improved and more nuanced understanding of metabolic regulation of chromatin and its roles in physiological and disease-related processes will emerge as these questions are answered.

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites

Protein succinylation is a biochemical reaction in which a succinyl group (-CO-CH2-CH2-CO-) is attached to the lysine residue of a protein molecule. Lysine succinylation plays important regulatory roles in living cells. However, studies in this field are limited by the difficulty in experimentally identifying the substrate site specificity of lysine succinylation. To facilitate this process, several tools have been proposed for the computational identification of succinylated lysine sites. In this study, we developed an approach to investigate the substrate specificity of lysine succinylated sites based on amino acid composition. Using experimentally verified lysine succinylated sites collected from public resources, the significant differences in position-specific amino acid composition between succinylated and non-succinylated sites were represented using the Two Sample Logo program. These findings enabled the adoption of an effective machine learning method, support vector machine, to train a predictive model with not only the amino acid composition, but also the composition of k-spaced amino acid pairs. After the selection of the best model using a ten-fold cross-validation approach, the selected model significantly outperformed existing tools based on an independent dataset manually extracted from published research articles. Finally, the selected model was used to develop a web-based tool, SuccSite, to aid the study of protein succinylation. Two proteins were used as case studies on the website to demonstrate the effective prediction of succinylation sites. We will regularly update SuccSite by integrating more experimental datasets. SuccSite is freely accessible at http://csb.cse.yzu.edu.tw/SuccSite/.

ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides

The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.

Modification of α-synuclein by lipid peroxidation products derived from polyunsaturated fatty acids promotes toxic oligomerization: its relevance to Parkinson disease

Recently, toxic α-synuclein oligomer, which can mediate cell-to-cell propagation is suggested to cause sporadic Parkinson disease. α-Synuclein interacts with membrane lipids especially polyunsaturated fatty acids to stabilize its three-dementional structure. Peroxidation of polyunsaturated fatty acids may reduce their affinity to α-synuclein and peroxidation byproducts might modify α-synuclein. 4-Hydroxy-2-nonenal derived from n-6 polyunsaturated fatty acids was reported to modify α-synuclein to produce a toxic oligomer. Moreover, the accumulation of 4-hydroxy-2-nonenal, which could induce oligomeriztion of α-synuclein, was found in parkinsonian brains. Docosahexaenoic acid, an n-3 polyunsaturated fatty acids abundant in the neuronal membrane, was also found to enhance α-synuclein oligomerization; however, the precise details of the chemical reaction involved are unclear. Propanoylated lysine, a specific indicator of docosahexaenoic acid oxidation, was increased in neuronal differentiated human neuroblastoma SH-SY5Y cells overexpressing α-synuclein. α-Synuclein might be modified by the peroxidation products and then, is degraded by the autophagy-lysosome system. In addition, in the cells overexpressing α-synuclein, the mitochondrial electrone transfer chain was found to be inhibited. Accumulation of abnormal α-synuclein modified by lipid radicals derived from polyunsaturated fatty acids may be not only an indicator of brain oxidative stress but also causative of neurodegeneration such as Parkinson disease by impairing mitochondrial function.

Development and application of oxidative stress biomarkers

Oxidative stress may cause a wide variety of free radical reactions to produce deleterious modifications in membranes, proteins, enzymes, and DNA. Reactive Oxygen Species (ROS) generated by myeloperoxidase (MPO) can induce lipid peroxidation and also play an important role in the generation of reactive chlorinating and brominating species. As the universal biomarkers, chemical, and immunochemical approach on oxidatively modified and halogenated tyrosines has been carried out. As amido-type adduct biomarkers, chemical, and immunochemical evaluation of hexanoyl- and propanoyl-lysines, hexanoyl- and propanoyl-dopamines and phospholipids were prepared and developed for application of evaluation of novel antioxidative functional food factors. We have also involved in application of oxidatively modified DNAs such as 8-hydroxy- and 8-halogenated deoxyguanosines as the useful biomarkers for age-related diseases using both in vitro and in vivo systems. Application of these oxidative stress biomarkers for novel type of functional food development and recent approach for development of novel evaluation systems are also discussed.

Quantitative Succinyl-Proteome Profiling of Camellia sinensis cv. 'Anji Baicha' During Periodic Albinism

Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. ‘Anji Baicha’ is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in ‘Anji Baicha’ has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in ‘Anji Baicha’, representing the first extensive data on the lysine succinylome in the tea plant. Eleven conserved succinylation motifs were enriched among the identified succinylated peptides. The protein-protein interaction maps were visualized using Cytoscape software. Comparison across three typical developmental stages of ‘Anji Baicha’ revealed that proteins exhibiting differential succinylation levels were primarily involved in photosynthesis, carbon fixation, biosynthesis of amino acids and porphyrin and chlorophyll metabolism, suggesting that these succinylated proteins are involved in ‘Anji Baicha’ leaf colour variability. These results not only deepen our understanding of the mechanism underlying ‘Anji Baicha’ albinism and the regulatory role of succinylation in the tea plant but also provide new insight into molecular breeding for leaf colour variety.

The growing landscape of lysine acetylation links metabolism and cell signalling

Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling. Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many biological processes through the regulation of protein interactions, activity and localization. In addition, proteins are frequently modified by other types of acylations, such as formylation, butyrylation, propionylation, succinylation, malonylation, myristoylation, glutarylation and crotonylation. The intricate link between lysine acylation and cellular metabolism has been clarified by the occurrence of several such metabolite-sensitive acylations and their selective removal by sirtuin deacylases. These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes.

Oleic acid promotes adaptability against oxidative stress in 3T3-L1 cells through lipohormesis

Although fatty acids are important components of biological membranes, energy sources, and signal transducers or precursors of lipid mediators, excess intake of fatty acids and their accumulation cause obesity and metabolic syndrome. Thus, fatty acid quantity is known to be an important factor for obesity-related diseases, but the effects of different types of fatty acids (i.e., fatty acid quality) on human health are not completely understood. We here focused on the relationship between fatty acid quality and oxidative stress by investigating whether resistibility to tert-butyl hydrperoxide (t-BuOOH)-induced oxidative stress in 3T3-L1 cells varied according to the fatty acid type. Among eight fatty acids (both saturated and unsaturated) tested, oleic acid (OA) exerted the most pronounced cytoprotective effects, with efficacy over a wide range of concentrations. OA treatment markedly enhanced the intracellular levels of lipid peroxidation markers, including N(ε)-(hexanoyl)lysine, 4-hydroxy-2-nonenal, and acrolein. The levels of these markers in OA-treated cells were decreased after t-BuOOH exposure, whereas the levels in untreated control cells were notably increased after t-BuOOH exposure. Our results suggested that unsaturated fatty acids, particularly OA, could promote an adaptive response and enhance cell tolerance through increased cellular antioxidative capacity via OA-induced mild lipid peroxidation (lipohormesis), and thus protect cells against subsequent oxidative stress-related injury.

Immunochemical detection of lipid hydroperoxide- and aldehyde-modified proteins in diseases

Polyunsaturated fatty acid (PUFA) is easily peroxidized by free radicals and enzymes. When this occurs, it results in the compromised integrity of cellular membranes and leads to lipid hydroperoxide as a major reaction product, which is decomposed into aldehyde. Lipid hydroperoxide-modified lysine is known to be an early product of the lipid peroxidation process, suggesting that it might be a PUFA-oxidative stress marker during the initial stage of oxidative stress. Lipid hydroperoxides cause or enhance ROS-mediated DNA fragmentation. The α,β-unsaturated aldehydes are end products of PUFA peroxidation. They are highly reactive and readily attack and modify the protein amino acid residues into aldehyde-modified proteins. Lipid peroxidation-derived α,β-unsaturated aldehydes are capable of inducing cellular stress-responsive processes such as cell signaling and apoptosis. The lipid hydroperoxide- and aldehyde-modified proteins have been immunohistochemically detected in diverse pathological situations such as atherosclerosis, Alzheimer's disease, Parkinson's disease, and chemical material-induced liver injury and renal tubular injury in humans and experimental animals. These findings suggest that the expression of the lipid hydroperoxide- and aldehyde-modified proteins is closely associated with the pathogenesis of these diseases in humans and experimental animals.

Lipid hydroperoxide-derived adduction to amino-phospholipid in biomembrane

Phospholipids such as phosphatidylethanolamine and phosphatidylcholine play crucial roles in the biological system to maintain the cellular environmental condition. Despite that, oxidative stress targets these phospholipids containing polyunsaturated fatty acids and accompanies the oxidized phospholipids. Recent studies have been suggested that oxidized phospholipids have the relationship with inflammation and might induce the atherosclerosis formation by uptake of oxidized LDL through scavenger receptor as ligands. Red blood cells, which have been studied the bilayer model, are also modified by oxidative stress because hemoglobin can mediate and produce the reactive oxygen species, which leads to lipid peroxidation of biomembrane. In these oxidation processes of biomolecules, hexanoylation against phosphatidylethanolamine and phosphatidylserine, which has the primary amine and is the target of this modification, generates the oxidized membrane such as erythrocyte ghosts. This unique structure of phosphatidylethanolamine and phosphatidylserine is possibly the useful biomarker to evaluate the oxidation of biomembrane in vivo using liquid chromatography tandem mass spectrometry and monoclonal antibody.

Role of lipid peroxide in the neurodegenerative disorders

Nervous system controls all the organs in the living like a symphony. In this chapter, the mechanism of neuronal death in aged is discussed in relation to oxidative stress. Polyunsaturated fatty acid (PUFA) is known to be rich in the membranous component of the neurons and plays an important role in maintaining the neuronal functions. Recent reports revealed that oxidation of omega-3 and omega-6 PUFAs, such as docosahexaenoic acid (DHA) and arachidonic acid (ARA), are potent antioxidant but simultaneously, their oxidation products are potentially toxic. In this chapter, the existence of early oxidation products of PUFA is examined in the samples from neurodegenerative disorders and the cellular model. Accumulation of proteins with abnormal conformation is suggested to induce neuronal death by disturbance of proteolysis and mitochondrial function. The role of lipid peroxide and lipid-derived aldehyde adduct proteins is discussed in relation to brain ageing and age-related neurodegeneration.

The formation of lipid hydroperoxide-derived amide-type lysine adducts on proteins: a review of current knowledge

Lipid peroxidation is an important biological reaction. In particular, polyunsaturated fatty acid (PUFA) can be oxidized easily. Peroxidized lipids often react with other amines accompanied by the formation of various covalent adducts. Novel amide-type lipid-lysine adducts have been identified from an in vitro reaction mixture of lipid hydroperoxide with a protein, biological tissues exposed to conditions of oxidative stress and human urine from a healthy person. In this chapter, the current knowledge of amide type adducts is reviewed with a focus on the evaluation of functional foods and diseases with a history of discovery of hexanoyl-lysine (HEL). Although there is extensive research on HEL and other amide-type adducts, the mechanism of generation of the amide bond remains unclear. We have found that the decomposed aldehyde plus peroxide combined with a lysine moiety does not fully explain the formation of the amide-type lipid-lysine adduct that is generated by lipid hydroperoxide. Singlet oxygen or an excited state of the ketone generated from the lipid hydroperoxide may also contribute to the formation of the amide linkage. The amide-adducts may prove useful not only for the detection of oxidative stress induced by disease but also for the estimation of damage caused by an excess intake of PUFA.

Oxidative modification of lipoproteins

Lipoproteins consist of lipids and apolipoproteins that have functional roles in lipid metabolism. It has been suggested that oxidation of lipoproteins by reactive oxygen species (ROS) may be involved in the inception of various diseases. In particular, the relationship between low-density lipoprotein (LDL) oxidation and atherosclerosis has been studied in great detail. The main target molecules of lipoprotein oxidation are polyunsaturated fatty acid residues of lipids and apolipoproteins. Extensive investigations have characterized oxidative modifications of apolipoprotein B100 (apo B100) in LDL. Furthermore, modifications of apo B100 by oxidized lipids have been confirmed in oxidized LDL and atherosclerotic lesions using immunological techniques. In this chapter, characteristics and oxidation mechanisms of lipoproteins by ROS are described from in vitro and in vivo studies. Oxidative modifications of apo B100 by lipid hydroperoxides, major products of lipid peroxidation at the early stage, are principally reported.

Amide-type adduct of dopamine - plausible cause of Parkinson diseases

Dopamine is the endogenous neurotransmitter produced by nigral neurons. Dopamine loss can trigger not only prominent secondary morphological changes, but also changes in the density and sensitivity of dopamine receptors; therefore, it is a sign of PD development. The reasons for dopamine loss are attributed to dopamine's molecular instability due to it is a member of catecholamine family, whose catechol structure contributes to high oxidative stress through enzymatic and non-enzymatic oxidation. Oxidative stress in the brain easily leads to the lipid peroxidation reaction due to a high concentration of polyunsaturated fatty acids (PUFA), such as docosahexaenoic acid (DHA, C22:6/ω-3) and arachidonic acid (AA, C18:4/ω-6). Recent studies have shown that lipid hydroperoxides, the primary peroxidative products, could non-specifically react with primary amino groups to form N-acyl-type (amide-linkage) adducts. Therefore, based on the NH2-teminals in dopamine's structure, the aims of this chapter are to describes the possibility that reactive LOOH species derived from DHA/AA lipid peroxidation may modify dopamine to form amide-linkage dopamine adducts, which might be related to etiology of Parkinson's diseases.

An update on lysine deacylases targeting the expanding "acylome"

Lysine ε-amino acetylation has long been recognized as an epigenetically relevant post-translational modification of multiple residues in histone proteins. However, it has become clear that lysine acetylation is not restricted to histones, and therefore, it may be involved in the regulation of a wide variety of proteins, some of which have been identified and studied in detail. More recently, post-translational modifications of lysine side chains by additional acyl groups have also been identified, and some of these appear to be regulated by histone deacetylases (HDACs) and/or sirtuins. In this Concept, new developments are discussed with emphasis on the enzymes that have been shown to catalyze the cleavage of these novel marks, including new assays and inhibitors. Ultimately, a deeper understand of these mechanisms should facilitate the development of ligands with therapeutic potential.

SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways

Protein function is regulated by diverse posttranslational modifications. The mitochondrial sirtuin SIRT5 removes malonyl and succinyl moieties from target lysines. The spectrum of protein substrates subject to these modifications is unknown. We report systematic profiling of the mammalian succinylome, identifying 2,565 succinylation sites on 779 proteins. Most of these do not overlap with acetylation sites, suggesting differential regulation of succinylation and acetylation. Our analysis reveals potential impacts of lysine succinylation on enzymes involved in mitochondrial metabolism; e.g., amino acid degradation, the tricarboxylic acid cycle (TCA) cycle, and fatty acid metabolism. Lysine succinylation is also present on cytosolic and nuclear proteins; indeed, we show that a substantial fraction of SIRT5 is extramitochondrial. SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase. Our data reveal widespread roles for lysine succinylation in regulating metabolism and potentially other cellular functions.

Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation

Recent studies have shown that lysines can be posttranslationally modified by various types of acylations. However, except for acetylation, very little is known about their scope and cellular distribution. We mapped thousands of succinylation sites in bacteria (E. coli), yeast (S. cerevisiae), human (HeLa) cells, and mouse liver tissue, demonstrating widespread succinylation in diverse organisms. A majority of succinylation sites in bacteria, yeast, and mouse liver were acetylated at the same position. Quantitative analysis of succinylation in yeast showed that succinylation was globally altered by growth conditions and mutations that affected succinyl-coenzyme A (succinyl-CoA) metabolism in the tricarboxylic acid cycle, indicating that succinylation levels are globally affected by succinyl-CoA concentration. We preferentially detected succinylation on abundant proteins, suggesting that succinylation occurs at a low level and that many succinylation sites remain unidentified. These data provide a systems-wide view of succinylation and its dynamic regulation and show its extensive overlap with acetylation.

Protein lysine acylation and cysteine succination by intermediates of energy metabolism

In the past few years, several new protein post-translational modifications that use intermediates in metabolism have been discovered. These include various acyl lysine modifications (formylation, propionylation, butyrylation, crotonylation, malonylation, succinylation, myristoylation) and cysteine succination. Here, we review the discovery and the current understanding of these modifications. Several of these modifications are regulated by the deacylases, sirtuins, which use nicotinamide adenine dinucleotide (NAD), an important metabolic small molecule. Interestingly, several of these modifications in turn regulate the activity of metabolic enzymes. These new modifications reveal interesting connections between metabolism and protein post-translational modifications and raise many questions for future investigations.

DHA Hydroperoxides as a Potential Inducer of Neuronal Cell Death: a Mitochondrial Dysfunction-Mediated Pathway

During the lipid peroxidation reaction, lipid hydroperoxides are formed as primary products. Several lines of evidence suggest that lipid hydroperoxides can trigger cell death in many cell types, including neurons. In a screening of lipid hydroperoxides which can induce toxicity in neuronal cells, we found docosahexaenoic acid hydroperoxides (DHA-OOH) induced much severe levels of reactive oxygen species generation and cell death in human neuroblastoma SH-SY5Y cells compared to the hydroperoxides of linoleic acid and arachidonic acid. Therefore, we focused on DHA-OOH, and demonstrated that DHA-OOH apparently induced an apoptosis in the neuronal cells through several apoptotic hallmarks including nuclei condensation, DNA fragmentation, poly (ADP-ribose) polymerase cleavage and increased activity of caspase-3. We also found the signaling changes in mitochondria-mediated apoptosis, such as cytochrome c release and increased expression of Bcl-2, as well as a dose-dependent attenuation of mitochondrial membrane potential in the DHA-OOH treated cells. These data indicated DHA hydroperoxide as a potential inducer of apoptosis in human neuroblastoma SH-SY5Y cells, which may be mediated by mitochondria dysfunction pathway.

Sulfo-N-hydroxysuccinimide interferes with bicinchoninic acid protein assay

This study revealed a major interference from sulfo-N-hydroxysuccinimide (sulfo-NHS) in the bicinchoninic acid (BCA) protein assay. Sulfo-NHS, a common reagent used in bioconjugation and analytical biochemistry, exhibited absorbance signals and absorbance peaks at 562 nm, comparable to bovine serum albumin (BSA). However, the combined absorbance of sulfo-NHS and BSA was not strictly additive. The sulfo-NHS interference was suggested to be caused by the reduction of Cu(2+) in the BCA Kit's reagent B (4% cupric sulfate) in a manner similar to that of the protein.

Elevated 4-hydroxyhexenal in Alzheimer's disease (AD) progression

Multiple studies have demonstrated elevations of α, β-unsaturated aldehydes including 4-hydroxynonenal (HNE) and acrolein, in vulnerable regions of mild cognitive impairment (MCI), preclinical Alzheimer's disease (PCAD), and late stage Alzheimer's disease (LAD) brain. However, there has been limited study of a third member, 4-hydroxyhexenal (HHE), a diffusible lipid peroxidation product of the ω-3 polyunstataturated fatty acids (PUFAs). In the present study levels of extractable and protein-bound HHE were quantified in the hippocampus/parahippocampal gyrus (HPG), superior and middle temporal gyri (SMTG), and cerebellum (CER) of MCI, PCAD, LAD, and normal control (NC) subjects. Levels of extractable and protein-bound HHE were increased in multiple regions in the progression of Alzheimer's disease (AD). Extractable HHE was significantly elevated in the hippocampus/parahippocampal gyrus (HPG) of PCAD and LAD subjects and protein-bound HHE was significantly higher in MCI, PCAD, and LAD HPG. A time- and concentration-dependent decrease in survival and a concentration-dependent decrease in glucose uptake were observed in primary cortical cultures treated with HHE. Together these data support a role for lipid peroxidation in the progression of Alzheimer's disease.

Detection of lipid-lysine amide-type adduct as a marker of PUFA oxidation and its applications

Research into lipid peroxidation-induced protein modification has been ongoing for many years. Recent studies on lipo-oxidation shows the occurrence of another type of protein modification, amide-type adduct formation by lipid hydroperoxide, as well as classical aldehyde-derived protein modifications. The amide-type modifications can be either classified as alkylamide and carboxyalkylamide according to the formed structures. As an alkylamide-type adduct, Nepsilon-(hexanoyl)lysine can be formed by the reaction of peroxidized n-6 fatty acid with lysine. Nepsilon-(propanoyl)lysine is considered to be generated from oxidation of n-3 fatty acid with lysine. The generation pattern of both might be useful for classification of which fatty acids are more involved in oxidation in vivo. Since the alkylamide type-adducts are relatively stable and detectable from biological specimens like urine, these adducts, especially Nepsilon-(hexanoyl)lysine, are used as reliable markers for not only oxidative stress evaluation but also development of functional food.

Increased levels of 4-hydroxynonenal and acrolein in the brain in preclinical Alzheimer disease

Previous studies demonstrate increased levels of 4-hydroxynonenal (HNE) and acrolein in vulnerable brain regions of subjects with mild cognitive impairment and late-stage Alzheimer disease (LAD). Recently preclinical AD (PCAD) subjects, who demonstrate normal antemortem neuropsychological test scores but abundant AD pathology at autopsy, have become the focus of increased study. Levels of extractable HNE and acrolein were quantified by gas chromatography-mass spectrometry with negative chemical ionization, and protein-bound HNE and acrolein were quantified by dot-blot immunohistochemistry in the hippocampus/parahippocampal gyrus (HPG), superior and middle temporal gyri (SMTG), and cerebellum (CER) of 10 PCAD and 10 age-matched normal control (NC) subjects. Results of the analyses show a significant (P<0.05) increase in levels of extractable acrolein in the HPG of PCAD subjects compared to age-matched NC subjects and a significant decrease in extractable acrolein in PCAD CER. Significant increases in protein-bound HNE in HPG and a significant decrease in CER of PCAD subjects compared to NC subjects were observed. No significant alterations were observed in either extractable or protein-bound HNE or acrolein in the SMTG of PCAD subjects. Additionally, no significant differences in levels of protein carbonyls were observed in the HPG, SMTG, or CER of PCAD subjects compared to NC subjects.

The immunological and chemical detection of N-(hexanoyl)phosphatidylethanolamine and N-(hexanoyl)phosphatidylserine in an oxidative model induced by carbon tetrachloride

Lipid peroxidation products have a high reactivity against the primary amino groups of biomolecules such as aminophospholipids, proteins, and DNA. Until now, many papers have reported about the modification of biomolecules derived from lipid peroxides. Our group has also reported that aminophospholipids, such as phosphatidylethanolamine (PE), can be modified by lipid peroxidation including 13-hydroperoxyoctadecadienoic acid (13-HPODE). The aim of this study was to examine the oxidative stress in vivo by detecting the formation of N-(hexanoyl)phosphatidylethanolamine (HEPE) and N-(hexanoyl)phosphatidylserine (HEPS), a novel hexanoyl adduct, using a liquid chromatography/tandem mass spectrometry (LC/MS/MS) and a monoclonal antibody. Consequently, we observed that the formation of HEPE and HEPS occurred in the red blood cell (RBC) ghosts modified by 13-HPODE and the oxidative stress model induced by carbon tetrachloride (CCl(4)) using LC/MS/MS monitoring hexanoyl ethanolamine (HEEA), a head group of HEPE, and hexanoyl serine (HESE) as a part of HEPS. Furthermore, we obtained a novel type of monoclonal antibody against HEPE. This antibody could recognize HEPE in the liver of rats with oxidative stress in vivo.

Assessing the neuroprotective effect of antioxidative food factors by application of lipid-derived dopamine modification adducts

Advances in understanding the neurodegenerative pathologies are creating new opportunities for the development of neuroprotective therapies, such as antioxidant food factors, lifestyle modification, and drugs. However, the biomarker by which to determine the effect of the agent on neurodegeneration is limited. We here address hexanoyl dopamine (HED), one of novel dopamine adducts derived from brain polyunsaturated acid, referring to its in vitro formation, potent toxicity to SH-SY5Y cells, and application to assess the neuroprotective effect of antioxidative food factors. Dopamine is a neurotransmitter and its deficiency is a characterized feature in Parkinson's disease (PD), thereby HED represents a new addition to understanding of dopamine biology and pathophysiology of PD and a novel biomarker for the assessment of neuroprotective therapies. We have established an analytical system using for the detection of HED and its toxicity to the neuroblstoma cell line, SH-SY5Y cells. Here, we discuss the characteristics of the system and its applications to investigate the neuroprotective effect of several antioxidants that originate from food.

Assessing the neuroprotective effect of antioxidant food factors by application of lipid-derived dopamine modification adducts

Advances in understanding the neurodegenerative pathologies are creating new opportunities for the development of neuroprotective therapies, such as antioxidant food factors, lifestyle modification and drugs. However, the biomarker by which the effect of the agent on neurodegeneration is determined is limited. We here address hexanoyl dopamine (HED), one of novel dopamine adducts derived from brain polyunsaturated acid, referring to its in vitro formation, potent toxicity to SH-SY5Y cells, and application to assess the neuroprotective effect of antioxidative food factors. Dopamine is a neurotransmitter, and its deficiency is a characterized feature in Parkinson's disease (PD); thus, HED provides a new insight into the understanding of dopamine biology and pathophysiology of PD and a novel biomarker for the assessment of neuroprotective therapies. We have established an analytical system for the detection of HED and its toxicity to the neuroblstoma cell line, SH-SY5Y cells. Here, we discuss the characteristics of the system and its applications to investigate the neuroprotective effect of several antioxidants that originate from food.

Chemical and immunochemical identification of propanoyllysine derived from oxidized n-3 polyunsaturated fatty acid

It is known that n-3 polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid and eicosapentaenoic acid, are rapidly oxidized in vitro. Nvarepsilon-(propanoyl)lysine (propionyllysine, or PRL) is formed from the reaction of the oxidized products of n-3 PUFAs and lysine. To evaluate the oxidized n-3 PUFA-derived protein modifications in vivo, we have developed detection methods using a novel monoclonal antibody against PRL as well as liquid chromatography-mass spectrometry (LC/MS/MS). The antibody obtained specifically recognized PRL. A strong positive staining in atherosclerotic lesions of hypercholesterolemic rabbits was observed. We have also simultaneously identified and quantified both urinary PRL and urinary Nvarepsilon-(hexanoyl)lysine, using LC/MS/MS using isotope dilution methods. The level of urinary PRL (21.6+/-10.6 micromol/mol of creatinine) significantly correlated with the other oxidative stress markers, 8-oxo-deoxyguanosine, dityrosine, and isoprostanes. The increase in the excretion of amide adducts into the urine of diabetic patients was also confirmed compared to healthy subjects. These results suggest that PRL may be good marker for n-3 PUFA-derived oxidative stress in vivo.

Detection of a lipid-lysine adduct family with an amide bond as the linkage: novel markers for lipid-derived protein modifications

An amide-type adduct, hexanoyl-lysine (HEL) is generated from the reaction between n-6 fatty acid (FA)-derived lipid peroxide and lysine. Immunochemical and chemical methods can be used to detect the formation of HEL. For example, an ELISA kit using the monoclonal antibody to HEL is now commercially available. We recently identified propanoyl-lysine (propionyl-lysine, PRL) from the reaction of an n-3 FA and a lysine residue. The antibody to PRL has been prepared and characterized. Using these monoclonal antibodies, the localization of adducts in tissues has been confirmed. Moreover, both amide-type adducts, HEL and PRL, can be simultaneously measured using liquid chromatography mass spectrometry (LC/MS/MS) with isotope dilution methods. The LC/MS/MS analysis reveals the rigid amounts of the adducts in human urine. Both the chemical and immunochemical methods are useful for the estimation of amide-type adducts in vivo.

Formation of dopamine adducts derived from brain polyunsaturated fatty acids: mechanism for Parkinson disease

Oxidative stress appears to be directly involved in the pathogenesis of the neurodegeneration of dopaminergic systems in Parkinson disease. In this study, we formed four dopamine modification adducts derived from docosahexaenoic acid (C22:6/omega-3) and arachidonic acid (C18:4/omega-6), which are known as the major polyunsaturated fatty acids in the brain. Upon incubation of dopamine with fatty acid hydroperoxides and an in vivo experiment using rat brain tissue, all four dopamine adducts were detected. Furthermore, hexanoyl dopamine (HED), an arachidonic acid-derived adduct, caused severe cytotoxicity in human dopaminergic neuroblastoma SH-SY5Y cells, whereas the other adducts were only slightly affected. The HED-induced cell death was found to include apoptosis, which also seems to be mediated by reactive oxygen species generation and mitochondrial abnormality. Additionally, the experiments using monoamine transporter inhibitor and mouse embryonic fibroblast NIH-3T3 cells that lack the monoamine transporter indicate that the HED-induced cytotoxicity might specially occur in the neuronal cells. These data suggest that the formation of the docosahexaenoic acid- and arachidonic acid-derived dopamine adducts in vitro and in vivo, and HED, the arachidonic acid-derived dopamine modification adduct, which caused selective cytotoxicity of neuronal cells, may indicate a novel mechanism responsible for the pathogenesis in Parkinson disease.

Structural characterization of alpha,beta-unsaturated aldehydes by GC/MS is dependent upon ionization method

alpha,beta-unsaturated aldehydes are toxic products of lipid peroxidation. Detection and characterization of these aldehydes is important in many human disease states as well as in the food industry. Our study shows that electron ionization-mass spectrometry (EI-MS) and positive-ion chemical ionization-mass spectrometry (PICI-MS), but not electron capture negative ionization-mass spectrometry (ECNI-MS), can be used to detect the C4-hydroxylation state of alpha,beta-unsaturated aldehydes derivatized with pentafluorobenzyl hydroxylamine alone. EI-MS and PICI-MS spectra of 4-hydroxy-2-alkenals contained a fragment with m/z 252, whereas spectra of 2-alkenals contained a fragment with m/z 250. These fragments are consistent with fragmentation between C3 and C4 with transfer of two hydrogens from C4 and the C4 hydroxyl group in the case of 4-hydroxy-2-alkenals. In addition, EI-MS and PICI-MS were able to distinguish 4-hydroxy-2-alkenals and 2-alkenals from 4-keto-2-alkenals and 4-hydroxyalkanals. On the other hand, ECNI-MS provided complex spectra regarding C4-hydroxylation state. Furthermore, the syn- and anti-configurations of PFB-oximes had different resultant spectra using ECNI-MS, but not with EI-MS or PICI-MS. These data indicate that EI-MS and PICI-MS are more amenable for structural analysis of alpha,beta-unsaturated aldehydes than ECNI-MS.

Formation of high-molecular-weight protein adducts by methyl docosahexaenoate peroxidation products

In the present study, the formation of modified proteins by methyl docosahexaenoate (DHA) peroxidation products in the presence of a metal-catalyzed oxidation system was investigated. Metal-catalyzed oxidation of mixtures containing bovine serum albumin (BSA) and DHA led to formation of two high molecular weight derivatives of BSA. One had a mass of 71.5 kDa as determined by two-dimensional electrophoresis, matrix assisted laser desorption and ionization mass spectrometer (MALDI MS) analysis. The other was estimated to be 93 kDa by SDS-PAGE electrophoresis. The exposure of BSA to DHA also led to the generation of carbonyl groups. Oxygen radical scavengers could inhibit these modifications induced by DHA peroxidation. Furthermore, there was little difference of the peptides mass fingerprinting between the two kinds of modified high-molecular-weight proteins. These results suggest that oxygen radicals formed during lipid peroxidation are involved in the formation of protein derivatives. Our study may be important in the understanding the specific role of docosahexaenoic acid in the formation of modified proteins during aging and its related diseases.