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Ding Y, Liu Y, Yang K, Zhao Y, Wen C, Yang Y, Zhang W. Proteomic Analysis of Lysine Acetylation and Succinylation to Investigate the Pathogenicity of Virulent Pseudomonas syringae pv. tomato DC3000 and Avirulent Line Pseudomonas syringae pv. tomato DC3000 avrRpm1 on Arabidopsis thaliana. Genes (Basel) 2024; 15:499. [PMID: 38674433 PMCID: PMC11050401 DOI: 10.3390/genes15040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is able to infect many economically important crops and thus causes substantial losses in the global agricultural economy. Pst DC3000 can be divided into virulent lines and avirulent lines. For instance, the pathogen effector avrRPM1 of avirulent line Pst-avrRpm1 (Pst DC3000 avrRpm1) can be recognized and detoxified by the plant. To further compare the pathogenicity mechanisms of virulent and avirulent Pst DC3000, a comprehensive analysis of the acetylome and succinylome in Arabidopsis thaliana was conducted following infection with virulent line Pst DC3000 and avirulent line Pst-avrRpm1. In this study, a total of 1625 acetylated proteins encompassing 3423 distinct acetylation sites were successfully identified. Additionally, 229 succinylated proteins with 527 unique succinylation sites were detected. A comparison of these modification profiles between plants infected with Pst DC3000 and Pst-avrRpm1 revealed significant differences. Specifically, modification sites demonstrated inconsistencies, with a variance of up to 10% compared to the control group. Moreover, lysine acetylation (Kac) and lysine succinylation (Ksu) displayed distinct preferences in their modification patterns. Lysine acetylation is observed to exhibit a tendency towards up-regulation in Arabidopsis infected with Pst-avrRpm1. Conversely, the disparity in the number of Ksu up-regulated and down-regulated sites was not as pronounced. Motif enrichment analysis disclosed that acetylation modification sequences are relatively conserved, and regions rich in polar acidic/basic and non-polar hydrophobic amino acids are hotspots for acetylation modifications. Functional enrichment analysis indicated that the differentially modified proteins are primarily enriched in the photosynthesis pathway, particularly in relation to light-capturing proteins. In conclusion, this study provides an insightful profile of the lysine acetylome and succinylome in A. thaliana infected with virulent and avirulent lines of Pst DC3000. Our findings revealed the potential impact of these post-translational modifications (PTMs) on the physiological functions of the host plant during pathogen infection. This study offers valuable insights into the complex interactions between plant pathogens and their hosts, laying the groundwork for future research on disease resistance and pathogenesis mechanisms.
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Affiliation(s)
- Yongqiang Ding
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yangxuan Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Kexin Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yiran Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Chun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Wei Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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Ma Q, Zeng Q, Wang K, Qian M, Li J, Wang H, Zhang H, Jiang J, Chen Z, Huang W. Acetyltransferase P300 Regulates Glucose Metabolic Reprogramming through Catalyzing Succinylation in Lung Cancer. Int J Mol Sci 2024; 25:1057. [PMID: 38256128 PMCID: PMC10816063 DOI: 10.3390/ijms25021057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Aberrant protein post-translational modification is a hallmark of malignant tumors. Lysine succinylation (Ksucc) plays a vital role in cell energy metabolism in various cancers. However, whether succinylation can be catalyzed by acetyltransferase p300 remains unclear. In this study, we unveiled that p300 is a "writer" for succinylation, and p300-mediated Ksucc promotes cell glycometabolism in lung adenocarcinoma (LUAD). Specifically, our succinylome data revealed that EP300 deficiency leads to the systemic reduction of Ksucc, and 79.55% of the p300-succinylated proteins were found in the cytoplasm, which were primarily enriched in the carbohydrate metabolism process. Interestingly, deleting EP300 led to a notable decrease in Ksucc levels on several glycolytic enzymes, especially Phosphoglycerate Kinase 1 (PGK1). Mutation of the succinylated site of PGK1 notably hindered cell glycolysis and lactic acid excretion. Metabolomics in vivo indicated that p300-caused metabolic reprogramming was mainly attributed to the altered carbohydrate metabolism. In addition, 89.35% of LUAD patients exhibited cytoplasmic localization of p300, with higher levels in tumor tissues than adjacent normal tissues. High levels of p300 correlated with advanced tumor stages and poor prognosis of LUAD patients. Briefly, we disclose the activity of p300 to catalyze succinylation, which contributes to cell glucose metabolic reprogramming and malignant progression of lung cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhinan Chen
- Department of Cell Biology, National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Xi’an 710032, China
| | - Wan Huang
- Department of Cell Biology, National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Xi’an 710032, China
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Kubatzky KF, Gao Y, Yu D. Post-translational modulation of cell signalling through protein succinylation. Explor Target Antitumor Ther 2023; 4:1260-1285. [PMID: 38213532 PMCID: PMC10776603 DOI: 10.37349/etat.2023.00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cells need to adapt their activities to extra- and intracellular signalling cues. To translate a received extracellular signal, cells have specific receptors that transmit the signal to downstream proteins so that it can reach the nucleus to initiate or repress gene transcription. Post-translational modifications (PTMs) of proteins are reversible or irreversible chemical modifications that help to further modulate protein activity. The most commonly observed PTMs are the phosphorylation of serine, threonine, and tyrosine residues, followed by acetylation, glycosylation, and amidation. In addition to PTMs that involve the modification of a certain amino acid (phosphorylation, hydrophobic groups for membrane localisation, or chemical groups like acylation), or the conjugation of peptides (SUMOylation, NEDDylation), structural changes such as the formation of disulphide bridge, protein cleavage or splicing can also be classified as PTMs. Recently, it was discovered that metabolites from the tricarboxylic acid (TCA) cycle are not only intermediates that support cellular metabolism but can also modify lysine residues. This has been shown for acetate, succinate, and lactate, among others. Due to the importance of mitochondria for the overall fitness of organisms, the regulatory function of such PTMs is critical for protection from aging, neurodegeneration, or cardiovascular disease. Cancer cells and activated immune cells display a phenotype of accelerated metabolic activity known as the Warburg effect. This metabolic state is characterised by enhanced glycolysis, the use of the pentose phosphate pathway as well as a disruption of the TCA cycle, ultimately causing the accumulation of metabolites like citrate, succinate, and malate. Succinate can then serve as a signalling molecule by directly interacting with proteins, by binding to its G protein-coupled receptor 91 (GPR91) and by post-translationally modifying proteins through succinylation of lysine residues, respectively. This review is focus on the process of protein succinylation and its importance in health and disease.
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Affiliation(s)
- Katharina F. Kubatzky
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yue Gao
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Dayoung Yu
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
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Wang Y, Yang M, Ge F, Jiang B, Hu R, Zhou X, Yang Y, Liu M. Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus. Mol Cell Proteomics 2023; 22:100490. [PMID: 36566904 PMCID: PMC9879794 DOI: 10.1016/j.mcpro.2022.100490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Mingkun Yang
- University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Feng Ge
- University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Hubei Optics Valley Laboratory, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
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Li S, Zhou Y, Xu Y, Ran S, Hou M, Li Q, Zhong X, Zhong F. The analysis of lysine succinylation modification reveals the mechanism of oxybenzone damaging of pakchoi (Brassica rapa L. ssp. chinensis). Front Plant Sci 2022; 13:1001935. [PMID: 36570927 PMCID: PMC9772522 DOI: 10.3389/fpls.2022.1001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under OBZ stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid (TCA) cycle. Comprehensive analysis shows that Ksuc mainly changes the carbon flow distribution, enhances the activity of the antioxidant system, affects the biosynthesis of amino acids, and increases the modification of histones. The results of this study first showed the profiling of the Kusc map under OBZ treatment and proposed the adaptive mechanism of pakchoi in response to pollutants and other abiotic stresses at the posttranslational level, which revealed the importance of Ksuc in the regulation of various life activities and provides a reference dataset for future research on molecular function.
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Affiliation(s)
- Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Maomao Hou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Qingming Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Cheng’du, China
| | - Xin Zhong
- Institute of Marine Science and Technology, Shandong University, Qing’dao, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
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Luo X, Huang S, Liang M, Xue Q, Rehman SU, Ren X, Li Y, Yang T, Shi D, Li X. The freezability of Mediterranean buffalo sperm is associated with lysine succinylation and lipid metabolism. FASEB J 2022; 36:e22635. [PMID: 36333987 DOI: 10.1096/fj.202201254r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Semen cryopreservation is used for the propagation of variety among species and domestic breeding. Mitochondria are implicated in sperm freezability, and their proteins are prone to succinylation, but the relationship between sperm freezability and mitochondrial protein succinylation is unclear. In this study, six bulls were classified as having good or poor freezability ejaculates (GFE or PFE, each 3 bulls). The fresh sperm mitochondrial membrane potential (MMP) and pan succinylation level of the two groups were first detected. Then the lysine succinylome and fatty acid content of the two groups were analyzed using label-free LC-MS/MS and GC-MS/MS in multiple reaction monitoring (MRM) modes, respectively. The results indicated that the GFE sperm had significantly higher MMPs than the PFE group (p < 0.05). A total of 1393 succinylation sites corresponding to 426 proteins were assessed and 5 succinylated peptides of the GFE group were markedly upregulated, while 3 were significantly downregulated (FC > 2.0 - < 0.5 and p-value < 0.05) when compared to the PFE group. Forty-six succinylated proteins were identified to have consistent presence/absence expression. The upregulated succinylated proteins in the GFE sperm were enriched in lipid metabolic processes. A total of 31 fatty acids were further subjected to quantitative analysis of which 23 including arachidic (C20:0), linolenic (C18:3n3), and docosahexaenoic acids (C22:6n3) were decreased in GFE sperm when compared with PFE (p < 0.05). These results suggest that lysine succinylation can potentially influence the sperm freezability of Mediterranean buffaloes through mitochondrial lipid metabolism. This novel study provides our understanding of sperm succinylation and the molecular basis for the mechanism of sperm freezability.
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Affiliation(s)
- Xi Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Shihai Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Mingming Liang
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Qingsong Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Saif Ur Rehman
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xuan Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yanfang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Ting Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xiangping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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Jia J, Wu G, Li M, Qiu W. pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module. BMC Bioinformatics 2022; 23:450. [PMCID: PMC9620660 DOI: 10.1186/s12859-022-05001-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Lysine succinylation is a newly discovered protein post-translational modifications. Predicting succinylation sites helps investigate the metabolic disease treatments. However, the biological experimental approaches are costly and inefficient, it is necessary to develop efficient computational approaches. Results In this paper, we proposed a novel predictor based on ensemble dense blocks and an attention module, called as pSuc-EDBAM, which adopted one hot encoding to derive the feature maps of protein sequences, and generated the low-level feature maps through 1-D CNN. Afterward, the ensemble dense blocks were used to capture feature information at different levels in the process of feature learning. We also introduced an attention module to evaluate the importance degrees of different features. The experimental results show that Acc reaches 74.25%, and MCC reaches 0.2927 on the testing dataset, which suggest that the pSuc-EDBAM outperforms the existing predictors. Conclusions The experimental results of ten-fold cross-validation on the training dataset and independent test on the testing dataset showed that pSuc-EDBAM outperforms the existing succinylation site predictors and can predict potential succinylation sites effectively. The pSuc-EDBAM is feasible and obtains the credible predictive results, which may also provide valuable references for other related research. To make the convenience of the experimental scientists, a user-friendly web server has been established (http://bioinfo.wugenqiang.top/pSuc-EDBAM/), by which the desired results can be easily obtained.
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Affiliation(s)
- Jianhua Jia
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 333403 China
| | - Genqiang Wu
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 333403 China
| | - Meifang Li
- grid.410729.90000 0004 1759 3199Computer Department, Nanchang Institute of Technology, Nanchang, 330044 China
| | - Wangren Qiu
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 333403 China
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Xia Y, Jiang M, Luo Y, Feng G, Jia G, Zhang H, Wang P, Ge R. SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm. J Comput Biol 2022; 29:1085-1094. [PMID: 35714347 DOI: 10.1089/cmb.2022.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Yixiao Xia
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Minchao Jiang
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Yizhang Luo
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Guanwen Feng
- Xi'an Key Laboratory of Big Data and Intelligent Vision, School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Gangyong Jia
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Hua Zhang
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Pu Wang
- Computer School, Hubei University of Arts and Science, Xiangyang, China
| | - Ruiquan Ge
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
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Wang H, Zhao H, Zhang J, Han J, Liu Z. A parallel model of DenseCNN and ordered-neuron LSTM for generic and species-specific succinylation site prediction. Biotechnol Bioeng 2022; 119:1755-1767. [PMID: 35320585 DOI: 10.1002/bit.28091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/12/2022] [Accepted: 03/19/2022] [Indexed: 11/07/2022]
Abstract
Lysine succinylation (Ksucc) regulates various metabolic processes, participates in vital life processes, ans is involved in the occurrence and development of numerous diseases. Accurate recognition of succinylation sites can reveal underlying functional mechanisms and pathogenesis. However, most remain undetected. Moreover, a deep learning architecture focusing on generic and species-specific predictions is still lacking. Thus, we proposed a deep learning-based framework named Deep-Ksucc, combining a dense convolutional network (DenseCNN) and ordered-neuron long short-term memory (OnLSTM) in parallel, which took the cascading characteristics of sequence information and physicochemical properties as the input. The results of the generic and species-specific predictions indicated that Deep-Ksucc can identify sequence patterns of different organisms and recognize plenty of succinylation sites. The case study showed that Deep-Ksucc can serve as a reliable tool for biology verification and computer-aided recognition of succinylation sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huiqing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Hong Zhao
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jing Zhang
- Engineering Training Center, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jiale Han
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Zhihao Liu
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
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Yang Y, Zhang H, Guo Z, Zou S, Long F, Wu J, Li P, Zhao GP, Zhao W. Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways. Mol Cell Proteomics 2021; 20:100148. [PMID: 34530157 PMCID: PMC8498004 DOI: 10.1016/j.mcpro.2021.100148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/08/2021] [Indexed: 02/09/2023] Open
Abstract
Lysine acylations are reversible and ubiquitous post-translational modifications that play critical roles in regulating multiple cellular processes. In the current study, highly abundant and dynamic acetylation, besides succinylation, was uncovered in a soil bacterium, Streptomyces coelicolor. By affinity enrichment using anti–acetyl-lysine antibody and the following LC−MS/MS analysis, a total of 1298 acetylation sites among 601 proteins were identified. Bioinformatics analyses suggested that these acetylated proteins have diverse subcellular localization and were enriched in a wide range of biological functions. Specifically, a majority of the acetylated proteins were also succinylated in the tricarboxylic acid cycle and protein translation pathways, and the bimodification occurred at the same sites in some proteins. The acetylation and succinylation sites were quantified by knocking out either the deacetylase ScCobB1 or the desuccinylase ScCobB2, demonstrating a possible competitive relationship between the two acylations. Moreover, in vitro experiments using synthetically modified peptides confirmed the regulatory crosstalk between the two sirtuins, which may be involved in the collaborative regulation of cell physiology. Collectively, these results provided global insights into the S. coelicolor acylomes and laid a foundation for characterizing the regulatory roles of the crosstalk between lysine acetylation and succinylation in the future. A highly abundant and dynamic acetylation is discovered in Streptomyces coelicolor. Quantitative acetylome and succinylome analyses in Streptomyces coelicolor. The bimodification proteins are enriched in multiple metabolic pathways.
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Affiliation(s)
- Yujiao Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhenyang Guo
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Siwei Zou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fei Long
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiacheng Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China.
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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11
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Frankovsky J, Keresztesová B, Bellová J, Kunová N, Čanigová N, Hanakova K, Bauer JA, Ondrovičová G, Lukáčová V, Siváková B, Zdrahal Z, Pevala V, Procházková K, Nosek J, Baráth P, Kutejova E, Tomaska L. The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids. J Biol Chem 2021; 297:101155. [PMID: 34480900 DOI: 10.1016/j.jbc.2021.101155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022] Open
Abstract
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.
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12
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Wang H, Zhao H, Yan Z, Zhao J, Han J. MDCAN-Lys: A Model for Predicting Succinylation Sites Based on Multilane Dense Convolutional Attention Network. Biomolecules 2021; 11:biom11060872. [PMID: 34208298 PMCID: PMC8231176 DOI: 10.3390/biom11060872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Lysine succinylation is an important post-translational modification, whose abnormalities are closely related to the occurrence and development of many diseases. Therefore, exploring effective methods to identify succinylation sites is helpful for disease treatment and research of related drugs. However, most existing computational methods for the prediction of succinylation sites are still based on machine learning. With the increasing volume of data and complexity of feature representations, it is necessary to explore effective deep learning methods to recognize succinylation sites. In this paper, we propose a multilane dense convolutional attention network, MDCAN-Lys. MDCAN-Lys extracts sequence information, physicochemical properties of amino acids, and structural properties of proteins using a three-way network, and it constructs feature space. For each sub-network, MDCAN-Lys uses the cascading model of dense convolutional block and convolutional block attention module to capture feature information at different levels and improve the abstraction ability of the network. The experimental results of 10-fold cross-validation and independent testing show that MDCAN-Lys can recognize more succinylation sites, which is consistent with the conclusion of the case study. Thus, it is worthwhile to explore deep learning-based methods for the recognition of succinylation sites.
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Siculella L, Giannotti L, Di Chiara Stanca B, Calcagnile M, Rochira A, Stanca E, Alifano P, Damiano F. Evidence for a Negative Correlation between Human Reactive Enamine-Imine Intermediate Deaminase A (RIDA) Activity and Cell Proliferation Rate: Role of Lysine Succinylation of RIDA. Int J Mol Sci 2021; 22:ijms22083804. [PMID: 33916919 PMCID: PMC8067581 DOI: 10.3390/ijms22083804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 01/17/2023] Open
Abstract
Reactive intermediate deaminase (Rid) proteins are enzymes conserved in all domains of life. UK114, a mammalian member of RidA subfamily, has been firstly identified as a component of liver perchloric acid-soluble proteins (L-PSP). Although still poorly defined, several functions have been attributed to the mammalian protein UK114/RIDA, including the reactive intermediate deamination activity. The expression of UK114/RIDA has been observed in some tumors, arousing interest in this protein as an evaluable tumor marker. However, other studies reported a negative correlation between UK114/RIDA expression, tumor differentiation degree and cell proliferation. This work addressed the question of UK114/RIDA expression in human non-tumor HEK293 cell lines and in some human tumor cell lines. Here we reported that human RIDA (hRIDA) was expressed in all the analyzed cell line and subjected to lysine (K-)succinylation. In HEK293, hRIDA K-succinylation was negatively correlated to the cell proliferation rate and was under the control of SIRT5. Moreover, K-succinylation clearly altered hRIDA quantification by immunoblotting, explaining, at least in part, some discrepancies about RIDA expression reported in previous studies. We found that hRIDA was able to deaminate reactive enamine-imine intermediates and that K-succinylation drastically reduced deaminase activity. As predicted by in silico analysis, the observed reduction of deaminase activity has been related to the drastic alterations of hRIDA structure inferred by K-succinylation. The role of hRIDA and the importance of its K-succinylation in cell metabolism, especially in cancer biology, have been discussed.
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Affiliation(s)
- Luisa Siculella
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
- Correspondence: (L.S.); (F.D.); Tel.: +39-0832-298-696 (L.S.); +39-0832-298-698 (F.D.)
| | - Laura Giannotti
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Benedetta Di Chiara Stanca
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Matteo Calcagnile
- Laboratory of Microbiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.C.); (P.A.)
| | - Alessio Rochira
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Eleonora Stanca
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Pietro Alifano
- Laboratory of Microbiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.C.); (P.A.)
| | - Fabrizio Damiano
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
- Correspondence: (L.S.); (F.D.); Tel.: +39-0832-298-696 (L.S.); +39-0832-298-698 (F.D.)
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14
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Abstract
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.
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Affiliation(s)
- Lanting Yang
- Department of Cardiovascular Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266000, China.,School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Shuo Miao
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Jing Zhang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Peiyan Wang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Gaoli Liu
- Department of Cardiovascular Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Jianxun Wang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
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15
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Zeng F, Pang H, Chen Y, Zheng H, Li W, Ramanathan S, Hoare R, Monaghan SJ, Lin X, Jian J. First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence. Front Cell Infect Microbiol 2021; 10:626574. [PMID: 33614530 PMCID: PMC7892601 DOI: 10.3389/fcimb.2020.626574] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
Recent studies have shown that a key strategy of many pathogens is to use post-translational modification (PTMs) to modulate host factors critical for infection. Lysine succinylation (Ksuc) is a major PTM widespread in prokaryotic and eukaryotic cells, and is associated with the regulation of numerous important cellular processes. Vibrio alginolyticus is a common pathogen that causes serious disease problems in aquaculture. Here we used the affinity enrichment method with LC-MS/MS to report the first identification of 2082 lysine succinylation sites on 671 proteins in V. alginolyticus, and compared this with the lysine acetylation of V. alginolyticus in our previous work. The Ksuc modification of SodB and PEPCK proteins were further validated by Co-immunoprecipitation combined with Western blotting. Bioinformatics analysis showed that the identified lysine succinylated proteins are involved in various biological processes and central metabolism pathways. Moreover, a total of 1,005 (25.4%) succinyl sites on 502 (37.3%) proteins were also found to be acetylated, which indicated that an extensive crosstalk between acetylation and succinylation in V. alginolyticus occurs, especially in three central metabolic pathways: glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism. Furthermore, we found at least 50 (7.45%) succinylated virulence factors, including LuxS, Tdh, SodB, PEPCK, ClpP, and the Sec system to play an important role in bacterial virulence. Taken together, this systematic analysis provides a basis for further study on the pathophysiological role of lysine succinylation in V. alginolyticus and provides targets for the development of attenuated vaccines.
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Affiliation(s)
- Fuyuan Zeng
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Huanying Pang
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Hongwei Zheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Srinivasan Ramanathan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rowena Hoare
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Sean J. Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jichang Jian
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Zhao Y, Han Y, Sun Y, Wei Z, Chen J, Niu X, An Q, Zhang L, Qi R, Gao X. Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis. Front Microbiol 2021; 11:632367. [PMID: 33597936 PMCID: PMC7882547 DOI: 10.3389/fmicb.2020.632367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background Lysine 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. Objectives The 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. Methods Using 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. Results A 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. Conclusion We 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).
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Affiliation(s)
- Yiping Zhao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Han
- Department of Dermatology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Yuzhe Sun
- Department of Dermatology, Dermatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhendong Wei
- Department of Dermatology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jialong Chen
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueli Niu
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qian An
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Zhang
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ruiqun Qi
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinghua Gao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
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17
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Zeng J, Wu L, Chen Q, Wang L, Qiu W, Zheng X, Yin X, Liu J, Ren Y, Li Y. Comprehensive profiling of protein lysine acetylation and its overlap with lysine succinylation in the Porphyromonas gingivalis fimbriated strain ATCC 33277. Mol Oral Microbiol 2020; 35:240-250. [PMID: 32939976 DOI: 10.1111/omi.12312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Porphyromonas gingivalis is a pathogen closely associated with periodontal and systemic infections. Recently, lysine acetylation (Kac) and lysine succinylation (Ksuc) have been identified in bacterial proteins with diverse biological and pathological functions. The Ksuc of P. gingivalis ATCC 33277 has been characterized in our previous work, and here, we report the systematic analysis of Kac and its crosstalk with Ksuc in this bacterium. A combination of the affinity enrichment by the acetyl-lysine antibody with highly sensitive LC-MS/MS was used to identify the lysine-acetylated proteins and sites in P. gingivalis ATCC 33277. A total of 1,112 lysine-acetylated sites matching 438 proteins were identified. These proteins involved in several cellular processes, especially those proteins related to protein biosynthesis and central metabolism had a high tendency to be lysine acetylated. Moreover, lysine sites flanked by tyrosine, phenylalanine, and histidine in the +1 position, as well as residue lysine in position +4 to +5, were the targets of Kac. Additionally, proteins involved in adhesins, gingipains, black pigmentation, and oxidative stress resistance were identified as substrates of Kac. Collectively, these results suggest Kac may play a critical role in the regulation of physiology and virulence of P. gingivalis. Furthermore, we discovered that, Ksuc and Kac were extensively overlapped in P. gingivalis ATCC 33277, especially in proteins related to ribosomes and metabolism. This study provides a significant beginning for further investigating the role of Kac and Ksuc in the pathogenicity of P. gingivalis.
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Affiliation(s)
- Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lingyun Wang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoming Yin
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jie Liu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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18
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Shi R, Wang Y, Gao Y, Xu X, Mao S, Xiao Y, Song S, Wang L, Tian B, Zhao Y, Hua Y, Xu H. Succinylation at a key residue of FEN1 is involved in the DNA damage response to maintain genome stability. Am J Physiol Cell Physiol 2020; 319:C657-C666. [PMID: 32783654 DOI: 10.1152/ajpcell.00137.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human flap endonuclease 1 (FEN1) is a structure-specific, multifunctional endonuclease essential for DNA replication and repair. Our previous study showed that in response to DNA damage, FEN1 interacts with the PCNA-like Rad9-Rad1-Hus1 complex instead of PCNA to engage in DNA repair activities, such as stalled DNA replication fork repair, and undergoes SUMOylation by SUMO-1. Here, we report that succinylation of FEN1 was stimulated in response to DNA replication fork-stalling agents, such as ultraviolet (UV) irradiation, hydroxyurea, camptothecin, and mitomycin C. K200 is a key succinylation site of FEN1 that is essential for gap endonuclease activity and could be suppressed by methylation and stimulated by phosphorylation to promote SUMO-1 modification. Succinylation at K200 of FEN1 promoted the interaction of FEN1 with the Rad9-Rad1-Hus1 complex to rescue stalled replication forks. Impairment of FEN1 succinylation led to the accumulation of DNA damage and heightened sensitivity to fork-stalling agents. Altogether, our findings suggest an important role of FEN1 succinylation in regulating its roles in DNA replication and repair, thus maintaining genome stability.
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Affiliation(s)
- Rongyi Shi
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yiyi Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ya Gao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Xiaoli Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Shuyu Mao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yue Xiao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Shuang Song
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
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19
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Qiu C, Wang Y, Sun JH, Qian WJ, Xie H, Ding YQ, Ding ZT. [A Qualitative Proteome-Wide Lysine Succinylation Profiling of Tea Revealed its Involvement in Primary Metabolism]. Mol Biol (Mosk) 2020; 54:164-176. [PMID: 32163400 DOI: 10.31857/s0026898420010127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/07/2019] [Indexed: 11/24/2022]
Abstract
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.
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Affiliation(s)
- C Qiu
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - Y Wang
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - J H Sun
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - W J Qian
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - H Xie
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - Y Q Ding
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China
| | - Z T Ding
- Tea Research Institute, Qingdao Agricultural University, Changcheng Road, Chengyang District, Qingdao, Shandong, 266109 China.,
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20
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Meng X, Mujahid H, Zhang Y, Peng X, Redoña ED, Wang C, Peng Z. Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds. Mol Cell Proteomics 2019; 18:2359-2372. [PMID: 31492684 PMCID: PMC6885699 DOI: 10.1074/mcp.ra119.001426] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/04/2019] [Indexed: 11/06/2022] Open
Abstract
Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.
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Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Yadong Zhang
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762; Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou 310018, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Mississippi State University, Stoneville MS, 38776
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762.
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21
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Zhang K, Xiong Y, Sun W, Wang GL, Liu W. Global Proteomic Analysis Reveals Widespread Lysine Succinylation in Rice Seedlings. Int J Mol Sci 2019; 20:E5911. [PMID: 31775301 DOI: 10.3390/ijms20235911] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 01/20/2023] Open
Abstract
Lysine succinylation (Ksu) is a dynamic and reversible post-translational modification that plays an important role in many biological processes. Although recent research has analyzed Ksu plant proteomes, little is known about the scope and cellular distribution of Ksu in rice seedlings. Here, we report high-quality proteome-scale Ksu data for rice seedlings. A total of 710 Ksu sites in 346 proteins with diverse biological functions and subcellular localizations were identified in rice samples. About 54% of the sites were predicted to be localized in the chloroplast. Six putative succinylation motifs were detected. Comparative analysis with succinylation data revealed that arginine (R), located downstream of Ksu sites, is the most conserved amino acid surrounding the succinylated lysine. KEGG pathway category enrichment analysis indicated that carbon metabolism, tricarboxylic acid cycle (TCA) cycle, oxidative phosphorylation, photosynthesis, and glyoxylate and dicarboxylate metabolism pathways were significantly enriched. Additionally, we compared published Ksu data from rice embryos with our data from rice seedlings and found conserved Ksu sites between the two rice tissues. Our in-depth survey of Ksu in rice seedlings provides the foundation for further understanding the biological function of lysine-succinylated proteins in rice growth and development.
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22
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Kurmi K, Hitosugi S, Wiese EK, Boakye-Agyeman F, Gonsalves WI, Lou Z, Karnitz LM, Goetz MP, Hitosugi T. Carnitine Palmitoyltransferase 1A Has a Lysine Succinyltransferase Activity. Cell Rep 2019; 22:1365-1373. [PMID: 29425493 PMCID: PMC5826573 DOI: 10.1016/j.celrep.2018.01.030] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/26/2017] [Accepted: 01/09/2018] [Indexed: 12/13/2022] Open
Abstract
Lysine succinylation was recently identified as a post-translational modification in cells. However, the molecular mechanism underlying lysine succinylation remains unclear. Here, we show that carnitine palmitoyltransferase 1A (CPT1A) has lysine succinyl-transferase (LSTase) activity in vivo and in vitro. Using a stable isotope labeling by amino acid in cell culture (SILAC)-based proteomics approach, we found that 101 proteins were more succinylated in cells expressing wild-type (WT) CPT1A compared with vector control cells. One of the most heavily succinylated proteins in this analysis was enolase 1. We found that CPT1A WT succinylated enolase 1 and reduced enolase enzymatic activity in cells and in vitro. Importantly, mutation of CPT1A Gly710 (G710E) selectively inactivated carnitine palmitoyltransferase (CPTase) activity but not the LSTase activity that decreased enolase activity in cells and promoted cell proliferation under glutamine depletion. These findings suggest that CPT1A acts as an LSTase that can regulate enzymatic activity of a substrate protein and metabolism independent of its classical CPTase activity.
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Affiliation(s)
- Kiran Kurmi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Sadae Hitosugi
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Elizabeth K Wiese
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Larry M Karnitz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Taro Hitosugi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA.
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23
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Wu L, Gong T, Zhou X, Zeng J, Huang R, Wu Y, Li Y. Global analysis of lysine succinylome in the periodontal pathogen Porphyromonas gingivalis. Mol Oral Microbiol 2019; 34:74-83. [PMID: 30672658 DOI: 10.1111/omi.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/22/2018] [Accepted: 01/21/2019] [Indexed: 02/05/2023]
Abstract
The gram-negative anaerobe Porphyromonas gingivalis is not only a keystone periodontal pathogen but also an emerging systemic pathogen. Although the newly discovered protein post-translational modification (PTM), lysine succinylation (Ksuc), appears to play an important role in modulating metabolic processes in bacteria, this PTM has not been investigated in P gingivalis. In this study, we used a highly sensitive proteomics approach combining affinity enrichment with high-resolution liquid chromatography coupled with tandem mass spectrometry to examine Ksuc in P gingivalis. In total, 345 Ksuc sites in 233 proteins were identified and determined to be involved in a variety of cellular processes. In the region surrounding Ksuc sites, lysine residues were drastically overrepresented and sequence motifs with succinyl-lysine flanked by a lysine at the +3 or +6 positions appear to be unique to this pathogen. Additionally, our results suggest a crosstalk between Ksuc and glycosylation, but the overlap between Ksuc and acetylation in P gingivalis is quite different from that observed in other organisms. Notably, Ksuc was observed in proteins associated with established virulence factors, including gingipains, fimbriae, RagB, and PorR. Moreover, products of the factors necessary for P gingivalis in vitro survival (18.5%) were found to be succinylated at lysine sites and the same was observed in products of fitness factors for P gingivalis survival in both abscess and epithelial cell colonization environments (12%). Collectively, these results suggest that Ksuc may be a new mechanism in modulating the virulence, adaptation, and fitness of P gingivalis.
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Affiliation(s)
- Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jumei Zeng
- Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ruijie Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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24
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Hasan MM, Khatun MS, Kurata H. Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites. Cells 2019; 8:cells8020095. [PMID: 30696115 PMCID: PMC6406724 DOI: 10.3390/cells8020095] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.
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Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
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25
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Suzuki S, Kondo N, Yoshida M, Nishiyama M, Kosono S. Dynamic changes in lysine acetylation and succinylation of the elongation factor Tu in Bacillus subtilis. Microbiology (Reading) 2018; 165:65-77. [PMID: 30394869 DOI: 10.1099/mic.0.000737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nε-lysine acetylation and succinylation are ubiquitous post-translational modifications in eukaryotes and bacteria. In the present study, we showed a dynamic change in acetylation and succinylation of TufA, the translation elongation factor Tu, from Bacillus subtilis. Increased acetylation of TufA was observed during the exponential growth phase in LB and minimal glucose conditions, and its acetylation level decreased upon entering the stationary phase, while its succinylation increased during the late stationary phase. TufA was also succinylated during vegetative growth under minimal citrate or succinate conditions. Mutational analysis showed that triple succinylation mimic mutations at Lys306, Lys308 and Lys316 in domain-3 of TufA had a negative effect on B. subtilis growth, whereas the non-acylation mimic mutations at these three lysine residues did not. Consistent with the growth phenotypes, the triple succinylation mimic mutant showed 67 % decreased translation activity in vitro, suggesting a possibility that succinylation at the lysine residues in domain-3 decreases the translation activity. TufA, including Lys308, was non-enzymatically succinylated by physiological concentrations of succinyl-CoA. Lys42 in the G-domain was identified as the most frequently modified acetylation site, though its acetylation was likely dispensable for TufA translation activity and growth. Determination of the intracellular levels of acetylating substrates and TufA acetylation revealed that acetyl phosphate was responsible for acetylation at several lysine sites of TufA, but not for Lys42 acetylation. It was speculated that acetyl-CoA was likely responsible for Lys42 acetylation, though AcuA acetyltransferase was not involved. Zn2+-dependent AcuC and NAD+-dependent SrtN deacetylases were responsible for deacetylation of TufA, including Lys42. These findings suggest the potential regulatory roles of acetylation and succinylation in controlling TufA function and translation in response to nutrient environments in B. subtilis.
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Affiliation(s)
- Shota Suzuki
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoko Kondo
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- 2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,3Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Makoto Nishiyama
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Saori Kosono
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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26
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Abstract
Candida albicans is the most common human fungal pathogen for both immunocompetent and immunocompromised individuals. Lysine succinylation is a frequently occurring post-translational modification that is found in many organisms; however, the role of succinylation is still under investigation. Here, we initiated a first screening of lysine succinylation in C. albicans. We identified 1550 succinylation sites from 389 proteins in C. albicans, demonstrating that succinylation is conservative in this organism. However, the lysine succinylation sites showed some difference in C. albicans, with the overlapping rates between C. albicans and other species ranging from 55% for Saccharomyces cerevisiae, 40% for human, 35% for mouse, and to only 16% for Escherichia coli. The further bioinformatics analysis indicated that the succinylated proteins were involved in a wide range of cellular functions with diverse subcellular localizations. Furthermore, we discovered that lysine succinylation could coexist with phosphorylation and/or acetylation in C. albicans. The KEGG enrichment pathway analysis of these succinylated proteins suggested that succinylation may play an indispensable role in the regulation of the tricarboxylic acid cycle. The bioinformatic data obtained from this study therefore enable the depth-resolved physiological roles of lysine succinylation in C. albicans.
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Affiliation(s)
- Hailin Zheng
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing, Jiangsu 210042, People's Republic of China
| | - Yun He
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China
| | - Xiaowei Zhou
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing, Jiangsu 210042, People's Republic of China
| | - Guanyu Qian
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China
| | - Guixia Lv
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China
| | - Yongnian Shen
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China
| | - Jiyun Liu
- Jingjie PTM Biolab (Hangzhou) Co., Ltd. , Hangzhou, Zhejiang 310018, People's Republic of China
| | - Dongmei Li
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China.,Department of Microbiology & Immunology, Georgetown University Medical Center , Washington, D.C. 20057, United States
| | - Xiaofang Li
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing, Jiangsu 210042, People's Republic of China
| | - Weida Liu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College , Nanjing, Jiangsu 210042 People's Republic of China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing, Jiangsu 210042, People's Republic of China
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27
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Fukushima A, Alrob OA, Zhang L, Wagg CS, Altamimi T, Rawat S, Rebeyka IM, Kantor PF, Lopaschuk GD. Acetylation and succinylation contribute to maturational alterations in energy metabolism in the newborn heart. Am J Physiol Heart Circ Physiol 2016; 311:H347-63. [PMID: 27261364 DOI: 10.1152/ajpheart.00900.2015] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/25/2016] [Indexed: 11/22/2022]
Abstract
Dramatic maturational changes in cardiac energy metabolism occur in the newborn period, with a shift from glycolysis to fatty acid oxidation. Acetylation and succinylation of lysyl residues are novel posttranslational modifications involved in the control of cardiac energy metabolism. We investigated the impact of changes in protein acetylation/succinylation on the maturational changes in energy metabolism of 1-, 7-, and 21-day-old rabbit hearts. Cardiac fatty acid β-oxidation rates increased in 21-day vs. 1- and 7-day-old hearts, whereas glycolysis and glucose oxidation rates decreased in 21-day-old hearts. The fatty acid oxidation enzymes, long-chain acyl-CoA dehydrogenase (LCAD) and β-hydroxyacyl-CoA dehydrogenase (β-HAD), were hyperacetylated with maturation, positively correlated with their activities and fatty acid β-oxidation rates. This alteration was associated with increased expression of the mitochondrial acetyltransferase, general control of amino acid synthesis 5 like 1 (GCN5L1), since silencing GCN5L1 mRNA in H9c2 cells significantly reduced acetylation and activity of LCAD and β-HAD. An increase in mitochondrial ATP production rates with maturation was associated with the decreased acetylation of peroxisome proliferator-activated receptor-γ coactivator-1α, a transcriptional regulator for mitochondrial biogenesis. In addition, hypoxia-inducible factor-1α, hexokinase, and phosphoglycerate mutase expression declined postbirth, whereas acetylation of these glycolytic enzymes increased. Phosphorylation rather than acetylation of pyruvate dehydrogenase (PDH) increased in 21-day-old hearts, accounting for the low glucose oxidation postbirth. A maturational increase was also observed in succinylation of PDH and LCAD. Collectively, our data are the first suggesting that acetylation and succinylation of the key metabolic enzymes in newborn hearts play a crucial role in cardiac energy metabolism with maturation.
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Affiliation(s)
- Arata Fukushima
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Osama Abo Alrob
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Liyan Zhang
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Cory S Wagg
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Tariq Altamimi
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Sonia Rawat
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Ivan M Rebeyka
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Paul F Kantor
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
| | - Gary D Lopaschuk
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada; and
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28
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Zhou M, Xie L, Yang Z, Zhou J, Xie J. Lysine succinylation of Mycobacterium tuberculosis isocitrate lyase (ICL) fine-tunes the microbial resistance to antibiotics. J Biomol Struct Dyn 2016; 35:1030-1041. [PMID: 27023679 DOI: 10.1080/07391102.2016.1169219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lysine succinylation (Ksucc) is a newly identified protein posttranslational modification (PTM), which may play an important role in cellular physiology. However, the role of lysine succinylation in antibiotic resistance remains elusive. Isocitrate lyase (ICL) is crucial for broad-spectrum antibiotics tolerance in Mycobacterium tuberculosis (Mtb). We previously found that MtbICL (Rv0467) has at least three succinylated lysine residues, namely K189, K322, and K334.To explore the effect of succinylation on the activity of MtbICL, mutants' mimicry of the lysine succinylation were generated by site-directed mutagenesis. ICL-K189E mutant strain is more sensitive than the wild-type to rifampicin and streptomycin, but not isoniazid. For the in vitro activity of the purified isocitrate lyase, only K189E mutant showed significantly decreased activity. Crystal structure analysis showed that Lys189 Glu dramatically increased the pKa of Glu188 and decreased the pKa of Lys190, whereas had negligible effect on other residues within 5 Å as well as disruption of the electrostatic interaction between Lys189 and Glu182, which might prevent the closure of the active site loop and cause severe reduction of the enzyme activity. Considering the genetic, biochemical, and crystallographical evidences together, the succinylation of specific ICL residue can fine-tune the bacterial resistance to selected antibiotics. The decreased enzymatic activity resulting from the succinylation-changed electrostatic interaction might underlie this phenotype. This study provided the first insight into the link between lysine succinylation and antibiotic resistance.
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Affiliation(s)
- Mingliang Zhou
- a State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences , Southwest University , Beibei, Chongqing 400715 , China
| | - Longxiang Xie
- a State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences , Southwest University , Beibei, Chongqing 400715 , China
| | - Zhaozhen Yang
- b State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032 , China
| | - Jiahai Zhou
- b State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032 , China
| | - Jianping Xie
- a State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences , Southwest University , Beibei, Chongqing 400715 , China
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Sadhukhan S, Liu X, Ryu D, Nelson OD, Stupinski JA, Li Z, Chen W, Zhang S, Weiss RS, Locasale JW, Auwerx J, Lin H. Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function. Proc Natl Acad Sci U S A 2016; 113:4320-5. [PMID: 27051063 DOI: 10.1073/pnas.1519858113] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular metabolites, such as acyl-CoA, can modify proteins, leading to protein posttranslational modifications (PTMs). One such PTM is lysine succinylation, which is regulated by sirtuin 5 (SIRT5). Although numerous proteins are modified by lysine succinylation, the physiological significance of lysine succinylation and SIRT5 remains elusive. Here, by profiling acyl-CoA molecules in various mouse tissues, we have discovered that different tissues have different acyl-CoA profiles and that succinyl-CoA is the most abundant acyl-CoA molecule in the heart. This interesting observation has prompted us to examine protein lysine succinylation in different mouse tissues in the presence and absence of SIRT5. Protein lysine succinylation predominantly accumulates in the heart whenSirt5is deleted. Using proteomic studies, we have identified many cardiac proteins regulated by SIRT5. Our data suggest that ECHA, a protein involved in fatty acid oxidation, is a major enzyme that is regulated by SIRT5 and affects heart function.Sirt5knockout (KO) mice have lower ECHA activity, increased long-chain acyl-CoAs, and decreased ATP in the heart under fasting conditions.Sirt5KO mice develop hypertrophic cardiomyopathy, as evident from the increased heart weight relative to body weight, as well as reduced shortening and ejection fractions. These findings establish that regulating heart metabolism and function is a major physiological function of lysine succinylation and SIRT5.
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Li X, Hu X, Wan Y, Xie G, Li X, Chen D, Cheng Z, Yi X, Liang S, Tan F. Systematic identification of the lysine succinylation in the protozoan parasite Toxoplasma gondii. J Proteome Res 2014; 13:6087-95. [PMID: 25377623 DOI: 10.1021/pr500992r] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lysine succinylation is a new posttranslational modification identified in histone proteins of Toxoplasma gondii, an obligate intracellular parasite of the phylum Apicomplexa. However, very little is known about their scope and cellular distribution. Here, using LC-MS/MS to identify parasite peptides enriched by immunopurification with succinyl lysine antibody, we produced the first lysine succinylome in this parasite. Overall, a total of 425 lysine succinylation sites that occurred on 147 succinylated proteins were identified in extracellular Toxoplasma tachyzoites, which is a proliferative stage that results in acute toxoplasmosis. With the bioinformatics analysis, it is shown that these succinylated proteins are evolutionarily conserved and involved in a wide variety of cellular functions such as metabolism and epigenetic gene regulation and exhibit diverse subcellular localizations. Moreover, we defined five types of definitively conserved succinylation site motifs, and the results imply that lysine residue of a polypeptide with lysine on the +3 position and without lysine at the -1 to +2 position is a preferred substrate of lysine succinyltransferase. In conclusion, our findings suggest that lysine succinylation in Toxoplasma involves a diverse array of cellular functions, although the succinylation occurs at a low level.
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Xie L, Liu W, Li Q, Chen S, Xu M, Huang Q, Zeng J, Zhou M, Xie J. First succinyl-proteome profiling of extensively drug-resistant Mycobacterium tuberculosis revealed involvement of succinylation in cellular physiology. J Proteome Res 2014; 14:107-19. [PMID: 25363132 DOI: 10.1021/pr500859a] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein lysine succinylation, an emerging protein post-translational modification widespread among eukaryotic and prokaryotic cells, represents an important regulator of cellular processes. However, the extent and function of lysine succinylation in Mycobacterium tuberculosis, especially extensively drug-resistant strain, remain elusive. Combining protein/peptide prefractionation, immunoaffinity enrichment, and LC-MS/MS analysis, a total of 686 succinylated proteins and 1739 succinylation sites of M. tuberculosis were identified, representing the first global profiling of M. tuberculosis lysine succinylation. The identified succinylated proteins are involved in a variety of cellular functions such as metabolic processes, transcription, translation, and stress responses and exhibit different subcellular localization via GO, protein interaction network, and other bioinformatic analysis. Notably, proteins involved in protein biosynthesis and carbon metabolism are preferred targets of lysine succinylation. Moreover, two prevalent sequence patterns: EK(suc) and K*****K(suc), can be found around the succinylation sites. There are 109 lysine-succinylated homologues in E. coli, suggesting highly conserved succinylated proteins. Succinylation was found to occur at the active sites predicted by Prosite signature including Rv0946c, indicating that lysine succinylation may affect their activities. There is extensive overlapping between acetylation sites and succinylation sites in M. tuberculosis. Many M. tuberculosis metabolic enzymes and antibiotic resistance proteins were succinylated. This study provides a basis for further characterization of the pathophysiological role of lysine succinylation in M. tuberculosis.
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Affiliation(s)
- Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715, China
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Tan M, Peng C, Anderson KA, Chhoy P, Xie Z, Dai L, Park J, Chen Y, Huang H, Zhang Y, Ro J, Wagner GR, Green MF, Madsen AS, Schmiesing J, Peterson BS, Xu G, Ilkayeva OR, Muehlbauer MJ, Braulke T, Mühlhausen C, Backos DS, Olsen CA, McGuire PJ, Pletcher SD, Lombard DB, Hirschey MD, Zhao Y. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab 2014; 19:605-17. [PMID: 24703693 PMCID: PMC4108075 DOI: 10.1016/j.cmet.2014.03.014] [Citation(s) in RCA: 542] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 11/17/2013] [Accepted: 01/27/2014] [Indexed: 01/20/2023]
Abstract
We report the identification and characterization of a five-carbon protein posttranslational modification (PTM) called lysine glutarylation (Kglu). This protein modification was detected by immunoblot and mass spectrometry (MS), and then comprehensively validated by chemical and biochemical methods. We demonstrated that the previously annotated deacetylase, sirtuin 5 (SIRT5), is a lysine deglutarylase. Proteome-wide analysis identified 683 Kglu sites in 191 proteins and showed that Kglu is highly enriched on metabolic enzymes and mitochondrial proteins. We validated carbamoyl phosphate synthase 1 (CPS1), the rate-limiting enzyme in urea cycle, as a glutarylated protein and demonstrated that CPS1 is targeted by SIRT5 for deglutarylation. We further showed that glutarylation suppresses CPS1 enzymatic activity in cell lines, mice, and a model of glutaric acidemia type I disease, the last of which has elevated glutaric acid and glutaryl-CoA. This study expands the landscape of lysine acyl modifications and increases our understanding of the deacylase SIRT5.
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Affiliation(s)
- Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kristin A Anderson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Peter Chhoy
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Zhongyu Xie
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Lunzhi Dai
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jeongsoon Park
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yue Chen
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yi Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jennifer Ro
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory R Wagner
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michelle F Green
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Andreas S Madsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Brett S Peterson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Guofeng Xu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Olga R Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christian A Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter J McGuire
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA.
| | - Yingming Zhao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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