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Ye Z, Liu R, Wang H, Zuo A, Jin C, Wang N, Sun H, Feng L, Yang H. Neuroprotective potential for mitigating ischemia-reperfusion-induced damage. Neural Regen Res 2025; 20:2199-2217. [PMID: 39104164 PMCID: PMC11759025 DOI: 10.4103/nrr.nrr-d-23-01985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/09/2024] [Accepted: 06/22/2024] [Indexed: 08/07/2024] Open
Abstract
Reperfusion following cerebral ischemia causes both structural and functional damage to brain tissue and could aggravate a patient's condition; this phenomenon is known as cerebral ischemia-reperfusion injury. Current studies have elucidated the neuroprotective role of the sirtuin protein family (Sirtuins) in modulating cerebral ischemia-reperfusion injury. However, the potential of utilizing it as a novel intervention target to influence the prognosis of cerebral ischemia-reperfusion injury requires additional exploration. In this review, the origin and research progress of Sirtuins are summarized, suggesting the involvement of Sirtuins in diverse mechanisms that affect cerebral ischemia-reperfusion injury, including inflammation, oxidative stress, blood-brain barrier damage, apoptosis, pyroptosis, and autophagy. The therapeutic avenues related to Sirtuins that may improve the prognosis of cerebral ischemia-reperfusion injury were also investigated by modulating Sirtuins expression and affecting representative pathways, such as nuclear factor-kappa B signaling, oxidative stress mediated by adenosine monophosphate-activated protein kinase, and the forkhead box O. This review also summarizes the potential of endogenous substances, such as RNA and hormones, drugs, dietary supplements, and emerging therapies that regulate Sirtuins expression. This review also reveals that regulating Sirtuins mitigates cerebral ischemia-reperfusion injury when combined with other risk factors. While Sirtuins show promise as a potential target for the treatment of cerebral ischemia-reperfusion injury, most recent studies are based on rodent models with circadian rhythms that are distinct from those of humans, potentially influencing the efficacy of Sirtuins-targeting drug therapies. Overall, this review provides new insights into the role of Sirtuins in the pathology and treatment of cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Zi Ye
- The Clinical Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Runqing Liu
- The Clinical Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Hangxing Wang
- Division of Infectious Diseases, Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aizhen Zuo
- The Clinical Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Cen Jin
- School of Medical Imaging, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Nan Wang
- Division of Gastroenterology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Huiqi Sun
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu Province, China
| | - Luqian Feng
- Department of Neurosurgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Hua Yang
- Department of Neurosurgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
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2
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Lou Y, Dong C, Jiang Q, He Z, Yang S. Protein succinylation mechanisms and potential targeted therapies in urinary disease. Cell Signal 2025; 131:111744. [PMID: 40090556 DOI: 10.1016/j.cellsig.2025.111744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 03/04/2025] [Accepted: 03/11/2025] [Indexed: 03/18/2025]
Abstract
Succinylation is a relatively common post-translational modification. It occurs in the cytoplasm, mitochondria, and the nucleus, where its essential precursor, succinyl-CoA, is present, allowing for the modification of non-histone and histone proteins. In normal cells, succinylation levels are carefully regulated to sustain a dynamic balance, necessitating the involvement of various regulatory mechanisms, including non-enzymatic reactions, succinyltransferases, and desuccinylases. Among these regulatory factors, sirtuin 5, the first identified desuccinylase, plays a significant role and has been extensively researched. The level of succinylation has a significant effect on multiple metabolic pathways, including the tricarboxylic acid cycle, redox balance, and fatty acid metabolism. Dysregulated succinylation can contribute to the progression or exacerbation of various urinary diseases. Succinylation predominantly affects disease progression by altering the expression of key genes and modulating the activity of enzymes involved in vital metabolic processes. Desuccinylases primarily affect enzymes associated with Warburg's effect, thereby affecting the energy supply of tumor cells, while succinyltransferases can regulate gene transcription to alter cell phenotype, thereby involving the development of urinary diseases. Considering these effects, targeting succinylation-related enzymes to regulate metabolic pathways or gene expression may offer a promising therapeutic strategy for treating urinary diseases.
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Affiliation(s)
- Yuanquan Lou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, People's Republic of China
| | - Caitao Dong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, People's Republic of China
| | - Qinhong Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, People's Republic of China
| | - Ziqi He
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, People's Republic of China.
| | - Sixing Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, People's Republic of China.
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Parashar S, Kaushik A, Ambasta RK, Kumar P. E2 conjugating enzymes: A silent but crucial player in ubiquitin biology. Ageing Res Rev 2025; 108:102740. [PMID: 40194666 DOI: 10.1016/j.arr.2025.102740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 03/14/2025] [Accepted: 03/19/2025] [Indexed: 04/09/2025]
Abstract
E2 conjugating enzymes serve as the linchpin of the Ubiquitin-Proteasome System (UPS), facilitating ubiquitin (Ub) transfer to substrate proteins and regulating diverse processes critical to cellular homeostasis. The interaction of E2s with E1 activating enzymes and E3 ligases singularly positions them as middlemen of the ubiquitin machinery that guides protein turnover. Structural determinants of E2 enzymes play a pivotal role in these interactions, enabling precise ubiquitin transfer and substrate specificity. Regulation of E2 enzymes is tightly controlled through mechanisms such as post-translational modifications (PTMs), allosteric control, and gene expression modulation. Specific residues that undergo PTMs highlight their impact on E2 function and their role in ubiquitin dynamics. E2 enzymes also cooperate with deubiquitinases (DUBs) to maintain proteostasis. Design of small molecule inhibitors to modulate E2 activity is emerging as promising avenue to restrict ubiquitination as a potential therapeutic intervention. Additionally, E2 enzymes have been implicated in the pathogenesis and progression of neurodegenerative disorders (NDDs), where their dysfunction contributes to disease mechanisms. In summary, examining E2 enzymes from structural and functional perspectives offers potential to advance our understanding of cellular processes and assist in discovery of new therapeutic targets.
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Affiliation(s)
- Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India.
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4
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Bian Y, Hu Z, Wang R, Xie S, Sun Y, Liu T, Ma S, Liu B, Tan M, Xu JY. Characterization of substrate distribution and functional implication of lysine acylations in Staphylococcus aureus. J Proteomics 2025; 316:105419. [PMID: 40057026 DOI: 10.1016/j.jprot.2025.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Revised: 03/04/2025] [Accepted: 03/05/2025] [Indexed: 03/14/2025]
Abstract
Staphylococcus aureus (S. aureus) is a major pathogen whose post-translational modifications (PTMs) regulate key biological processes that exert a substantial impact on protein function within this pathogen. In this study, we comprehensively analyzed the overall patterns of three lysine acylation in S. aureus including acetylation, succinylation, and malonylation. Using mass spectrometry, we identified 1249 acetylated, 871 succinylated, and 67 malonylated sites. Bioinformatic analysis furtherly revealed that both lysine acetylation and succinylation exhibited a preferential association with glutamate residues near the modified lysine positions. Pathway enrichment showed that modified substrates were associated with ribosomes and metabolic functions. Additional functional exploration showed that lysine succinylation significantly regulates the enzymatic activity of Glutamyl-tRNA amidotransferase and Carbamoyl phosphate synthase. In conclusion, our study enhanced the comprehension of lysine succinylation in S. aureus and highlights potential targets related to its pathogenicity at the post-translational modification level. SIGNIFICANCE NEW: Lysine acylations play important roles in regulating bacterial survival and pathogenicity in Staphylococcus aureus. However, comprehensive and systematic investigations of the lysine acylomes in S. aureus remain insufficient. In this study, we conducted a comprehensive analysis of three lysine acylation modifications in Staphylococcus aureus subspecies aureus ATCC 25923 using mass spectrometry-based proteomic techniques. The objective was to investigate the potential impact of these modifications on protein function. Our bioinformatics analysis identified a significant correlation between lysine acylations and both ribosomal and metabolic pathways. Through additional experimental validation, we have substantiated that lysine succinylation plays a significant regulatory role in the activities of Glutamyl-tRNA amidinotransferase and Carbamoyl phosphate synthetase, consequently exerting a profound impact on cellular energy metabolism and protein synthesis in S. aureus. Collectively, our study underscores the pivotal role of lysine acylation modifications in S. aureus in modulating enzyme function, thereby offering valuable insights into the biology of S. aureus and informing potential therapeutic strategies.
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Affiliation(s)
- Yunxu Bian
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Zunli Hu
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China
| | - Rongzhen Wang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuyu Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yewen Sun
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Tianqi Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Shaojie Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Minjia Tan
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China; Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jun-Yu Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China; Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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5
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Wang B, Wang X, Guo M, Xu H. Succinate reduces biological activity and mitochondrial function of human adipose-derived stem cells. Cell Cycle 2025:1-13. [PMID: 40394998 DOI: 10.1080/15384101.2025.2508109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 05/22/2025] Open
Abstract
Elevated succinate accumulation has been demonstrated to be associated with metabolic and inflammatory disorders. Our previous study revealed that adipose-derived stem cells (ADSC) from obese individuals exhibit high succinate, reduced biological activity, and mitochondrial dysfunction. However, the precise role of succinate in these processes remains unclear. Here, we investigated the effects of excess succinate on cellular biological activity, immunomodulatory capacity, and mitochondrial function of ADSC. We found that elevated succinate levels in ADSC decreased proliferation and differentiation potential, while promoting M1 macrophage polarization. Furthermore, succinate accumulation impaired mitochondrial biogenesis and metabolism, increasing in reactive oxygen species (ROS) production and inflammatory responses. Transcriptome sequencing analysis further confirmed that succinate upregulated inflammatory pathways, suppressed mitochondrial biogenesis and metabolism, and enhanced cellular apoptosis and senescence, accompanied by reduced DNA replication and repair. Overall, these findings imply that succinate accumulation in ADSC triggers inflammatory response and mitochondrial dysfunction, potentially contributing to a decline of cellular biological activity. Targeting succinate may offer therapeutic potential for metabolic disorders.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Laboratory of Systems Medicine for Cancer, Renji-MedX Clinical Stem Cell Research Center, RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxin Wang
- State Laboratory of Systems Medicine for Cancer, Renji-MedX Clinical Stem Cell Research Center, RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huiming Xu
- State Laboratory of Systems Medicine for Cancer, Renji-MedX Clinical Stem Cell Research Center, RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Barik S, Aldar KS, Chakraborty A, Panda AK, Kar RK, Biswas A. Understanding the structural and functional implications of lysine succinylation in Mycobacterium tuberculosis heat shock protein 16.3. Int J Biol Macromol 2025; 307:142046. [PMID: 40089242 DOI: 10.1016/j.ijbiomac.2025.142046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 03/10/2025] [Accepted: 03/11/2025] [Indexed: 03/17/2025]
Abstract
Heat shock protein 16.3 (Hsp16.3), a major immunodominant antigen of Mycobacterium tuberculosis, exhibits molecular chaperone function that is essential for pathogen's survival and slow growth inside hosts, as well as for enhancing the efficacy of Bacillus Calmette-Guérin (BCG) vaccine. Proteomic studies revealed that Hsp16.3 undergoes lysine succinylation in vivo at all lysine residues (K47, K64, K78, K85, K114, K119 and K132) except K136. However, the effects of succinylation on its structure and function remain unexplored. This study investigated the impact of succinylation, induced by physiological (succinyl-CoA) and/or non-physiological (succinic anhydride) donors, on the structure, stability and chaperone function of Hsp16.3. Succinylation of all eight lysine residues, affirmed via fluorescamine assay and mass spectrometry, led to structural (secondary and tertiary) alterations, as indicated by circular dichroism (CD), fluorescence and in-silico analyses. Succinylation induced oligomeric dissociation (dodecamer to dimer) and enhanced surface hydrophobicity of Hsp16.3. Moreover, succinylation reduced protein stability, making it more conformationally flexible and less compact, as revealed by urea-denaturation, chymotrypsin-digestion and computational studies. Despite this reduced stability, succinylated Hsp16.3 exhibited enhanced chaperone activity, offering improved protection to stressed-prone client proteins. These findings provide useful insights into this modification, offering potential therapeutic avenues for targeting Hsp16.3 in M. tuberculosis infection.
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Affiliation(s)
- Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, India
| | - Kunal Shivaji Aldar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Ayon Chakraborty
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali 140413, India
| | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, Kalinga Institute of Industrial Technology, Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, India.
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Liu H, Binoy A, Ren S, Martino TC, Miller AE, Willis CRG, Veerabhadraiah SR, Bons J, Rose JP, Schilling B, Jurynec MJ, Zhu S. Regulation of Chondrocyte Metabolism and Osteoarthritis Development by Sirt5 Through Protein Lysine Malonylation. Arthritis Rheumatol 2025. [PMID: 40176311 DOI: 10.1002/art.43164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 02/11/2025] [Accepted: 03/14/2025] [Indexed: 04/04/2025]
Abstract
OBJECTIVE Chondrocytemetabolic dysfunction plays an important role in osteoarthritis (OA) development during aging and obesity. Protein posttranslational modifications (PTMs) have recently emerged as an important regulator of cellular metabolism. We aim to study one type of PTM, lysine malonylation (MaK), and its regulator sirtuin 5 (Sirt5) in OA development. METHODS Human and mouse cartilage tissues were used to measure SIRT5 and MaK levels. Both systemic and cartilage-specific conditional knockout mouse models were subject to high-fat diet treatment to induce obesity and OA. Proteomics analysis was performed in Sirt5-/- and wild-type chondrocytes. SIRT5 mutation was identified in the Utah Population Database. RESULTS We found that SIRT5 decreases while MaK increases in the cartilage during aging. A combination of Sirt5 deficiency and obesity exacerbates joint degeneration in a sex-dependent manner in mice. We further delineate the malonylome in chondrocytes, pinpointing MaK's predominant impact on various metabolic pathways, such as carbon metabolism and glycolysis. Lastly, we identified a rare coding mutation in SIRT5 that dominantly segregates in a family with OA. The mutation results in substitution of an evolutionally invariant phenylalanine to leucine (F101L) in the catalytic domain. The mutant protein results in a higher MaK level and decreased expression of cartilage extracellular matrix genes and upregulation of inflammation-associated genes. CONCLUSION We found that Sirt5-mediated MaK is an important regulator of chondrocyte cellular metabolism, and dysregulation of Sirt5-MaK could be an important mechanism underlying aging- and obesity-associated OA development.
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Affiliation(s)
- Huanhuan Liu
- Heritage College of Osteopathic Medicine, Ohio University, Athens
| | - Anupama Binoy
- Heritage College of Osteopathic Medicine, Ohio University, Athens
| | - Siqi Ren
- Heritage College of Osteopathic Medicine, Ohio University, Athens
| | - Thomas C Martino
- Heritage College of Osteopathic Medicine, Ohio University, Athens
| | - Anna E Miller
- Heritage College of Osteopathic Medicine, Ohio University, Athens
| | - Craig R G Willis
- University of Bradford, Bradford, University of Exeter, Exeter, United Kingdom
| | | | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Jacob P Rose
- Buck Institute for Research on Aging, Novato, California
| | | | | | - Shouan Zhu
- Heritage College of Osteopathic Medicine, Ohio University, Athens
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Yang N, Li L, Shi XL, Liu YP, Wen R, Yang YH, Zhang T, Yang XR, Xu YF, Liu CF, Ning W, Zhang TN. Succinylation of SERCA2a at K352 Promotes Its Ubiquitinoylation and Degradation by Proteasomes in Sepsis-Induced Heart Dysfunction. Circ Heart Fail 2025; 18:e012180. [PMID: 39996319 DOI: 10.1161/circheartfailure.124.012180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 01/28/2025] [Indexed: 02/26/2025]
Abstract
BACKGROUND Intracellular Ca2+ cycling governs effective myocardial systolic contraction and diastolic relaxation. SERCA2a (sarco/endoplasmic reticulum Ca2+ ATPase type 2a), which plays a crucial role in controlling intracellular Ca2+ signaling and myocardial cell function, is downregulated and inactivated during sepsis-induced heart dysfunction. However, the cause of this dysregulation remains unclear. In this study, we investigated the effect of lysine succinylation in lipopolysaccharide-induced septic heart dysfunction through global succinylome analysis of myocardial tissues from septic rats. METHODS We conducted a succinylome profiling and developed a protein language model-based framework to prioritize succinylation at a functionally important site, and further analysis revealed crosstalk between ubiquitination and succinylation of SERCA2a. The succinylation of SERCA2a in septic rats or lipopolysaccharide-treated cells were detected by co-immunoprecipitation. Thereafter, a desuccinylated SERCA2aK352R was introduced and its function and stability were determined by Ca2+ transient and Western blot, respectively. Meanwhile, the effect on SERCA2aK352R on heart function was assessed in vivo by echocardiography and hemodynamics. RESULTS We identified 10 324 succinylated lysine sites in heart tissues, including 1042 differentially succinylated lysine sites, in response to lipopolysaccharide. SERCA2a was hypersuccinylated in the myocardial tissues of septic rats and lipopolysaccharide-treated cardiomyocytes. Increased ubiquitination level, reduced protein level, and activity of SERCA2a were observed, along with increased succinylation of SERCA2a in vivo and in vitro. K352 was essential for SERCA2a succinylation, which reduced SERCA2a protein level by promoting formation of the K48 ubiquitin chain on SERCA2a and its degradation by proteasomes. Co-immunoprecipitation combined with liquid chromatography-tandem mass spectrometry identified that SIRT2 (sirtuin2), a deacylase, exhibited interaction with SERCA2a. Furthermore, SIRT2 decreased K352 succinylation of SERCA2a, suggesting that SIRT2 may function as a desuccinylase for SERCA2a. CONCLUSIONS Succinylation of SERCA2a at K352, which was controlled by SIRT2, promotes its ubiquitinoylation and degradation by proteasomes in sepsis-induced heart dysfunction.
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Affiliation(s)
- Ni Yang
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Linus Li
- Institute for Clinical Medical Research, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, China (L.L., W.N.)
| | - Xiao-Lu Shi
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing (X.-L.S.)
| | - Yong-Ping Liu
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Ri Wen
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Yu-Hang Yang
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Tao Zhang
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Xin-Ru Yang
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Yang-Fan Xu
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Chun-Feng Liu
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
| | - Wanshan Ning
- Institute for Clinical Medical Research, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, China (L.L., W.N.)
| | - Tie-Ning Zhang
- Department of Pediatrics, Pediatric Intensive Care Unit, Shengjing Hospital of China Medical University, Shenyang (N.Y., Y.-P.L., R.W., Y.-H.Y., T.Z., X.-R.Y., Y.-F.X., C.-F.L., T.-N.Z.)
- Institute for Clinical Medical Research, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, China (L.L., W.N.)
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9
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Guo L, Du Y, Li H, He T, Yao L, Yang G, Yang X. Metabolites-mediated posttranslational modifications in cardiac metabolic remodeling: Implications for disease pathology and therapeutic potential. Metabolism 2025; 165:156144. [PMID: 39864796 DOI: 10.1016/j.metabol.2025.156144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 01/20/2025] [Accepted: 01/22/2025] [Indexed: 01/28/2025]
Abstract
The nonenergy - producing functions of metabolism are attracting increasing attention, as metabolic changes are involved in discrete pathways modulating enzyme activity and gene expression. Substantial evidence suggests that myocardial metabolic remodeling occurring during diabetic cardiomyopathy, heart failure, and cardiac pathological stress (e.g., myocardial ischemia, pressure overload) contributes to the progression of pathology. Within the rewired metabolic network, metabolic intermediates and end-products can directly alter protein function and/or regulate epigenetic modifications by providing acyl groups for posttranslational modifications, thereby affecting the overall cardiac stress response and providing a direct link between cellular metabolism and cardiac pathology. This review provides a comprehensive overview of the functional diversity and mechanistic roles of several types of metabolite-mediated histone and nonhistone acylation, namely O-GlcNAcylation, lactylation, crotonylation, β-hydroxybutyrylation, and succinylation, as well as fatty acid-mediated modifications, in regulating physiological processes and contributing to the progression of heart disease. Furthermore, it explores the potential of these modifications as therapeutic targets for disease intervention.
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Affiliation(s)
- Lifei Guo
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; Cadet Team 6 of School of Basic Medicine, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Yuting Du
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Heng Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Li Yao
- Department of Pathology, Xi' an No. 3 Hospital, The Affiliated Hospital of Northwest University, Xi' an 710018, China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China.
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China.
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10
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Zhang K, Jagannath C. Crosstalk between metabolism and epigenetics during macrophage polarization. Epigenetics Chromatin 2025; 18:16. [PMID: 40156046 PMCID: PMC11954343 DOI: 10.1186/s13072-025-00575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Accepted: 02/17/2025] [Indexed: 04/01/2025] Open
Abstract
Macrophage polarization is a dynamic process driven by a complex interplay of cytokine signaling, metabolism, and epigenetic modifications mediated by pathogens. Upon encountering specific environmental cues, monocytes differentiate into macrophages, adopting either a pro-inflammatory (M1) or anti-inflammatory (M2) phenotype, depending on the cytokines present. M1 macrophages are induced by interferon-gamma (IFN-γ) and are characterized by their reliance on glycolysis and their role in host defense. In contrast, M2 macrophages, stimulated by interleukin-4 (IL-4) and interleukin-13 (IL-13), favor oxidative phosphorylation and participate in tissue repair and anti-inflammatory responses. Metabolism is tightly linked to epigenetic regulation, because key metabolic intermediates such as acetyl-coenzyme A (CoA), α-ketoglutarate (α-KG), S-adenosylmethionine (SAM), and nicotinamide adenine dinucleotide (NAD+) serve as cofactors for chromatin-modifying enzymes, which in turn, directly influences histone acetylation, methylation, RNA/DNA methylation, and protein arginine methylation. These epigenetic modifications control gene expression by regulating chromatin accessibility, thereby modulating macrophage function and polarization. Histone acetylation generally promotes a more open chromatin structure conducive to gene activation, while histone methylation can either activate or repress gene expression depending on the specific residue and its methylation state. Crosstalk between histone modifications, such as acetylation and methylation, further fine-tunes macrophage phenotypes by regulating transcriptional networks in response to metabolic cues. While arginine methylation primarily functions in epigenetics by regulating gene expression through protein modifications, the degradation of methylated proteins releases arginine derivatives like asymmetric dimethylarginine (ADMA), which contribute directly to arginine metabolism-a key factor in macrophage polarization. This review explores the intricate relationships between metabolism and epigenetic regulation during macrophage polarization. A better understanding of this crosstalk will likely generate novel therapeutic insights for manipulating macrophage phenotypes during infections like tuberculosis and inflammatory diseases such as diabetes.
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Affiliation(s)
- Kangling Zhang
- Department of Pharmacology and Toxicology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA.
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA.
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11
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Pajares MÁ. Posttranslational Regulation of Mammalian Sulfur Amino Acid Metabolism. Int J Mol Sci 2025; 26:2488. [PMID: 40141131 PMCID: PMC11942099 DOI: 10.3390/ijms26062488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 03/05/2025] [Accepted: 03/09/2025] [Indexed: 03/28/2025] Open
Abstract
Metabolism of the mammalian proteinogenic sulfur amino acids methionine and cysteine includes the methionine cycle and reverse transsulfuration pathway, establishing many connections with other important metabolic routes. The main source of these amino acids is the diet, which also provides B vitamins required as cofactors for several enzymes of the metabolism of these amino acids. While methionine is considered an essential amino acid, cysteine can be produced from methionine in a series of reactions that also generate homocysteine, a non-proteinogenic amino acid linking reverse transsulfuration with the methionine and folate cycles. These pathways produce key metabolites that participate in synthesizing a large variety of compounds and important regulatory processes (e.g., epigenetic methylations). The impairment of sulfur amino acid metabolism manifests in many pathological processes, mostly correlated with oxidative stress and alterations in glutathione levels that also depend on this part of the cellular metabolism. This review analyzes the current knowledge on the posttranslational regulation of mammalian sulfur amino acid metabolism, highlighting the large number of modification sites reported through high-throughput studies and the surprisingly limited knowledge of their functional impact.
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Affiliation(s)
- María Ángeles Pajares
- Department of Molecular and Cellular Biosciences, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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12
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Abdeen AH, Trist BG, Nikseresht S, Harwood R, Roudeau S, Rowlands BD, Kreilaus F, Cottam V, Mor D, Richardson M, Siciliano J, Forkgen J, Schaffer G, Genoud S, Li AA, Proschogo N, Antonio B, Falkenberg G, Brueckner D, Kysenius K, Liddell JR, Fat SCM, Wu S, Fifita J, Lockwood TE, Bishop DP, Blair I, Ortega R, Crouch PJ, Double KL. Parkinson-like wild-type superoxide dismutase 1 pathology induces nigral dopamine neuron degeneration in a novel murine model. Acta Neuropathol 2025; 149:22. [PMID: 40042537 PMCID: PMC11882636 DOI: 10.1007/s00401-025-02859-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 02/12/2025] [Accepted: 02/12/2025] [Indexed: 03/09/2025]
Abstract
Atypical wild-type superoxide dismutase 1 (SOD1) protein misfolding and deposition occurs specifically within the degenerating substantia nigra pars compacta (SNc) in Parkinson disease. Mechanisms driving the formation of this pathology and relationship with SNc dopamine neuron health are yet to be fully understood. We applied proteomic mass spectrometry and synchrotron-based biometal quantification to post-mortem brain tissues from the SNc of Parkinson disease patients and age-matched controls to uncover key factors underlying the formation of wild-type SOD1 pathology in this disorder. We also engineered two of these factors - brain copper deficiency and upregulated SOD1 protein levels - into a novel mouse strain, termed the SOCK mouse, to verify their involvement in the development of Parkinson-like wild-type SOD1 pathology and their impact on dopamine neuron health. Soluble SOD1 protein in the degenerating Parkinson disease SNc exhibited altered post-translational modifications, which may underlie changes to the enzymatic activity and aggregation of the protein in this region. These include decreased copper binding, dysregulation of physiological glycosylation, and atypical oxidation and glycation of key SOD1 amino acid residues. We demonstrated that the biochemical profile introduced in SOCK mice promotes the same post-translational modifications and the development of Parkinson-like wild-type SOD1 pathology in the midbrain and cortex. This pathology accumulates progressively with age and is accompanied by nigrostriatal degeneration and dysfunction, which occur in the absence of α-synuclein deposition. These mice do not exhibit weight loss nor spinal cord motor neuron degeneration, distinguishing them from transgenic mutant SOD1 mouse models. This study provides the first in vivo evidence that mismetallation and altered post-translational modifications precipitates wild-type SOD1 misfolding, dysfunction, and deposition in the Parkinson disease brain, which may contribute to SNc dopamine neuron degeneration. Our data position this pathology as a novel drug target for this disorder, with a particular focus on therapies capable of correcting alterations to SOD1 post-translational modifications.
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Affiliation(s)
- Amr H Abdeen
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Benjamin G Trist
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Sara Nikseresht
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Richard Harwood
- Sydney Microscopy and Microanalysis, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stéphane Roudeau
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, 33170, Gradignan, France
| | - Benjamin D Rowlands
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Fabian Kreilaus
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Veronica Cottam
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - David Mor
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Miriam Richardson
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Joel Siciliano
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Julia Forkgen
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Greta Schaffer
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Sian Genoud
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Anne A Li
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Nicholas Proschogo
- Mass Spectrometry Facility, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Bernadeth Antonio
- Mass Spectrometry Facility, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dennis Brueckner
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Kai Kysenius
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jeffrey R Liddell
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sandrine Chan Moi Fat
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Sharlynn Wu
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Jennifer Fifita
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Thomas E Lockwood
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - David P Bishop
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Ian Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Richard Ortega
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, 33170, Gradignan, France
| | - Peter J Crouch
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kay L Double
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia.
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13
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Zuo Y, Fang X, Chen J, Ji J, Li Y, Wu Z, Liu X, Zeng X, Deng Z, Yin H, Zhao A. MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human. Brief Bioinform 2025; 26:bbaf189. [PMID: 40285360 PMCID: PMC12031725 DOI: 10.1093/bib/bbaf189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 03/27/2025] [Accepted: 04/03/2025] [Indexed: 04/29/2025] Open
Abstract
In post-translational modification, covalent bonds on lysine and attached chemical groups significantly change proteins' physical and chemical properties. They shape protein structures, enhance function and stability, and are vital for physiological processes, affecting health and disease through mechanisms like gene expression, signal transduction, protein degradation, and cell metabolism. Although lysine (K) modification sites are considered among the most common types of post-translational modifications in proteins, research on K-PTMs has largely overlooked the synergistic effects between different modifications and lacked the techniques to address the problem of sample imbalance. Based on this, the Extreme Point Deviation Compensated Clustering (EPDCC) Undersampling algorithm was proposed in this study and combined with Cross-Scale Convolutional Neural Networks (CSCNNs) to develop a novel computational tool, MlyPredCSED, for simultaneously predicting multiple lysine modification sites. MlyPredCSED employs Multi-Label Position-Specific Triad Amino Acid Propensity and the physicochemical properties of amino acids to enhance the richness of sequence information. To address the challenge of sample imbalance, the innovative EPDCC Undersampling technique was introduced to adjust the majority class samples. The model's training and testing phase relies on the advanced CSCNN framework. MlyPredCSED, through cross-validation and testing, outperformed existing models, especially in complex categories with multiple modification sites. This research not only provides an efficient method for the identification of lysine modification sites but also demonstrates its value in biological research and drug development. To facilitate efficient use of MlyPredCSED by researchers, we have specifically developed an accessible free web tool: http://www.mlypredcsed.com.
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Affiliation(s)
- Yun Zuo
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Xingze Fang
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Jiankang Chen
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Jiayi Ji
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Yuwen Li
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Zeyu Wu
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Xiangrong Liu
- Department of Computer Science and Technology, National Institute for Data Science in Health and Medicine, Xiamen Key Laboratory of Intelligent Storage and Computing, Xiamen University, Xiamen 361005, China
| | - Xiangxiang Zeng
- School of Information Science and Engineering, Hunan University, Changsha, China
| | - Zhaohong Deng
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi 214000, China
| | - Hongwei Yin
- Department of Oncology, The First Affiliated Hospital of Naval Military Medical University, Shanghai 200000, China
| | - Anjing Zhao
- Department of Oncology, The First Affiliated Hospital of Naval Military Medical University, Shanghai 200000, China
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14
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Li L, Liu Y, Liu D, Wang J, Wang M, Xiang B, Qin J, Yao T, Li W, Wu P, Wang Q, Zhang J, Xu Y, Liu M, Wang Y, Ma G, Liu R, Li X, Huai Z, Huang Y, Guo H, Yang B, Feng L, Huang D, Zhang K, Wang L, Liu B. Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation. Nat Microbiol 2025; 10:749-764. [PMID: 39891012 DOI: 10.1038/s41564-025-01931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/13/2025] [Indexed: 02/03/2025]
Abstract
Succinate upregulates enterohaemorrhagic Escherichia coli (EHEC) virulence. Lysine succinylation, a post-translational modification, regulates cellular function in eukaryotes but is less characterized in bacteria. We hypothesized that lysine succinylation regulates EHEC virulence. Here we used SILAC-based proteomics and characterized the EHEC succinylome to show that the transcription factor, PurR, is succinylated at K24 and K55. Succinylation of PurR inhibited its ability to directly bind DNA and repress expression of a major virulence factor, the Type 3 Secretion System (T3SS), thus increasing T3SS expression. Deletion of purR, or K24E or K55E mutation, increased EHEC adherence to cells and colonization of infant rabbits. Using mice treated with streptomycin to deplete succinate, or colonized with succinate-producing Prevotella copri to increase succinate levels, we showed that microbiota-derived succinate increased succinylation of PurR to promote virulence of Citrobacter rodentium, a model for EHEC, in mice. Lastly, we identified CitC as the succinyltransferase required for PurR modification.
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Affiliation(s)
- Linxing Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, P. R. China
- Nankai International Advanced Research Institute, Shenzhen, P. R. China
| | - Yutao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Dan Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Jing Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Min Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Binbin Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Jingliang Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Ting Yao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Wanwu Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Pan Wu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Qian Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Jianji Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yanli Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Miaomiao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Yanling Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Guozhen Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Ruiying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Xiaoya Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Zimeng Huai
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Yu Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Han Guo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Bin Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Lu Feng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, P. R. China
- Nankai International Advanced Research Institute, Shenzhen, P. R. China
| | - Di Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China.
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, P. R. China.
- Nankai International Advanced Research Institute, Shenzhen, P. R. China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Lei Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China.
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, P. R. China.
- Nankai International Advanced Research Institute, Shenzhen, P. R. China.
| | - Bin Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China.
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, P. R. China.
- Nankai International Advanced Research Institute, Shenzhen, P. R. China.
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15
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Zhang B, Qi T, Lin J, Zhai S, Wang X, Zhou L, Deng X. KLF6-mediated recruitment of the p300 complex enhances H3K23su and cooperatively upregulates SEMA3C with FOSL2 to drive 5-FU resistance in colon cancer cells. Exp Mol Med 2025; 57:667-685. [PMID: 40082673 PMCID: PMC11958781 DOI: 10.1038/s12276-025-01424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 11/17/2024] [Accepted: 12/23/2024] [Indexed: 03/16/2025] Open
Abstract
Histone lysine succinylation, an emerging epigenetic marker, has been implicated in diverse cellular functions, yet its role in cancer drug resistance is not well understood. Here we investigated the genome-wide alterations in histone 3 lysine 23 succinylation (H3K23su) and its impact on gene expression in 5-fluorouracil (5-FU)-resistant HCT15 colon cancer cells. We utilized CUT&Tag assays to identify differentially enriched regions (DERs) of H3K23su in 5-FU-resistant HCT15 cells via integration with ATAC-seq and RNA sequencing data. The regulatory network involving transcription factors (TFs), notably FOSL2 and KLF6, and their downstream target genes was dissected using motif enrichment analysis and chromatin immunoprecipitation assays. Our results revealed a strong positive correlation between H3K23su DERs, differentially expressed genes (DEGs) and H3K27ac, indicating that H3K23su enrichment is closely related to gene activation. The DEGs associated with the H3K23su GAIN regions were significantly enriched in pathways related to colorectal cancer, including the Wnt, MAPK and p53 signaling pathways. FOSL2 and KLF6 emerged as pivotal TFs potentially modulating DEGs associated with H3K23su DERs and were found to be essential for sustaining 5-FU resistance. Notably, we discovered that FOSL2 and KLF6 recruit the PCAF-p300/CBP complex to synergistically regulate SEMA3C expression, which subsequently modulates the canonical Wnt-β-catenin signaling pathway, leading to the upregulation of MYC and FOSL2. This study demonstrated that H3K23su is a critical epigenetic determinant of 5-FU resistance in colon cancer cells, exerting its effects through the modulation of critical genes and TFs. These findings indicate that interventions aimed at targeting TFs or enzymes involved in H3K23su modification could represent potential therapeutic strategies for treating colorectal cancers that are resistant to 5-FU treatment.
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Affiliation(s)
- Bishu Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tuoya Qi
- Jinshan Hospital of Fudan University, Shanghai, China
| | - Jiewei Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuyu Zhai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelong Wang
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Lingang laboratory, Shanghai, China.
| | - Leqi Zhou
- Shanghai Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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16
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Wang Z, Liu Z, Lv M, Luan Z, Li T, Hu J. Novel histone modifications and liver cancer: emerging frontiers in epigenetic regulation. Clin Epigenetics 2025; 17:30. [PMID: 39980025 PMCID: PMC11841274 DOI: 10.1186/s13148-025-01838-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 02/08/2025] [Indexed: 02/22/2025] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide, and its onset and progression are closely associated with epigenetic modifications, particularly post-translational modifications of histones (HPTMs). In recent years, advances in mass spectrometry (MS) have revealed a series of novel HPTMs, including succinylation (Ksuc), citrullination (Kcit), butyrylation (Kbhb), lactylation (Kla), crotonylation (Kcr), and 2-hydroxyisobutyrylation (Khib). These modifications not only expand the histone code but also play significant roles in key carcinogenic processes such as tumor proliferation, metastasis, and metabolic reprogramming in HCC. This review provides the first comprehensive analysis of the impact of novel HPTMs on gene expression, cellular metabolism, immune evasion, and the tumor microenvironment. It specifically focuses on their roles in promoting tumor stem cell characteristics, epithelial-mesenchymal transition (EMT), and therapeutic resistance. Additionally, the review highlights the dynamic regulation of these modifications by specific enzymes, including "writers," "readers," and "erasers."
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Affiliation(s)
- Zhonghua Wang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China
| | - Ziwen Liu
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China
| | - Mengxin Lv
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China
| | - Zhou Luan
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China
| | - Tao Li
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China
| | - Jinhua Hu
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, 250021, Shandong, People's Republic of China.
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17
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Li YX, Shao BY, Hou MY, Dong DJ. Succinylation enables IDE to act as a hub of larval tissue destruction and adult tissue reconstruction during insect metamorphosis. SCIENCE ADVANCES 2025; 11:eads0643. [PMID: 39908369 PMCID: PMC11797550 DOI: 10.1126/sciadv.ads0643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 01/03/2025] [Indexed: 02/07/2025]
Abstract
Metamorphosis is an important way for insects to adapt to the environment. In this process, larval tissue destruction regulated by 20-hydroxyecdysone (20E) and adult tissue reconstruction regulated by insulin-like peptides (ILPs) occur simultaneously, but the detailed mechanism is still unclear. Here, the results of succinylome, subcellular localization, and protein interaction analysis show that non-succinylated insulin-degrading enzyme (IDE) localizes in the cytoplasm, binds to insulin-like growth factor 2 (IGF-2-like), and degrades it. When the metamorphosis is initiated, 20E up-regulated carnitine palmitoyltransferase 1A (Cpt1a) through transcription factor Krüppel-like factor 15 (KLF15), thus increasing the level of IDE succinylation on K179. Succinylated IDE translocated from cytoplasm to nucleus, combined with ecdysone receptor to promote 20E signaling pathway, causing larval tissue destruction, while IGF-2-like was released to promote adult tissue proliferation. That is, succinylation alters subcellular localization of IDE so that it can bind to different target proteins and act as a hub of metamorphosis.
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Affiliation(s)
| | | | - Ming-Ye Hou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, China
| | - Du-Juan Dong
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, China
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18
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Meng X, Zhu X, Wang X, Zhang R, Zhang Z, Sun Y. Comprehensive analysis of the succinylome in Vero cells infected with peste des petits ruminants virus Nigeria 75/1 vaccine strain. BMC Vet Res 2025; 21:45. [PMID: 39885502 PMCID: PMC11784008 DOI: 10.1186/s12917-025-04496-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/14/2025] [Indexed: 02/01/2025] Open
Abstract
BACKGROUND Peste des petits ruminants virus (PPRV) is currently the only member of the Morbillivirus caprinae species within the genus Morbillivirus of the family Paramyoxviridae. PPRV causes a highly contagious disease in small ruminants, especially goats and sheep. Succinylation is a newly identified and conserved modification and plays an important role in host cell response to pathogen infection. However, the extent and function of succinylation in Vero cells during PPRV infection remains unknown. RESULTS In this study, a global profile of the succinylome in Vero cells infected with PPRV Nigeria 75/1 vaccine strain (PPRVvac) was performed by dimethylation labeling-based quantitative proteomics analysis. A total of 2633 succinylation sites derived from 823 proteins were quantified. The comparative analysis of differentially succinylated sites revealed that 228 down-regulated succinylation sites on 139 proteins and 44 up-regulated succinylation sites on 38 proteins were significantly modified in response to PPRVvac infection, seven succinylation motifs were identified. GO classification indicated that the differentially succinylated proteins (DSuPs) mainly participated in cellular respiration, biosynthetic process and transmembrane transporter activity. KEGG pathway analysis indicated that DSuPs were related to protein processing in the endoplasmic reticulum. Protein-protein interaction networks of the identified proteins provided further evidence that various ATP synthase subunits and carbon metabolism were modulated by succinylation, while the overlapped proteins between succinylation and acetylation are involved in glyoxylate and dicarboxylate metabolism. CONCLUSIONS The findings of the present study provide the first report of the succinylome in Vero cells infected with PPRVvac and provided a foundation for investigating the role of succinylation alone and its overlap with acetylation in response to PPRVvac.
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Affiliation(s)
- Xuelian Meng
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, Gansu, China.
| | - Xueliang Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, Gansu, China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, Gansu, China
| | - Rui Zhang
- College of Animal and Veterinary Sciences, Southwest Minzu University, #16, South Section, 1st Ring Road, Chengdu, 610041, Sichuan, China
| | - Zhidong Zhang
- College of Animal and Veterinary Sciences, Southwest Minzu University, #16, South Section, 1st Ring Road, Chengdu, 610041, Sichuan, China.
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Yanchangpu, Chengguan District, Lanzhou, 730046, Gansu, China
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19
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Koubek J, Kaur J, Bhandarkar S, Lewis CJT, Niederer RO, Stanciu A, Aitken CE, Gilbert WV. Cellular translational enhancer elements that recruit eukaryotic initiation factor 3. RNA (NEW YORK, N.Y.) 2025; 31:193-207. [PMID: 39626887 PMCID: PMC11789482 DOI: 10.1261/rna.080310.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 11/04/2024] [Indexed: 12/06/2024]
Abstract
Translation initiation is a highly regulated process that broadly affects eukaryotic gene expression. Eukaryotic initiation factor 3 (eIF3) is a central player in canonical and alternative pathways for ribosome recruitment. Here, we have investigated how direct binding of eIF3 contributes to the large and regulated differences in protein output conferred by different 5'-untranslated regions (5' UTRs) of cellular mRNAs. Using an unbiased high-throughput approach to determine the affinity of budding yeast eIF3 for native 5' UTRs from 4252 genes, we demonstrate that eIF3 binds specifically to a subset of 5' UTRs that contain a short unstructured binding motif, AMAYAA. eIF3-binding mRNAs have higher ribosome density in growing cells and are preferentially translated under certain stress conditions, supporting the functional relevance of this interaction. Our results reveal a new class of translational enhancers and suggest a mechanism by which changes in core initiation factor activity enact mRNA-specific translation programs.
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Affiliation(s)
- Jiří Koubek
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jaswinder Kaur
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Shivani Bhandarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Cole J T Lewis
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Rachel O Niederer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Andrei Stanciu
- Biology Department and Biochemistry Program, Vassar College, Poughkeepsie, New York 12604, USA
| | - Colin Echeverría Aitken
- Biology Department and Biochemistry Program, Vassar College, Poughkeepsie, New York 12604, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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20
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Hansen TN, Yuan X, I Santana MS, Olsen CA. Mechanism-based inactivators of sirtuin 5: A focused structure-activity relationship study. Bioorg Med Chem Lett 2025; 115:130017. [PMID: 39521149 DOI: 10.1016/j.bmcl.2024.130017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 11/01/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024]
Abstract
Sirtuin 5 (SIRT5) is a lysine deacylase enzyme that cleaves negatively charged ε-N-acyllysine posttranslational modifications, arising from short dicarboxylic acids. Inhibition of SIRT5 has been suggested as a target for treatment of leukemia and breast cancer. In this work, we performed a focused structure-activity relationship study that identified highly potent inhibitors of SIRT5. Examples of these inhibitors were shown by kinetic evaluation to function as mechanism-based inactivators. Masking of a crucial carboxylate functionality in the inhibitors provided prodrugs, which were demonstrated to bind SIRT5 in cells. This work underscores the importance of kinetic characterization of enzyme inhibitors and provides insights for the further optimization of inhibitors of SIRT5 with potential for in vivo applications.
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Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark.
| | - Xinyi Yuan
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Marc S I Santana
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark.
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21
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Zhang X, Ling C, Xiong Z, Gong T, Luo S, Liu X, Zhang L, Liao C, Lu Y, Huang X, Zhou W, Zhou S, Liu Y, Tang J. Desuccinylation of TBK1 by SIRT5 regulates inflammatory response of macrophages in sepsis. Cell Rep 2024; 43:115060. [PMID: 39673708 DOI: 10.1016/j.celrep.2024.115060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 08/19/2024] [Accepted: 11/21/2024] [Indexed: 12/16/2024] Open
Abstract
Tank-binding kinase 1 (TBK1) is a critical signal transducer in the nuclear factor κB (NF-κB) and interferon regulatory factor (IRF) pathways, essential for innate immunity. However, its negative regulation mechanisms remain unclear. This study demonstrates that TBK1 succinylation, regulated by desuccinylase SIRT5, inhibits lipopolysaccharide (LPS)/Toll-like receptor 4 (TLR4)-mediated NF-κB and IRF signaling activation. We identified three key succinylation sites on TBK1: K38, K154, and K692. In endotoxemia and sepsis models, reduced SIRT5 levels in macrophages increased TBK1 succinylation, inhibiting its binding to IRF3 and TRAF2 and suppressing the inflammatory response. In vivo, adoptive transfer of macrophages expressing the succinylation-resistant TBK1-2KR (K154/692R) mutant reversed the inflammatory cytokine suppression caused by SIRT5 deficiency, exacerbating sepsis-induced lung injury. These findings reveal a novel mechanism by which SIRT5 modulates TBK1 activity and macrophage-mediated inflammation during sepsis.
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Affiliation(s)
- Xuedi Zhang
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China; Department of Anesthesiology, Shenzhen Hospital of Southern Medical University, No. 1333, Xinhu Road, Baoan District, Shenzhen, Guangdong 518110, China; The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chunxiu Ling
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Ziying Xiong
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Ting Gong
- Department of Anesthesiology, Shenzhen Hospital of Southern Medical University, No. 1333, Xinhu Road, Baoan District, Shenzhen, Guangdong 518110, China; The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shuhua Luo
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Xiaolei Liu
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Lina Zhang
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Chaoxiong Liao
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Yue Lu
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Xiao Huang
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Wending Zhou
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China
| | - Shuangnan Zhou
- Senior Department of Infectious Disease, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China.
| | - Youtan Liu
- Department of Anesthesiology, Shenzhen Hospital of Southern Medical University, No. 1333, Xinhu Road, Baoan District, Shenzhen, Guangdong 518110, China; The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| | - Jing Tang
- The Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China; Guang Dong Medical University, Zhanjiang, Guangdong 524000, China.
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22
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Ye T, Wang D, Sun Y, Xie S, Liu T, Tian N, Tan M, Xu JY. Characterization of acidic lysine acylations in mycobacteria. Front Microbiol 2024; 15:1503184. [PMID: 39720477 PMCID: PMC11667787 DOI: 10.3389/fmicb.2024.1503184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 11/27/2024] [Indexed: 12/26/2024] Open
Abstract
Introduction Protein acetylation is an extensively investigated post-translational modification (PTM). In addition to lysine acetylation, three new types of lysine acylations characterized by the presence of an acidic carboxylic group have been recently identified and validated. These included lysine malonylation (Kmal), lysine succinylation (Ksucc) and lysine glutarylation (Kglu). Pathogens belonging to the genus Mycobacterium elicit severe diseases in mammalian hosts through the modulation of energy metabolism pathways. Throughout this process, malonyl-CoA, succinyl-CoA and glutaryl-CoA are important intermediates in metabolic pathways, including the tricarboxylic acid (TCA) cycle, amino acid and lipid metabolism. These short-chain acyl-CoAs serve as substrates for corresponding acidic lysine acylation reactions. However, the landscape of these acyl-CoAs dependent acidic lysine acylomes remains unclear. Methods We used the high-affinity antibody enrichment combined with high-resolution LC-MS/MS analysis to systematically investigate the global proteomic characteristics of the three acidic lysine acylations in Mycobacterium smegmatis. Subsequently, we employed in vitro enzymatic assays to validate the functional impact of acylated substrates, adenylate kinase and proteasome-associated ATPase. Furthermore, we investigated the effects of overexpressing these two substrates on the in vitro growth of Mycobacterium smegmatis, its invasion of THP-1 cells, and the influence on inflammatory cytokines. Results We systematically investigated the global substrate characterization of 1,703 lysine malonylated sites, 5,320 lysine succinylated sites and 269 lysine glutarylated sites in the non-pathogenic model strain Mycobacterium smegmatis. Bioinformatics analysis demonstrated a correlation between these acidic lysine acylations and the functional roles of ribosomes, in addition to their roles in various metabolic pathways. Furthermore, we investigated the impact of lysine acylations on the functional activity of adenylate kinase and proteasome-associated ATPase, as well as their roles in mycobacterial infection process. Discussion Collectively, our study provided an important resource on substrate characterization and functional regulation of acidic lysine acylations in Mycobacterium smegmatis, giving valuable insights into their interrelation with the biology of infectious process.
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Affiliation(s)
- Tong Ye
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Danfeng Wang
- School of Pharmacy, Zunyi Medical University, Zhuhai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Yewen Sun
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Shuyu Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Tianqi Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Nana Tian
- School of Pharmacy, Zunyi Medical University, Zhuhai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Minjia Tan
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Zunyi Medical University, Zhuhai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Jun-Yu Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Zunyi Medical University, Zhuhai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
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23
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Sieber A, Parr M, von Ehr J, Dhamotharan K, Kielkowski P, Brewer T, Schäpers A, Krafczyk R, Qi F, Schlundt A, Frishman D, Lassak J. EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences. Nat Commun 2024; 15:10465. [PMID: 39622818 PMCID: PMC11611912 DOI: 10.1038/s41467-024-54556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 11/13/2024] [Indexed: 12/06/2024] Open
Abstract
Polyproline sequences are deleterious to cells because they stall ribosomes. In bacteria, EF-P plays an important role in overcoming such polyproline sequence-induced ribosome stalling. Additionally, numerous bacteria possess an EF-P paralog called EfpL (also known as YeiP) of unknown function. Here, we functionally and structurally characterize EfpL from Escherichia coli and demonstrate its role in the translational stress response. Through ribosome profiling, we analyze the EfpL arrest motif spectrum and find additional sequences beyond the canonical polyproline motifs that both EF-P and EfpL can resolve. Notably, the two factors can also induce pauses. We further report that EfpL can sense the metabolic state of the cell via lysine acylation. Overall, our work characterizes the role of EfpL in ribosome rescue at proline-containing sequences, and provides evidence that co-occurrence of EF-P and EfpL is an evolutionary driver for higher bacterial growth rates.
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Affiliation(s)
- Alina Sieber
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Julian von Ehr
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
- IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Institut für Chemische Epigenetik (ICEM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tess Brewer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Anna Schäpers
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ralph Krafczyk
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Fei Qi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jürgen Lassak
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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Pham L, Arroum T, Wan J, Pavelich L, Bell J, Morse PT, Lee I, Grossman LI, Sanderson TH, Malek MH, Hüttemann M. Regulation of mitochondrial oxidative phosphorylation through tight control of cytochrome c oxidase in health and disease - Implications for ischemia/reperfusion injury, inflammatory diseases, diabetes, and cancer. Redox Biol 2024; 78:103426. [PMID: 39566165 PMCID: PMC11617887 DOI: 10.1016/j.redox.2024.103426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/04/2024] [Accepted: 11/09/2024] [Indexed: 11/22/2024] Open
Abstract
Mitochondria are essential to cellular function as they generate the majority of cellular ATP, mediated through oxidative phosphorylation, which couples proton pumping of the electron transport chain (ETC) to ATP production. The ETC generates an electrochemical gradient, known as the proton motive force, consisting of the mitochondrial membrane potential (ΔΨm, the major component in mammals) and ΔpH across the inner mitochondrial membrane. Both ATP production and reactive oxygen species (ROS) are linked to ΔΨm, and it has been shown that an imbalance in ΔΨm beyond the physiological optimal intermediate range results in excessive ROS production. The reaction of cytochrome c oxidase (COX) of the ETC with its small electron donor cytochrome c (Cytc) is the proposed rate-limiting step in mammals under physiological conditions. The rate at which this redox reaction occurs controls ΔΨm and thus ATP and ROS production. Multiple mechanisms are in place that regulate this reaction to meet the cell's energy demand and respond to acute stress. COX and Cytc have been shown to be regulated by all three main mechanisms, which we discuss in detail: allosteric regulation, tissue-specific isoforms, and post-translational modifications for which we provide a comprehensive catalog and discussion of their functional role with 55 and 50 identified phosphorylation and acetylation sites on COX, respectively. Disruption of these regulatory mechanisms has been found in several common human diseases, including stroke and myocardial infarction, inflammation including sepsis, and diabetes, where changes in COX or Cytc phosphorylation lead to mitochondrial dysfunction contributing to disease pathophysiology. Identification and subsequent targeting of the underlying signaling pathways holds clear promise for future interventions to improve human health. An example intervention is the recently discovered noninvasive COX-inhibitory infrared light therapy that holds promise to transform the current standard of clinical care in disease conditions where COX regulation has gone awry.
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Affiliation(s)
- Lucynda Pham
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Lauren Pavelich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
| | - Jamie Bell
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Division of Pediatric Critical Care, Children's Hospital of Michigan, Central Michigan University, Detroit, MI, 48201, USA.
| | - Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, 31116, Republic of Korea.
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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Liu Y, Zhang F, Hassan A, Zhou X, Huang Q. Accessory gland protein regulates pairing process and oviposition in the subterranean termite Reticulitermes chinensis after swarming. INSECT SCIENCE 2024; 31:1889-1907. [PMID: 38576063 DOI: 10.1111/1744-7917.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 04/06/2024]
Abstract
Swarming and pairing behaviors are significant to population dispersal of termites. Tandem running is a key process in pairing behavior of dealates to find a mate. Succinylation can lead to significant changes in protein structure and function, which is widely involved in metabolism and behavior regulation in many organisms. However, whether succinylation modification regulates termites' tandem running is currently unknown. In this research, we performed quantitative modified proteomics of the subterranean termite Reticulitermes chinensis Snyder before and after alate swarming. The succinylation levels of accessory gland protein (ACP) were significantly altered after alate swarming. We found that ACP is enriched in male accessory gland and female oocytes of termites. The acetylation and succinylation sites of ACP affected tandem running of dealates. The transcriptome and metabolome analyses of alates injected with ACP and its mutant proteins showed that β-alanine metabolism pathway was the major downstream pathway of ACP. Silencing the significantly differentially expressed genes in the β-alanine metabolic pathway (acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-hydroxyisobutyrate dehydrogenase, methylmalonate-semialdehyde dehydrogenase) suppressed tandem running and altered oviposition of paired dealates. These findings demonstrate that protein translation modification is an important regulator of tandem running behavior of termites, which implies that the succinylation and acetylation modification sites of ACP could be potential targets for insecticide action. Our research offers a potential approach for developing novel dispersal inhibitors against social insect pests.
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Affiliation(s)
- Yutong Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ali Hassan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Qiuying Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
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26
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Kienle SM, Schneider T, Bernecker C, Bracker J, Marx A, Kovermann M, Scheffner M, Stuber K. Biochemical and Structural Consequences of NEDD8 Acetylation. Chembiochem 2024; 25:e202400478. [PMID: 39022855 DOI: 10.1002/cbic.202400478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 07/20/2024]
Abstract
Similar to ubiquitin, the ubiquitin-like protein NEDD8 is not only conjugated to other proteins but is itself subject to posttranslational modifications including lysine acetylation. Yet, compared to ubiquitin, only little is known about the biochemical and structural consequences of site-specific NEDD8 acetylation. Here, we generated site-specifically mono-acetylated NEDD8 variants for each known acetylation site by genetic code expansion. We show that, in particular, acetylation of K11 has a negative impact on the usage of NEDD8 by the NEDD8-conjugating enzymes UBE2M and UBE2F and that this is likely due to electrostatic and steric effects resulting in conformational changes of NEDD8. Finally, we provide evidence that p300 acts as a position-specific NEDD8 acetyltransferase.
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Affiliation(s)
- Simon Maria Kienle
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Christine Bernecker
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Janina Bracker
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Katrin Stuber
- Departments of Biology and Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
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27
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Prieto-Garcia C, Matkovic V, Mosler T, Li C, Liang J, Oo JA, Haidle F, Mačinković I, Cabrera-Orefice A, Berkane R, Giuliani G, Xu F, Jacomin AC, Tomaskovic I, Basoglu M, Hoffmann ME, Rathore R, Cetin R, Boutguetait D, Bozkurt S, Hernández Cañás MC, Keller M, Busam J, Shah VJ, Wittig I, Kaulich M, Beli P, Galej WP, Ebersberger I, Wang L, Münch C, Stolz A, Brandes RP, Tse WKF, Eimer S, Stainier DYR, Legewie S, Zarnack K, Müller-McNicoll M, Dikic I. Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy. Science 2024; 386:768-776. [PMID: 39541449 DOI: 10.1126/science.adi5295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/22/2024] [Accepted: 10/14/2024] [Indexed: 11/16/2024]
Abstract
RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanisms and cellular responses remain poorly understood. In this work, we report that deficiency of ubiquitin-specific protease 39 (USP39) in human cell lines, zebrafish larvae, and mice led to impaired spliceosome assembly and a cytotoxic splicing profile characterized by the use of cryptic 5' splice sites. Disruptive cryptic variants evaded messenger RNA (mRNA) surveillance pathways and were translated into misfolded proteins, which caused proteotoxic aggregates, endoplasmic reticulum (ER) stress, and, ultimately, cell death. The detrimental consequence of splicing-induced proteotoxicity could be mitigated by up-regulating the ubiquitin-proteasome system and selective autophagy. Our findings provide insight into the molecular pathogenesis of spliceosome-associated diseases.
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Affiliation(s)
- Cristian Prieto-Garcia
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Vigor Matkovic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Thorsten Mosler
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Congxin Li
- Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Jie Liang
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - James A Oo
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhine-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Haidle
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Igor Mačinković
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Alfredo Cabrera-Orefice
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany
- Center for Functional Proteomics, Goethe University Frankfurt, Frankfurt, Germany
| | - Rayene Berkane
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Giulio Giuliani
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Fenfen Xu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P.R. China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Anne-Claire Jacomin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Ines Tomaskovic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Marion Basoglu
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Rajeshwari Rathore
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Ronay Cetin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Doha Boutguetait
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Jonas Busam
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Varun Jayeshkumar Shah
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Ilka Wittig
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhine-Main, Frankfurt, Germany
- Center for Functional Proteomics, Goethe University Frankfurt, Frankfurt, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University, Mainz, Germany
| | | | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Likun Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Center for Functional Proteomics, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhine-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Stefan Eimer
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Didier Y R Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Stefan Legewie
- Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
- Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Max-Planck Institute for Biophysics, Frankfurt, Germany
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28
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Fang F, Xu T, Chien Hagar HT, Hovde S, Kuo MH, Sun L. Pilot Study for Deciphering Post-Translational Modifications and Proteoforms of Tau Protein by Capillary Electrophoresis-Mass Spectrometry. J Proteome Res 2024; 23:5085-5095. [PMID: 39327902 PMCID: PMC11536466 DOI: 10.1021/acs.jproteome.4c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/11/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
Abnormal accumulation of tau protein in the brain is one pathological hallmark of Alzheimer's disease (AD). Many tau protein post-translational modifications (PTMs) are associated with the development of AD, such as phosphorylation, acetylation, and methylation. Therefore, a complete picture of the PTM landscape of tau is critical for understanding the molecular mechanisms of AD progression. Here, we offered a pilot study of combining two complementary analytical techniques, capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) and reversed-phase liquid chromatography (RPLC)-MS/MS, for bottom-up proteomics of recombinant human tau-0N3R. We identified 50 phosphorylation sites of tau-0N3R in total, which is about 25% higher than that from RPLC-MS/MS alone. CZE-MS/MS provided more PTM sites (i.e., phosphorylation) and modified peptides of tau-0N3R than RPLC-MS/MS, and its predicted electrophoretic mobility helped improve the confidence of the identified modified peptides. We developed a highly efficient capillary isoelectric focusing (cIEF)-MS technique to offer a bird's-eye view of tau-0N3R proteoforms, with 11 putative tau-0N3R proteoforms carrying up to nine phosphorylation sites and lower pI values from more phosphorylated proteoforms detected. Interestingly, under native-like cIEF-MS conditions, we observed three putative tau-0N3R dimers carrying phosphate groups. The findings demonstrate that CE-MS is a valuable analytical technique for the characterization of tau PTMs, proteoforms, and even oligomerization.
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Affiliation(s)
- Fei Fang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Hsiao-Tien Chien Hagar
- Department
of Biochemistry and Molecular Biology, Michigan
State University, 603 Wilson Road, Room 401, East Lansing, Michigan 48824, United States
| | - Stacy Hovde
- Department
of Biochemistry and Molecular Biology, Michigan
State University, 603 Wilson Road, Room 401, East Lansing, Michigan 48824, United States
| | - Min-Hao Kuo
- Department
of Biochemistry and Molecular Biology, Michigan
State University, 603 Wilson Road, Room 401, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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29
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Birhanu AG, Riaz T, Støen M, Tønjum T. Differential Abundance of Protein Acylation in Mycobacterium tuberculosis Under Exposure to Nitrosative Stress. Proteomics Clin Appl 2024; 18:e202300212. [PMID: 39082596 DOI: 10.1002/prca.202300212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 11/15/2024]
Abstract
BACKGROUND Human macrophages generate antimicrobial reactive nitrogen species in response to infection by Mycobacterium tuberculosis (Mtb). Exposure to these redox-reactive compounds induces stress response in Mtb, which can affect posttranslational modifications (PTM). METHODS Here, we present the global analysis of the PTM acylation of Mtb proteins in response to a sublethal dose of nitrosative stress in the form of nitric oxide (NO) using label free quantification. RESULTS A total of 6437 acylation events were identified on 1496 Mtb proteins, and O-acylation accounted for 92.2% of the events identified, while 7.8% were N-acylation events. About 22% of the sites identified were found to be acylated by more than one acyl-group. Furthermore, the abundance of each acyl-group decreased as their molecular weight increased. Quantitative PTM analysis revealed differential abundance of acylation in proteins involved in stress response, iron ion homeostasis, growth, energy metabolism, and antimicrobial resistance (AMR) induced by nitrosative stress over time. CONCLUSIONS The results reveal a potential role of Mtb protein acylation in the bacterial stress responses and AMR. To our knowledge, this is the first report on global O-acylation profile of Mtb in response to NO. This will significantly improve our understanding of the changes in Mtb acylation under nitrosative stress, highly relevant for global health.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
| | - Mari Støen
- Department of Microbiology, Oslo University Hospital, Nydalen, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Nydalen, Oslo, Norway
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30
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Gan Z, van der Stelt I, Li W, Hu L, Song J, Grefte S, van de Westerlo E, Zhang D, van Schothorst EM, Claahsen-van der Grinten HL, Teerds KJ, Adjobo-Hermans MJW, Keijer J, Koopman WJH. Mitochondrial Nicotinamide Nucleotide Transhydrogenase: Role in Energy Metabolism, Redox Homeostasis, and Cancer. Antioxid Redox Signal 2024; 41:927-956. [PMID: 39585234 DOI: 10.1089/ars.2024.0694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2024]
Abstract
Significance: Dimeric nicotinamide nucleotide transhydrogenase (NNT) is embedded in the mitochondrial inner membrane and couples the conversion of NADP+/NADH into NADPH/NAD+ to mitochondrial matrix proton influx. NNT was implied in various cancers, but its physiological role and regulation still remain incompletely understood. Recent Advances: NNT function was analyzed by studying: (1) NNT gene mutations in human (adrenal) glucocorticoid deficiency 4 (GCCD4), (2) Nnt gene mutation in C57BL/6J mice, and (3) the effect of NNT knockdown/overexpression in (cancer) cells. In these three models, altered NNT function induced both common and differential aberrations. Critical Issues: Information on NNT protein expression in GCCD4 patients is still scarce. Moreover, NNT expression levels are tissue-specific in humans and mice and the functional consequences of NNT deficiency strongly depend on experimental conditions. In addition, data from intact cells and isolated mitochondria are often unsuited for direct comparison. This prevents a proper understanding of NNT-linked (patho)physiology in GCCD4 patients, C57BL/6J mice, and cancer (cell) models, which complicates translational comparison. Future Directions: Development of mice with conditional NNT deletion, cell-reprogramming-based adrenal (organoid) models harboring specific NNT mutations, and/or NNT-specific chemical inhibitors/activators would be useful. Moreover, live-cell analysis of NNT substrate levels and mitochondrial/cellular functioning with fluorescent reporter molecules might provide novel insights into the conditions under which NNT is active and how this activity links to other metabolic and signaling pathways. This would also allow a better dissection of local signaling and/or compartment-specific (i.e., mitochondrial matrix, cytosol, nucleus) effects of NNT (dys)function in a cellular context. Antioxid. Redox Signal. 41, 927-956.
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Affiliation(s)
- Zhuohui Gan
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Inge van der Stelt
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Weiwei Li
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Liangyu Hu
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Jingyi Song
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Els van de Westerlo
- Department of Medical BioSciences, Radboudumc, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Deli Zhang
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Katja J Teerds
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Merel J W Adjobo-Hermans
- Department of Medical BioSciences, Radboudumc, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Werner J H Koopman
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
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31
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Chen F, He X, Xu W, Zhou L, Liu Q, Chen W, Zhu W, Zhang J. Chromatin lysine acylation: On the path to chromatin homeostasis and genome integrity. Cancer Sci 2024; 115:3506-3519. [PMID: 39155589 PMCID: PMC11531963 DOI: 10.1111/cas.16321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024] Open
Abstract
The fundamental role of cells in safeguarding the genome's integrity against DNA double-strand breaks (DSBs) is crucial for maintaining chromatin homeostasis and the overall genomic stability. Aberrant responses to DNA damage, known as DNA damage responses (DDRs), can result in genomic instability and contribute significantly to tumorigenesis. Unraveling the intricate mechanisms underlying DDRs following severe damage holds the key to identify therapeutic targets for cancer. Chromatin lysine acylation, encompassing diverse modifications such as acetylation, lactylation, crotonylation, succinylation, malonylation, glutarylation, propionylation, and butyrylation, has been extensively studied in the context of DDRs and chromatin homeostasis. Here, we delve into the modifying enzymes and the pivotal roles of lysine acylation and their crosstalk in maintaining chromatin homeostasis and genome integrity in response to DDRs. Moreover, we offer a comprehensive perspective and overview of the latest insights, driven primarily by chromatin acylation modification and associated regulators.
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Affiliation(s)
- Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Xingkai He
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Linmin Zhou
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Qi Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
- Cancer Research Institute, School of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Weicheng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Wei‐Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
| | - Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhenChina
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32
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Duchovni L, Shmunis G, Lobel L. Posttranslational modifications: an emerging functional layer of diet-host-microbe interactions. mBio 2024; 15:e0238724. [PMID: 39254316 PMCID: PMC11481575 DOI: 10.1128/mbio.02387-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
The microbiome plays a vital role in human health, with changes in its composition impacting various aspects of the body. Posttranslational modification (PTM) regulates protein activity by attaching chemical groups to amino acids in an enzymatic or non-enzymatic manner. PTMs offer fast and dynamic regulation of protein expression and can be influenced by specific dietary components that induce PTM events in gut microbiomes and their hosts. PTMs on microbiome proteins have been found to contribute to host-microbe interactions. For example, in Escherichia coli, S-sulfhydration of tryptophanase regulates uremic toxin production and chronic kidney disease in mice. On a broader microbial scale, the microbiomes of patients with inflammatory bowel disease exhibit distinct PTM patterns in their metaproteomes. Moreover, pathogens and commensals can alter host PTM profiles through protein secretion and diet-regulated metabolic shifts. The emerging field of metaPTMomics focuses on understanding PTM profiles in the microbiota, their association with lifestyle factors like diet, and their functional effects on host-microbe interactions.
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Affiliation(s)
- Lirit Duchovni
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Genrieta Shmunis
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Lior Lobel
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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33
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Sun L, Meng H, Liu T, Zhao Q, Xia M, Zhao Z, Qian Y, Cui H, Zhong X, Chai K, Tian Y, Sun Y, Zhu B, Di J, Shui G, Zhang L, Zheng J, Guo S, Liu Y. Nucleolin malonylation as a nuclear-cytosol signal exchange mechanism to drive cell proliferation in Hepatocarcinoma by enhancing AKT translation. J Biol Chem 2024; 300:107785. [PMID: 39305961 PMCID: PMC11525140 DOI: 10.1016/j.jbc.2024.107785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/30/2024] [Accepted: 09/04/2024] [Indexed: 10/18/2024] Open
Abstract
Cancer cells undergo metabolic reprogramming that is intricately linked to malignancy. Protein acylations are especially responsive to metabolic changes, influencing signal transduction pathways and fostering cell proliferation. However, as a novel type of acylations, the involvement of malonylation in cancer remains poorly understood. In this study, we observed a significant reduction in malonyl-CoA levels in hepatocellular carcinoma (HCC), which correlated with a global decrease in malonylation. Subsequent nuclear malonylome analysis unveiled nucleolin (NCL) malonylation, which was notably enhanced in HCC biopsies. we demonstrated that NCL undergoes malonylation at lysine residues 124 and 398. This modification triggers the translocation of NCL from the nucleolus to nucleoplasm and cytoplasm, binding to AKT mRNA, and promoting AKT translation in HCC. Silencing AKT expression markedly attenuated HCC cell proliferation driven by NCL malonylation. These findings collectively highlight nuclear signaling in modulating AKT expression, suggesting NCL malonylation as a novel mechanism through which cancer cells drive cell proliferation.
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Affiliation(s)
- Liang Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hanjing Meng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tao Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Qiong Zhao
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Mingyi Xia
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhongjun Zhao
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuting Qian
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hao Cui
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xuefei Zhong
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Keli Chai
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yang Tian
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yang Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Bao Zhu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiehui Di
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lianjun Zhang
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, Jiangsu, China; Key Laboratory of Synthetic Biology Regulatory Element, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, Jiangsu, China
| | - Junnian Zheng
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Shutao Guo
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, China.
| | - Yong Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.
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Zhu L, Liu YP, Huang YT, Zhou ZJ, Liu JF, Yu LM, Wang HS. Cellular and molecular biology of posttranslational modifications in cardiovascular disease. Biomed Pharmacother 2024; 179:117374. [PMID: 39217836 DOI: 10.1016/j.biopha.2024.117374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
Cardiovascular disease (CVD) has now become the leading cause of death worldwide, and its high morbidity and mortality rates pose a great threat to society. Although numerous studies have reported the pathophysiology of CVD, the exact pathogenesis of all types of CVD is not fully understood. Therefore, much more research is still needed to explore the pathogenesis of CVD. With the development of proteomics, many studies have successfully identified the role of posttranslational modifications in the pathogenesis of CVD, including key processes such as apoptosis, cell metabolism, and oxidative stress. In this review, we summarize the progress in the understanding of posttranslational modifications in cardiovascular diseases, including novel protein posttranslational modifications such as succinylation and nitrosylation. Furthermore, we summarize the currently identified histone deacetylase (HDAC) inhibitors used to treat CVD, providing new perspectives on CVD treatment modalities. We critically analyze the roles of posttranslational modifications in the pathogenesis of CVD-related diseases and explore future research directions related to posttranslational modifications in cardiovascular diseases.
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Affiliation(s)
- Li Zhu
- Graduate School of Dalian Medical University, Dalian 116000, Liaoning, China; State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Yong-Ping Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Yu-Ting Huang
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Zi-Jun Zhou
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Jian-Feng Liu
- First School of Clinical Medicine, Shenyang Medical College, Shenyang 110034, Liaoning, China
| | - Li-Ming Yu
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China.
| | - Hui-Shan Wang
- Graduate School of Dalian Medical University, Dalian 116000, Liaoning, China; State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China.
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Querl L, Krebber H. Defenders of the Transcriptome: Guard Protein-Mediated mRNA Quality Control in Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:10241. [PMID: 39408571 PMCID: PMC11476243 DOI: 10.3390/ijms251910241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 10/20/2024] Open
Abstract
Cell survival depends on precise gene expression, which is controlled sequentially. The guard proteins surveil mRNAs from their synthesis in the nucleus to their translation in the cytoplasm. Although the proteins within this group share many similarities, they play distinct roles in controlling nuclear mRNA maturation and cytoplasmic translation by supporting the degradation of faulty transcripts. Notably, this group is continuously expanding, currently including the RNA-binding proteins Npl3, Gbp2, Hrb1, Hrp1, and Nab2 in Saccharomyces cerevisiae. Some of the human serine-arginine (SR) splicing factors (SRSFs) show remarkable similarities to the yeast guard proteins and may be considered as functional homologues. Here, we provide a comprehensive summary of their crucial mRNA surveillance functions and their implications for cellular health.
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Affiliation(s)
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany;
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36
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Li Y, Jiang Y, Yan H, Qin Z, Peng Y, Lv D, Zhang H. Global isonicotinylome analysis identified SMAD3 isonicotinylation promotes liver cancer cell epithelial-mesenchymal transition and invasion. iScience 2024; 27:110775. [PMID: 39286495 PMCID: PMC11403401 DOI: 10.1016/j.isci.2024.110775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/02/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
Histone lysine isonicotinylation (Kinic) induced by isoniazid (INH) was recently identified as a post-translational modification in cells. However, global cellular non-histone proteins Kinic remains unclear. Using proteomic technology, we identified 11,442 Kinic sites across 2,792 proteins and demonstrated that Kinic of non-histone proteins is involved in multiple function pathways. Non-histone proteins Kinic can be regulated by isonicotinyl-transferases, including CBP and Tip60, and deisonicotinylases, including HDAC8 and HDAC6. In particular, the Kinic of poly (ADP-ribose) (PAR) polymerase 1 (PARP1) can be catalyzed by CBP and deisonicotinylation can be catalyzed by HDAC8. Tip60 and HDAC6 are isonicotinyl-transferase and the deisonicotinylase of SMAD3, respectively. Importantly, we found the K378inic of SMAD3 increases its phosphorylation, activates TGFβ pathway, and promotes liver cancer cells migration and invasion. In conclusion, our study demonstrated non-histone proteins Kinic occur extensively in cells and plays an important role in regulation of various cellular functions, including cancer progression.
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Affiliation(s)
- Yixiao Li
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Yuhan Jiang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Haoyi Yan
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Ziheng Qin
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Yidi Peng
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Danyu Lv
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
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Cao D, Sun W, Li X, Jian L, Zhou X, Bode AM, Luo X. The role of novel protein acylations in cancer. Eur J Pharmacol 2024; 979:176841. [PMID: 39033839 DOI: 10.1016/j.ejphar.2024.176841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024]
Abstract
Novel protein acylations are a class of protein post-translational modifications, such as lactylation, succinylation, crotonylation, palmitoylation, and β-hydroxybutyrylation. These acylation modifications are common in prokaryotes and eukaryotes and play pivotal roles in various key cellular processes by regulating gene transcription, protein subcellular localization, stability and activity, protein-protein interactions, and protein-DNA interactions. The diversified acylations are closely associated with various human diseases, especially cancer. In this review, we provide an overview of the distinctive characteristics, effects, and regulatory factors of novel protein acylations. We also explore the various mechanisms through which novel protein acylations are involved in the occurrence and progression of cancer. Furthermore, we discuss the development of anti-cancer drugs targeting novel acylations, offering promising avenues for cancer treatment.
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Affiliation(s)
- Dan Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Wenxuan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinyi Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Lian Jian
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinran Zhou
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China; Molecular Imaging Research Center of Central South University, Changsha, Hunan, 410078, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan, 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410078, China.
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Liu J, Zhai M, Chen Y, Wei Y, Li F, Chen Y, Duan B, Xing L, Du H, Jiang M, Li H, Ren G. Acetylation-dependent deubiquitinase USP26 stabilizes BAG3 to promote breast cancer progression. Cancer Lett 2024; 597:217005. [PMID: 38880224 DOI: 10.1016/j.canlet.2024.217005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024]
Abstract
Deubiquitylases (DUBs) have emerged as promising targets for cancer therapy due to their role in stabilizing substrate proteins within the ubiquitin machinery. Here, we identified ubiquitin-specific protease 26 (USP26) as an oncogene via screening prognostic DUBs in breast cancer. Through in vitro and in vivo experiments, we found that depletion of USP26 inhibited breast cancer cell proliferation and invasion, and suppressed tumor growth and metastasis in nude mice. Further investigation identified co-chaperone Bcl-2-associated athanogene 3 (BAG3) as the direct substrate of USP26, and ectopic expression of BAG3 partially reversed antitumor effect induced by USP26 knockdown. Mechanistically, the lysine acetyltransferase Tip60 targeted USP26 at K134 for acetylation, which enhanced USP26 binding affinity to BAG3, leading to BAG3 deubiquitination and increased protein stability. Importantly, we employed a structure-based virtual screening and discovered a drug-like molecule called 5813669 that targets USP26, destabilizing BAG3 and effectively mitigating tumor growth and metastasis in vivo. Clinically, high expression levels of USP26 were correlated with elevated BAG3 levels and poor prognosis in breast cancer patients. Overall, our findings highlight the critical role of USP26 in BAG3 protein stabilization and provide a promising therapeutic target for breast cancer.
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Affiliation(s)
- Jiazhou Liu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Mo Zhai
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Department of Orthopedics, Qijiang Hospital of the First Affiliated Hospital of Chongqing Medical University, Qijiang, Chongqing, 400016, China
| | - Yanyu Chen
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yuxian Wei
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Fan Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yuru Chen
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Bixia Duan
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Lei Xing
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Huimin Du
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Min Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Hongzhong Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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Liu H, Binoy A, Ren S, Martino TC, Miller AE, Willis CRG, Veerabhadraiah SR, Sukul A, Bons J, Rose JP, Schilling B, Jurynec MJ, Zhu S. Sirt5 regulates chondrocyte metabolism and osteoarthritis development through protein lysine malonylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604872. [PMID: 39091806 PMCID: PMC11291161 DOI: 10.1101/2024.07.23.604872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Objectives Chondrocyte metabolic dysfunction plays an important role in osteoarthritis (OA) development during aging and obesity. Protein post-translational modifications (PTMs) have recently emerged as an important regulator of cellular metabolism. We aim to study one type of PTM, lysine malonylation (MaK) and its regulator Sirt5 in OA development. Methods Human and mouse cartilage tissues were used to measure SIRT5 and MaK levels. Both systemic and cartilage-specific conditional knockout mouse models were subject to high-fat diet (HFD) treatment to induce obesity and OA. Proteomics analysis was performed in Sirt5 -/- and WT chondrocytes. SIRT5 mutation was identified in the Utah Population Database (UPDB). Results We found that SIRT5 decreases while MAK increases in the cartilage during aging. A combination of Sirt5 deficiency and obesity exacerbates joint degeneration in a sex dependent manner in mice. We further delineate the malonylome in chondrocytes, pinpointing MaK's predominant impact on various metabolic pathways such as carbon metabolism and glycolysis. Lastly, we identified a rare coding mutation in SIRT5 that dominantly segregates in a family with OA. The mutation results in substitution of an evolutionally invariant phenylalanine (Phe-F) to leucine (Leu-L) (F101L) in the catalytic domain. The mutant protein results in higher MaK level and decreased expression of cartilage ECM genes and upregulation of inflammation associated genes. Conclusions We found that Sirt5 mediated MaK is an important regulator of chondrocyte cellular metabolism and dysregulation of Sirt5-MaK could be an important mechanism underlying aging and obesity associated OA development.
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Affiliation(s)
- Huanhuan Liu
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Anupama Binoy
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Siqi Ren
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Thomas C. Martino
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Anna E. Miller
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Craig R. G. Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, UK
| | | | - Abhijit Sukul
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob P. Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Michael J. Jurynec
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, 84108 USA
| | - Shouan Zhu
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
- Diabetes Institute (DI), Heritage College of Osteopathic Medicine (HCOM), Ohio University, Athens, OH, 45701, USA
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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Mikkat S, Kreutzer M, Patenge N. Lysine Phoshoglycerylation Is Widespread in Bacteria and Overlaps with Acylation. Microorganisms 2024; 12:1556. [PMID: 39203397 PMCID: PMC11356508 DOI: 10.3390/microorganisms12081556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Phosphoglycerylation is a non-enzymatic protein modification in which a phosphoglyceryl moiety is covalently bound to the ε-amino group of lysine. It is enriched in glycolytic enzymes from humans and mice and is thought to provide a feedback mechanism for regulating glycolytic flux. We report the first proteomic analysis of this post-translational modification in bacteria by profiling phosphoglyceryl-lysine during the growth of Streptococcus pyogenes in different culture media. The identity of phosphoglyceryl-lysine was confirmed by a previously unknown diagnostic cyclic immonium ion generated during MS/MS. We identified 370 lysine phosphoglycerylation sites in 123 proteins of S. pyogenes. Growth in a defined medium on 1% fructose caused a significant accumulation of phosphoglycerylation compared to growth in a rich medium containing 0.2% glucose. Re-analysis of phosphoproteomes from 14 bacterial species revealed that phosphoglycerylation is generally widespread in bacteria. Many phosphoglycerylation sites were conserved in several bacteria, including S. pyogenes. There was considerable overlap between phosphoglycerylation, acetylation, succinylation, and other acylations on the same lysine residues. Despite some exceptions, most lysine phosphoglycerylations in S. pyogenes occurred with low stoichiometry. Such modifications may be meaningless, but it is also conceivable that phosphoglycerylation, acetylation, and other acylations jointly contribute to the overall regulation of metabolism.
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Affiliation(s)
- Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, 18057 Rostock, Germany
| | - Michael Kreutzer
- Medical Research Center, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany;
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Panja S, Nahomi RB, Rankenberg J, Michel CR, Nagaraj RH. Thiol-Mediated Enhancement of N ε-Acetyllysine Formation in Lens Proteins. ACS Chem Biol 2024; 19:1495-1505. [PMID: 38904252 DOI: 10.1021/acschembio.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Lysine acetylation (AcK) is a prominent post-translational modification in eye lens crystallins. We have observed that AcK formation is preferred in some lysine residues over others in crystallins. In this study, we have investigated the role of thiols in such AcK formation. Upon incubation with acetyl-CoA (AcCoA), αA-Crystallin, which contains two cysteine residues, showed significantly higher levels of AcK than αB-Crystallin, which lacks cysteine residues. Incubation with thiol-rich γS-Crystallin resulted in higher AcK formation in αB-Crystallin from AcCoA. External free thiol (glutathione and N-acetyl cysteine) increased the AcK content in AcCoA-incubated αB-Crystallin. Reductive alkylation of cysteine residues significantly decreased (p < 0.001) the AcCoA-mediated AcK formation in αA-Crystallin. Introduction of cysteine residues within ∼5 Å of lysine residues (K92C, E99C, and V169C) in αB-Crystallin followed by incubation with AcCoA resulted in a 3.5-, 1.3- and 1.3-fold increase in the AcK levels when compared to wild-type αB-Crystallin, respectively. Together, these results suggested that AcK formation in α-Crystallin is promoted by the proximal cysteine residues and protein-free thiols through an S → N acetyl transfer mechanism.
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Fang F, Xu T, Hagar HTC, Hovde S, Kuo MH, Sun L. A pilot study for deciphering post-translational modifications and proteoforms of tau protein by capillary electrophoresis-mass spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602093. [PMID: 39026802 PMCID: PMC11257423 DOI: 10.1101/2024.07.04.602093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Abnormal accumulation of tau proteins is one pathological hallmark of Alzheimer□s disease (AD). Many tau protein post-translational modifications (PTMs) are associated with the development of AD, such as phosphorylation, acetylation, and methylation. Therefore, a complete picture of PTM landscape of tau is critical for understanding the molecular mechanisms of AD progression. Here, we offered a pilot study of combining two complementary analytical techniques, capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) and reversed-phase liquid chromatography (RPLC)-MS/MS, for bottom-up proteomics of recombinant human tau-0N3R. We identified 53 phosphorylation sites of tau-0N3R in total, which is about 30% higher than that from RPLC-MS/MS alone. CZE-MS/MS provided more PTM sites (i.e., phosphorylation) and modified peptides of tau-0N3R than RPLC-MS/MS, and its predicted electrophoretic mobility helped improve the confidence of the identified modified peptides. We developed a highly efficient capillary isoelectric focusing (cIEF)-MS technique to offer a bird's-eye view of tau-0N3R proteoforms, with 11 putative tau-0N3R proteoforms carrying up to nine phosphorylation sites and lower pI values from more phosphorylated proteoforms detected. Interestingly, under a native-like cIEF-MS condition, we observed three putative tau-0N3R dimers carrying phosphate groups. The findings demonstrate that CE-MS is a valuable analytical technique for the characterization of tau PTMs, proteoforms, and even oligomerization.
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Pang H, Zhang W, Lin X, Zeng F, Xiao X, Wei Z, Wang S, Jian J, Wang N, Li W. Vibrio alginolyticus PEPCK Mediates Florfenicol Resistance through Lysine Succinylation Modification. J Proteome Res 2024; 23:2397-2407. [PMID: 38904328 DOI: 10.1021/acs.jproteome.4c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Protein succinylation modification is a common post-translational modification (PTM) that plays an important role in bacterial metabolic regulation. In this study, quantitative analysis was conducted on the succinylated proteome of wild-type and florfenicol-resistant Vibrio alginolyticus to investigate the mechanism of succinylation regulating antibiotic resistance. Bioinformatic analysis showed that the differentially succinylated proteins were mainly enriched in energy metabolism, and it was found that the succinylation level of phosphoenolpyruvate carboxyl kinase (PEPCK) was highly expressed in the florfenicol-resistant strain. Site-directed mutagenesis was used to mutate the lysine (K) at the succinylation site of PEPCK to glutamic acid (E) and arginine (R), respectively, to investigate the function of lysine succinylation of PEPCK in the florfenicol resistance of V. alginolyticus. The detection of site-directed mutagenesis strain viability under florfenicol revealed that the survival rate of the E mutant was significantly higher than that of the R mutant and wild type, indicating that succinylation modification of PEPCK protein may affect the resistance of V. alginolyticus to florfenicol. This study indicates the important role of PEPCK during V. alginolyticus antibiotic-resistance evolution and provides a theoretical basis for the prevention and control of vibriosis and the development of new antibiotics.
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Affiliation(s)
- Huanying Pang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Weijie Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Xuelian Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Fuyuan Zeng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Xing Xiao
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Zhiqing Wei
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Shi Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Jichang Jian
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang 524025, Guangdong, China
| | - Na Wang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Wanxin Li
- School of Public Health, Fujian Medical University, Fujian 350122, China
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Xie D, Zheng J, Sun Y, Li X, Ren S. Effects of Ca 2+ signal on the activities of key enzymes and expression of related genes in yeast ethanol metabolism and mitochondrial function during high sugar fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5077-5088. [PMID: 38284794 DOI: 10.1002/jsfa.13341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND During high sugar fermentation, yeast is mainly affected by high sugar stress in the early stage. It becomes jointly affected by high sugar and ethanol stress as ethanol accumulates during fermentation. Ca2+, as the second messenger of the cell, mediates various metabolic processes. In this study, the effects of the Ca2+ signal on the activities of key enzymes, expression of related genes of ethanol metabolism, and mitochondrial function were investigated. RESULTS The results showed a significant increase in the activities of enzymes related to ethanol metabolism in yeast cells under a high sugar environment. Ca2+ significantly promoted the activities of enzymes related to mitochondrial respiratory metabolism and regulated the carbon flow between ethanol metabolism and the tricarboxylic acid cycle. The high sugar environment affected the expression of genes related to carbon metabolism, while the addition of Ca2+ stabilized the expression of related genes. CONCLUSION Ca2+ signal participated in ethanol and mitochondrial metabolism and regulated the key enzymes and related gene expression to enhance the resistance of yeast to stress during high sugar fermentation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Xie
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Jiaxin Zheng
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yingqi Sun
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Xing Li
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Shuncheng Ren
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
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Ito M, Nishida Y, Iwamoto T, Kanai A, Aoyama S, Ueki K, Uzawa H, Iida H, Watada H. Protein acylations induced by a ketogenic diet demonstrate diverse patterns depending on organs and differ between histones and global proteins. Biochem Biophys Res Commun 2024; 712-713:149960. [PMID: 38640734 DOI: 10.1016/j.bbrc.2024.149960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
An essential ketone body, β-hydroxybutyrate (BOHB), plays various roles in physiological regulations via protein acylations such as lysine acetylation and β-hydroxybutyrylation. Here, to understand how BOHB systemically regulates acylations from an overarching perspective, we administered a ketogenic diet to mice to increase BOHB concentration and examined acylations. We found that global acetylation and β-hydroxybutyrylation dramatically increase in various organs except for the brains, where the increase was much smaller than in the other organs. Interestingly, we observe no increase in histone acetylation in the organs where significant global protein acetylation occurs despite a substantial rise in histone β-hydroxybutyrylation. Finally, we compared the transcriptome data of the mice's liver after the ketogenic diet to the public databases, showing that upregulated genes are enriched in those related to histone β-hydroxybutyrylation in starvation. Our data indicate that a ketogenic diet induces diverse patterns of acylations depending on organs and protein localizations, suggesting that different mechanisms regulate acylations and that the ketogenic diet is associated with starvation in terms of protein modifications.
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Affiliation(s)
- Minami Ito
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuya Nishida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Tatsuya Iwamoto
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Akiko Kanai
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shuhei Aoyama
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyosei Ueki
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotsugu Uzawa
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hitoshi Iida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotaka Watada
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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47
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Huang L, Guo H. Acetylation modification in the regulation of macroautophagy. ADVANCED BIOTECHNOLOGY 2024; 2:19. [PMID: 39883319 PMCID: PMC11740868 DOI: 10.1007/s44307-024-00027-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 01/31/2025]
Abstract
Macroautophagy, commonly referred to as autophagy, is an evolutionarily conserved cellular process that plays a crucial role in maintaining cellular homeostasis. It orchestrates the delivery of dysfunctional or surplus cellular materials to the vacuole or lysosome for degradation and recycling, particularly during adverse conditions. Over the past few decades, research has unveiled intricate regulatory mechanisms governing autophagy through various post-translational modifications (PTMs). Among these PTMs, acetylation modification has emerged as a focal point in yeast and animal studies. It plays a pivotal role in autophagy by directly targeting core components within the central machinery of autophagy, including autophagy initiation, nucleation, phagophore expansion, and autophagosome maturation. Additionally, acetylation modulates autophagy at the transcriptional level by modifying histones and transcription factors. Despite its well-established significance in yeast and mammals, the role of acetylation in plant autophagy remains largely unexplored, and the precise regulatory mechanisms remain enigmatic. In this comprehensive review, we summarize the current understanding of the function and underlying mechanisms of acetylation in regulating autophagy across yeast, mammals, and plants. We particularly highlight recent advances in deciphering the impact of acetylation on plant autophagy. These insights not only provide valuable guidance but also inspire further scientific inquiries into the intricate role of acetylation in plant autophagy.
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Affiliation(s)
- Li Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hongwei Guo
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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48
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Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem 2024; 16:913-921. [PMID: 38531969 PMCID: PMC11164685 DOI: 10.1038/s41557-024-01500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to -1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein-DNA and protein-protein interactions in biological processes from replication to ubiquitin signalling.
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Affiliation(s)
- Maria Weyh
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marie-Lena Jokisch
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tuan-Anh Nguyen
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maximilian Fottner
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Kathrin Lang
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany.
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Yan W, Xie C, Sun S, Zheng Q, Wang J, Wang Z, Man CH, Wang H, Yang Y, Wang T, Shi L, Zhang S, Huang C, Xu S, Wang YP. SUCLG1 restricts POLRMT succinylation to enhance mitochondrial biogenesis and leukemia progression. EMBO J 2024; 43:2337-2367. [PMID: 38649537 PMCID: PMC11183053 DOI: 10.1038/s44318-024-00101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Mitochondria are cellular powerhouses that generate energy through the electron transport chain (ETC). The mitochondrial genome (mtDNA) encodes essential ETC proteins in a compartmentalized manner, however, the mechanism underlying metabolic regulation of mtDNA function remains unknown. Here, we report that expression of tricarboxylic acid cycle enzyme succinate-CoA ligase SUCLG1 strongly correlates with ETC genes across various TCGA cancer transcriptomes. Mechanistically, SUCLG1 restricts succinyl-CoA levels to suppress the succinylation of mitochondrial RNA polymerase (POLRMT). Lysine 622 succinylation disrupts the interaction of POLRMT with mtDNA and mitochondrial transcription factors. SUCLG1-mediated POLRMT hyposuccinylation maintains mtDNA transcription, mitochondrial biogenesis, and leukemia cell proliferation. Specifically, leukemia-promoting FMS-like tyrosine kinase 3 (FLT3) mutations modulate nuclear transcription and upregulate SUCLG1 expression to reduce succinyl-CoA and POLRMT succinylation, resulting in enhanced mitobiogenesis. In line, genetic depletion of POLRMT or SUCLG1 significantly delays disease progression in mouse and humanized leukemia models. Importantly, succinyl-CoA level and POLRMT succinylation are downregulated in FLT3-mutated clinical leukemia samples, linking enhanced mitobiogenesis to cancer progression. Together, SUCLG1 connects succinyl-CoA with POLRMT succinylation to modulate mitochondrial function and cancer development.
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Affiliation(s)
- Weiwei Yan
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Chengmei Xie
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Sijun Sun
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Quan Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingyi Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Zihao Wang
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Cheuk-Him Man
- Division of Haematology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haiyan Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Yunfan Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Tianshi Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Leilei Shi
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Shengjie Zhang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
| | - Shuangnian Xu
- Department of Hematology, Southwest Hospital, Army Medical University, 400038, Chongqing, China.
| | - Yi-Ping Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China.
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50
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Chen C, Han P, Qing Y. Metabolic heterogeneity in tumor microenvironment - A novel landmark for immunotherapy. Autoimmun Rev 2024; 23:103579. [PMID: 39004158 DOI: 10.1016/j.autrev.2024.103579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/10/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
The surrounding non-cancer cells and tumor cells that make up the tumor microenvironment (TME) have various metabolic rhythms. TME metabolic heterogeneity is influenced by the intricate network of metabolic control within and between cells. DNA, protein, transport, and microbial levels are important regulators of TME metabolic homeostasis. The effectiveness of immunotherapy is also closely correlated with alterations in TME metabolism. The response of a tumor patient to immunotherapy is influenced by a variety of variables, including intracellular metabolic reprogramming, metabolic interaction between cells, ecological changes within and between tumors, and general dietary preferences. Although immunotherapy and targeted therapy have made great strides, their use in the accurate identification and treatment of tumors still has several limitations. The function of TME metabolic heterogeneity in tumor immunotherapy is summarized in this article. It focuses on how metabolic heterogeneity develops and is regulated as a tumor progresses, the precise molecular mechanisms and potential clinical significance of imbalances in intracellular metabolic homeostasis and intercellular metabolic coupling and interaction, as well as the benefits and drawbacks of targeted metabolism used in conjunction with immunotherapy. This offers insightful knowledge and important implications for individualized tumor patient diagnosis and treatment plans in the future.
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Affiliation(s)
- Chen Chen
- The First Affiliated Hospital of Ningbo University, Ningbo 315211, Zhejiang, China
| | - Peng Han
- Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang, China.
| | - Yanping Qing
- The First Affiliated Hospital of Ningbo University, Ningbo 315211, Zhejiang, China.
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