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Li C, Teng P, Sun S, Cui K, Yao S, Fei B, Ling F, Huang Z. Acetylation of aldehyde dehydrogenase ALDH1L2 regulates cellular redox balance and the chemosensitivity of colorectal cancer to 5-fluorouracil. J Biol Chem 2023; 299:105090. [PMID: 37507016 PMCID: PMC10470206 DOI: 10.1016/j.jbc.2023.105090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Folate-mediated one-carbon metabolism (FOCM) is crucial in sustaining rapid proliferation and survival of cancer cells. The folate cycle depends on a series of key cellular enzymes, including aldehyde dehydrogenase 1 family member L2 (ALDH1L2) that is usually overexpressed in cancer cells, but the regulatory mechanism of ALDH1L2 remains undefined. In this study, we observed the significant overexpression of ALDH1L2 in colorectal cancer (CRC) tissues, which is associated with poor prognosis. Mechanistically, we identified that the acetylation of ALDH1L2 at the K70 site is an important regulatory mechanism inhibiting the enzymatic activity of ALDH1L2 and disturbing cellular redox balance. Moreover, we revealed that sirtuins 3 (SIRT3) directly binds and deacetylates ALDH1L2 to increase its activity. Interestingly, the chemotherapeutic agent 5-fluorouracil (5-Fu) inhibits the expression of SIRT3 and increases the acetylation levels of ALDH1L2 in colorectal cancer cells. 5-Fu-induced ALDH1L2 acetylation sufficiently inhibits its enzymatic activity and the production of NADPH and GSH, thereby leading to oxidative stress-induced apoptosis and suppressing tumor growth in mice. Furthermore, the K70Q mutant of ALDH1L2 sensitizes cancer cells to 5-Fu both in vitro and in vivo through perturbing cellular redox and serine metabolism. Our findings reveal an unknown 5-Fu-SIRT3-ALDH1L2 axis regulating redox homeostasis, and suggest that targeting ALDH1L2 is a promising therapeutic strategy to sensitize tumor cells to chemotherapeutic agents.
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Affiliation(s)
- Chaoqun Li
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Peng Teng
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Shengbai Sun
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Bojian Fei
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Feng Ling
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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Li R, Wang Z, Wang Y, Sun R, Zou B, Tian X, Liu D, Zhao X, Zhou J, Zhao Y, Yao J. SIRT3 regulates mitophagy in liver fibrosis through deacetylation of PINK1/NIPSNAP1. J Cell Physiol 2023; 238:2090-2102. [PMID: 37417912 DOI: 10.1002/jcp.31069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/08/2023]
Abstract
Damaged mitochondria, a key factor in liver fibrosis, can be removed by the mitophagy pathway to maintain homeostasis of the intracellular environment to alleviate the development of fibrosis. PINK1 (PTEN-induced kinase 1) and NIPSNAP1 (nonneuronal SNAP25-like protein 1), which cooperatively regulate mitophagy, have been predicted to include the sites of lysine acetylation related to SIRT3 (mitochondrial deacetylase sirtuin 3). Our study aimed to discuss whether SIRT3 deacetylates PINK1 and NIPSNAP1 to regulate mitophagy in liver fibrosis. Carbon tetrachloride (CCl4 )-induced liver fibrosis as an in vivo model and LX-2 cells as activated cells were used to simulate liver fibrosis. SIRT3 expression was significantly decreased in mice in response to CCl4 , and SIRT3 knockout in vivo significantly deepened the severity of liver fibrosis, as indicated by increased α-SMA and Col1a1 levels both in vivo and in vitro. SIRT3 overexpression decreased α-SMA and Col1a1 levels. Furthermore, SIRT3 significantly regulated mitophagy in liver fibrosis, as demonstrated by LC3-Ⅱ/Ⅰ and p62 expression and colocalization between TOM20 and LAMP1. Importantly, PINK1 and NIPSNAP1 expression was also decreased in liver fibrosis, and PINK1 and NIPSNAP1 overexpression significantly improved mitophagy and attenuated ECM production. Furthermore, after simultaneously interfering with PINK1 or NIPSNAP1 and overexpressing SIRT3, the effect of SIRT3 on improving mitophagy and alleviating liver fibrosis was disrupted. Mechanistically, we show that SIRT3, as a mitochondrial deacetylase, specifically regulates the acetylation of PINK1 and NIPSNAP1 to mediate the mitophagy pathway in liver fibrosis. SIRT3-mediated PINK1 and NIPSNAP1 deacetylation is a novel molecular mechanism in liver fibrosis.
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Affiliation(s)
- Ruixi Li
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhecheng Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Yue Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Ruimin Sun
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Boyang Zou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Xinyao Tian
- Department of General Surgery, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Deshun Liu
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xuzi Zhao
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Junjun Zhou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Yan Zhao
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Jihong Yao
- Department of Pharmacology, Dalian Medical University, Dalian, China
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53
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Tang C, Wang P, Zhu X, Qi K, Xie Z, Zhang H, Li X, Gao H, Gu T, Gu C, Li S, de Graaf BHJ, Zhang S, Wu J. Acetylation of inorganic pyrophosphatase by S-RNase signaling induces pollen tube tip swelling by repressing pectin methylesterase. THE PLANT CELL 2023; 35:3544-3565. [PMID: 37306489 PMCID: PMC10473231 DOI: 10.1093/plcell/koad162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Self-incompatibility (SI) is a widespread genetically determined system in flowering plants that prevents self-fertilization to promote gene flow and limit inbreeding. S-RNase-based SI is characterized by the arrest of pollen tube growth through the pistil. Arrested pollen tubes show disrupted polarized growth and swollen tips, but the underlying molecular mechanism is largely unknown. Here, we demonstrate that the swelling at the tips of incompatible pollen tubes in pear (Pyrus bretschneideri [Pbr]) is mediated by the SI-induced acetylation of the soluble inorganic pyrophosphatase (PPA) PbrPPA5. Acetylation at Lys-42 of PbrPPA5 by the acetyltransferase GCN5-related N-acetyltransferase 1 (GNAT1) drives accumulation of PbrPPA5 in the nucleus, where it binds to the transcription factor PbrbZIP77, forming a transcriptional repression complex that inhibits the expression of the pectin methylesterase (PME) gene PbrPME44. The function of PbrPPA5 as a transcriptional repressor does not require its PPA activity. Downregulating PbrPME44 resulted in increased levels of methyl-esterified pectins in growing pollen tubes, leading to swelling at their tips. These observations suggest a mechanism for PbrPPA5-driven swelling at the tips of pollen tubes during the SI response. The targets of PbrPPA5 include genes encoding cell wall-modifying enzymes, which are essential for building a continuous sustainable mechanical structure for pollen tube growth.
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Affiliation(s)
- Chao Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Zhihua Xie
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Hao Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Xiaoqiang Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Hongru Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Shan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Shaoling Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Na AY, Choi SY, Paudel S, Bae JS, Tan M, Lee S. Integrative Profiling of Lysine Acylome in Sepsis-Induced Liver Injury. J Proteome Res 2023; 22:2860-2870. [PMID: 37523266 DOI: 10.1021/acs.jproteome.3c00130] [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: 08/02/2023]
Abstract
Sepsis is one of the life-threatening diseases worldwide. Despite the continuous progress in medicine, the specific mechanism of sepsis remains unclear. A key strategy of pathogens is to use post-translational modification to modulate host factors critical for infection. We employed global immunoprecipitation technology for lysine acetylation (Kac), succinylation (Ksu), and malonylation (Kmal) for the first global lysine acylation (Kacy) analysis in a cecum ligation and puncture (CLP) model in mouse. This was performed to reveal the pathogenic mechanism of integrative Kacy and the changes in modification sites. In total, 2230 sites of 1,235 Kac proteins, 1,887 sites of 433 Ksu proteins, and 499 sites of 276 Kmal proteins were quantified and normalized by their protein levels. We focused on 379 sites in 219 upregulated proteins as the integrative Kacy sites of Kac, Ksu, and Kmal on the basis of sirtuins decreased in the CLP group. KEGG pathway analysis of integrative Kacy in 219 upregulated proteins revealed three central metabolic pathways: glycolysis/gluconeogenesis, pyruvate metabolism, and tricarboxylic acid cycle. These findings reveal the key pathogenic mechanism of integrative PTM alteration in terms of the decreased sirtuins level and provide an important foundation for an in-depth study of the biological function of Kacy in sepsis.
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Affiliation(s)
- Ann-Yae Na
- Global Drug Development Research Institute, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - So Young Choi
- Mass Spectrometry Convergence Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sanjita Paudel
- College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Sup Bae
- College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Sangkyu Lee
- Global Drug Development Research Institute, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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55
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Coluccino G, Muraca VP, Corazza A, Lippe G. Cyclophilin D in Mitochondrial Dysfunction: A Key Player in Neurodegeneration? Biomolecules 2023; 13:1265. [PMID: 37627330 PMCID: PMC10452829 DOI: 10.3390/biom13081265] [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: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the "powerhouse of the cell" turns into the "factory of death" is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein CyPD is a peptidylprolyl cis-trans isomerase involved in the regulation of the permeability transition pore (mPTP). The mPTP is a multi-conductance channel in the inner mitochondrial membrane whose dysregulated opening can ultimately lead to cell death and whose involvement in pathology has been extensively documented over the past few decades. Moreover, several mPTP-independent CyPD interactions have been identified, indicating that CyPD could be involved in the fine regulation of several biochemical pathways. To further enrich the picture, CyPD undergoes several post-translational modifications that regulate both its activity and interaction with its clients. Here, we will dissect what is currently known about CyPD and critically review the most recent literature about its involvement in neurodegenerative disorders, focusing on Alzheimer's Disease and Parkinson's Disease, supporting the notion that CyPD could serve as a promising therapeutic target for the treatment of such conditions. Notably, significant efforts have been made to develop CyPD-specific inhibitors, which hold promise for the treatment of such complex disorders.
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Affiliation(s)
- Gabriele Coluccino
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
| | | | | | - Giovanna Lippe
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
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56
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Tan Y, Liu W, Chen Y, Zhou Y, Song K, Cao S, Zhang Y, Song Y, Deng H, Yang R, Du Z. Comparative Lysine Acetylome Analysis of Y. pestis YfiQ/CobB Mutants Reveals that Acetylation of SlyA Lys73 Significantly Promotes Biofilm Formation of Y. pestis. Microbiol Spectr 2023; 11:e0046023. [PMID: 37458592 PMCID: PMC10433856 DOI: 10.1128/spectrum.00460-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/10/2023] [Indexed: 08/19/2023] Open
Abstract
Increasing evidence shows that protein lysine acetylation is involved in almost every aspect of cellular physiology in bacteria. Yersinia pestis is a flea-borne pathogen responsible for millions of human deaths in three global pandemics. However, the functional role of lysine acetylation in this pathogen remains unclear. Here, we found more acetylated proteins and a higher degree of acetylation in Y. pestis grown under mammalian host (Mh) conditions than under flea vector (Fv) conditions, suggesting that protein acetylation could significantly change during fleabite transmission. Comparative acetylome analysis of mutants of YfiQ and CobB, the major acetyltransferase and deacetylase of Y. pestis, respectively, identified 23 YfiQ-dependent and 315 CobB-dependent acetylated proteins. Further results demonstrated that acetylation of Lys73 of the SlyA protein, a MarR-family transcriptional regulator, inhibits its binding to the promoter of target genes, including hmsT that encodes diguanylate cyclase responsible for the synthesis of c-di-GMP, and significantly enhances biofilm formation of Y. pestis. Our study presents the first extensive acetylome data of Y. pestis and a critical resource for the functional study of lysine acetylation in this pathogen. IMPORTANCE Yersinia pestis is the etiological agent of plague, historically responsible for three global pandemics. The 2017 plague epidemic in Madagascar was a reminder that Y. pestis remains a real threat in many parts of the world. Plague is a zoonotic disease that primarily infects rodents via fleabite, and transmission of Y. pestis from infected fleas to mammals requires rapid adaptive responses to adverse host environments to establish infection. Our study provides the first global profiling of lysine acetylation derived from mass spectrometry analysis in Y. pestis. Our data set can serve as a critical resource for the functional study of lysine acetylation in Y. pestis and provides new molecular insight into the physiological role of lysine acetylation in proteins. More importantly, we found that acetylation of Lys73 of SlyA significantly promotes biofilm formation of Y. pestis, indicating that bacteria can use lysine acetylation to fine-tune the expression of genes to improve adaptation.
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Affiliation(s)
- Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wanbing Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yazhou Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shiyang Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Fu G, Li ST, Jiang Z, Mao Q, Xiong N, Li X, Hao Y, Zhang H. PGAM5 deacetylation mediated by SIRT2 facilitates lipid metabolism and liver cancer proliferation. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1370-1379. [PMID: 37580952 PMCID: PMC10520483 DOI: 10.3724/abbs.2023155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/13/2023] [Indexed: 08/16/2023] Open
Abstract
Tumor metabolic reprogramming and epigenetic modification work together to promote tumorigenesis and development. Protein lysine acetylation, which affects a variety of biological functions of proteins, plays an important role under physiological and pathological conditions. Here, through immunoprecipitation and mass spectrum data, we show that phosphoglycerate mutase 5 (PGAM5) deacetylation enhances malic enzyme 1 (ME1) metabolic enzyme activity to promote lipid synthesis and proliferation of liver cancer cells. Mechanistically, we demonstrate that the deacetylase SIRT2 mediates PGAM5 deacetylation to activate ME1 activity, leading to ME1 dephosphorylation, subsequent lipid accumulation and the proliferation of liver cancer cells. Taken together, our study establishes an important role for the SIRT2-PGAM5-ME1 axis in the proliferation of liver cancer cells, suggesting a potential innovative cancer therapy.
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Affiliation(s)
- Gongyu Fu
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Shi-Ting Li
- Guangdong Cardiovascular InstituteGuangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou510080China
| | - Zetan Jiang
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Qiankun Mao
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Nanchi Xiong
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Yijie Hao
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Huafeng Zhang
- Anhui Key Laboratory of Hepatopancreatobiliary SurgeryDepartment of General SurgeryAnhui Provincial Hospitalthe First Affiliated Hospital of USTCDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Hefei National Laboratory for Physical Sciences at Microscalethe Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
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58
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Muñoz JP, Basei FL, Rojas ML, Galvis D, Zorzano A. Mechanisms of Modulation of Mitochondrial Architecture. Biomolecules 2023; 13:1225. [PMID: 37627290 PMCID: PMC10452872 DOI: 10.3390/biom13081225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial network architecture plays a critical role in cellular physiology. Indeed, alterations in the shape of mitochondria upon exposure to cellular stress can cause the dysfunction of these organelles. In this scenario, mitochondrial dynamics proteins and the phospholipid composition of the mitochondrial membrane are key for fine-tuning the modulation of mitochondrial architecture. In addition, several factors including post-translational modifications such as the phosphorylation, acetylation, SUMOylation, and o-GlcNAcylation of mitochondrial dynamics proteins contribute to shaping the plasticity of this architecture. In this regard, several studies have evidenced that, upon metabolic stress, mitochondrial dynamics proteins are post-translationally modified, leading to the alteration of mitochondrial architecture. Interestingly, several proteins that sustain the mitochondrial lipid composition also modulate mitochondrial morphology and organelle communication. In this context, pharmacological studies have revealed that the modulation of mitochondrial shape and function emerges as a potential therapeutic strategy for metabolic diseases. Here, we review the factors that modulate mitochondrial architecture.
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Affiliation(s)
- Juan Pablo Muñoz
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
| | - Fernanda Luisa Basei
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, 13083-871 Campinas, SP, Brazil
| | - María Laura Rojas
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - David Galvis
- Programa de Química Farmacéutica, Universidad CES, Medellín 050031, Colombia
| | - Antonio Zorzano
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
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59
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Yayli G, Bernardini A, Sanchez PKM, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA coactivator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551787. [PMID: 37577620 PMCID: PMC10418265 DOI: 10.1101/2023.08.03.551787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
To understand the function of multisubunit complexes it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the core modules of ATAC (ADA-Two-A-Containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histones proteins. In contrast, fully assembled ATAC complex cannot be detected in the cytoplasm of mammalian cells. However, endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related coactivators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic abundance and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - HT Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
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Huang Y, Zhu C, Pan L, Zhang Z. The role of Mycobacterium tuberculosis acetyltransferase and protein acetylation modifications in tuberculosis. Front Cell Infect Microbiol 2023; 13:1218583. [PMID: 37560320 PMCID: PMC10407107 DOI: 10.3389/fcimb.2023.1218583] [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: 05/07/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis (M. tb), which has been a significant burden for a long time. Post-translational modifications (PTMs) are essential for protein function in both eukaryotic and prokaryotic cells. This review focuses on the contribution of protein acetylation to the function of M. tb and its infected macrophages. The acetylation of M. tb proteins plays a critical role in virulence, drug resistance, regulation of metabolism, and host anti-TB immune response. Similarly, the PTMs of host proteins induced by M. tb are crucial for the development, treatment, and prevention of diseases. Host protein acetylation induced by M. tb is significant in regulating host immunity against TB, which substantially affects the disease's development. The review summarizes the functions and mechanisms of M. tb acetyltransferase in virulence and drug resistance. It also discusses the role and mechanism of M. tb in regulating host protein acetylation and immune response regulation. Furthermore, the current scenario of isoniazid usage in M. tb therapy treatment is examined. Overall, this review provides valuable information that can serve as a preliminary basis for studying pathogenic research, developing new drugs, exploring in-depth drug resistance mechanisms, and providing precise treatment for TB.
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Affiliation(s)
| | | | - Liping Pan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Johan MF. Proteomic Alteration in the Progression of Multiple Myeloma: A Comprehensive Review. Diagnostics (Basel) 2023; 13:2328. [PMID: 37510072 PMCID: PMC10378430 DOI: 10.3390/diagnostics13142328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/18/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy. Most MM patients are diagnosed at a late stage because the early symptoms of the disease can be uncertain and nonspecific, often resembling other, more common conditions. Additionally, MM patients are commonly associated with rapid relapse and an inevitable refractory phase. MM is characterized by the abnormal proliferation of monoclonal plasma cells in the bone marrow. During the progression of MM, massive genomic alterations occur that target multiple signaling pathways and are accompanied by a multistep process involving differentiation, proliferation, and invasion. Moreover, the transformation of healthy plasma cell biology into genetically heterogeneous MM clones is driven by a variety of post-translational protein modifications (PTMs), which has complicated the discovery of effective treatments. PTMs have been identified as the most promising candidates for biomarker detection, and further research has been recommended to develop promising surrogate markers. Proteomics research has begun in MM, and a comprehensive literature review is available. However, proteomics applications in MM have yet to make significant progress. Exploration of proteomic alterations in MM is worthwhile to improve understanding of the pathophysiology of MM and to search for new treatment targets. Proteomics studies using mass spectrometry (MS) in conjunction with robust bioinformatics tools are an excellent way to learn more about protein changes and modifications during disease progression MM. This article addresses in depth the proteomic changes associated with MM disease transformation.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman P.O. Box 382, Sudan
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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Kamelnia R, Goliaei B, Peyman Shariatpanahi S, Mehrnejad F, Ghasemi A, Zare Karizak A, Ebrahim-Habibi A. Chemical Modification of the Amino Groups of Human Insulin: Investigating Structural Properties and Amorphous Aggregation of Acetylated Species. Protein J 2023:10.1007/s10930-023-10131-7. [PMID: 37395911 DOI: 10.1007/s10930-023-10131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2023] [Indexed: 07/04/2023]
Abstract
The efficacy of human recombinant insulin can be affected by its aggregation. Effects of acetylation were observed on insulin structure, stability, and aggregation at 37 and 50 °C and pH of 5.0 and 7.4 with the use of spectroscopy, circular dichroism (CD), dynamic light scattering (DLS), and atomic force microscopy (AFM). Raman and FTIR results were indicative of structural changes in AC-INS, and CD analyses showed a slight increase in β-sheet content in AC-INS. Melting temperature (Tm) measurements indicated an overall more stable structure and spectroscopic assessment showed a more compact one. Formation of amorphous aggregates was followed over time and kinetics parameters showed a longer nucleation phase (higher t* amount) and lower aggregates amount (lower Alim) for acetylated insulin (AC-INS) compared to native (N-INS) in all tested conditions. The results of amyloid-specific probes approved the formation of amorphous aggregates. Size particle and microscopic analysis suggested that AC-INS was less prone to form aggregates, which were smaller if formed. In conclusion, this study has demonstrated that controlled acetylation of insulin may lead to its higher stability and lower propensity toward amorphous aggregation and has provided insight into the result of this type of post-translational protein modification.
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Affiliation(s)
- Reyhane Kamelnia
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran
| | - Bahram Goliaei
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran.
| | - Seyed Peyman Shariatpanahi
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ashkan Zare Karizak
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Jalal Al Ahmad Highway, Tehran, 1411713137, Iran.
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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Zhang S, Chen J, Li Q, Zeng W. Opioid growth factor receptor promotes adipose tissue thermogenesis via enhancing lipid oxidation. LIFE METABOLISM 2023; 2:load018. [PMID: 39872016 PMCID: PMC11749475 DOI: 10.1093/lifemeta/load018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/23/2023] [Accepted: 05/01/2023] [Indexed: 01/29/2025]
Abstract
The thermogenic brown and beige adipocytes consume fatty acids and generate heat to maintain core body temperature in the face of cold challenges. Since their validated presence in humans, the activation of thermogenic fat has been an attractive target for treating obesity and related metabolic diseases. Here, we reported that the opioid growth factor receptor (Ogfr) was highly expressed in adipocytes and promoted thermogenesis. The mice with genetic deletion of Ogfr in adipocytes displayed an impaired capacity to counter environmental cold challenges. Meanwhile, Ogfr ablation in adipocytes led to reduced fatty acid oxidation, enhanced lipid accumulation, impaired glucose tolerance, and exacerbated tissue inflammation under chronic high-fat diet (HFD)-fed conditions. At the cellular level, OGFr enhanced the production of mitochondrial trifunctional protein subunit α (MTPα) and also interacted with MTPα, thus promoting fatty acid oxidation. Together, our study demonstrated the important role of OGFr in fatty acid metabolism and adipose thermogenesis.
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Affiliation(s)
- Shan Zhang
- Institute for Immunology, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Jianhui Chen
- Institute for Immunology, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Qingqing Li
- Institute for Immunology, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Wenwen Zeng
- Institute for Immunology, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
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64
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Li S, Sheng ZH. Oligodendrocyte-derived transcellular signaling regulates axonal energy metabolism. Curr Opin Neurobiol 2023; 80:102722. [PMID: 37028201 PMCID: PMC10225329 DOI: 10.1016/j.conb.2023.102722] [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: 11/22/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
The unique morphology and functionality of central nervous system (CNS) neurons necessitate specialized mechanisms to maintain energy metabolism throughout long axons and extensive terminals. Oligodendrocytes (OLs) enwrap CNS axons with myelin sheaths in a multilamellar fashion. Apart from their well-established function in action potential propagation, OLs also provide intercellular metabolic support to axons by transferring energy metabolites and delivering exosomes consisting of proteins, lipids, and RNAs. OL-derived metabolic support is crucial for the maintenance of axonal integrity; its dysfunction has emerged as an important player in neurological disorders that are associated with axonal energy deficits and degeneration. In this review, we discuss recent advances in how these transcellular signaling pathways maintain axonal energy metabolism in health and neurological disorders.
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Affiliation(s)
- Sunan Li
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA. https://twitter.com/@sunan_li
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA.
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Wang Y, Abrol R, Mak JYW, Das Gupta K, Ramnath D, Karunakaran D, Fairlie DP, Sweet MJ. Histone deacetylase 7: a signalling hub controlling development, inflammation, metabolism and disease. FEBS J 2023; 290:2805-2832. [PMID: 35303381 PMCID: PMC10952174 DOI: 10.1111/febs.16437] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/02/2022] [Accepted: 03/16/2022] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) catalyse removal of acetyl groups from lysine residues on both histone and non-histone proteins to control numerous cellular processes. Of the 11 zinc-dependent classical HDACs, HDAC4, 5, 7 and 9 are class IIa HDAC enzymes that regulate cellular and developmental processes through both enzymatic and non-enzymatic mechanisms. Over the last two decades, HDAC7 has been associated with key roles in numerous physiological and pathological processes. Molecular, cellular, in vivo and disease association studies have revealed that HDAC7 acts through multiple mechanisms to control biological processes in immune cells, osteoclasts, muscle, the endothelium and epithelium. This HDAC protein regulates gene expression, cell proliferation, cell differentiation and cell survival and consequently controls development, angiogenesis, immune functions, inflammation and metabolism. This review focuses on the cell biology of HDAC7, including the regulation of its cellular localisation and molecular mechanisms of action, as well as its associative and causal links with cancer and inflammatory, metabolic and fibrotic diseases. We also review the development status of small molecule inhibitors targeting HDAC7 and their potential for intervention in different disease contexts.
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Affiliation(s)
- Yizhuo Wang
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Rishika Abrol
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Jeffrey Y. W. Mak
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
| | - Kaustav Das Gupta
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Divya Ramnath
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Denuja Karunakaran
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - David P. Fairlie
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
| | - Matthew J. Sweet
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
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Park JW, Tyl MD, Cristea IM. Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection. Biomolecules 2023; 13:biom13050869. [PMID: 37238738 DOI: 10.3390/biom13050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.
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Affiliation(s)
- Ji Woo Park
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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Hao K, Chen F, Zhao L, Xu S, Xiong Y, Xu R, Xie X, Huang H, Shu C, Liu Z, Wang H, Wang G. Nicotinamide ameliorates mitochondria-related neuronal apoptosis and cognitive impairment via the NAD +/SIRT3 pathway. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2023; 9:32. [PMID: 37210391 DOI: 10.1038/s41537-023-00357-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 05/22/2023]
Abstract
Emerging evidence suggests that mitochondria play a central role in mental health disorders including schizophrenia. Here we investigated whether nicotinamide (NAM) normalized cognitive impairment via a mechanism involving the mitochondrial Sirtuin 3 (SIRT3) pathway. The 24 h maternal separation (MS) rat model was used to mimic schizophrenia-associate phenotypes. Schizophrenia-like behaviors and memory impairments were detected using the pre-pulse inhibition test, novel object recognition test, and Barnes maze test, and neuronal apoptosis was characterized using multiple assays. SIRT3 activity was inhibited pharmacologically or by knockdown in HT22 cells, and BV2 microglia and SIRT3-knockdown HT22 cells were co-cultured in vitro. Mitochondrial molecules were measured by western blotting, and mitochondrial damage was measured with reactive oxygen species and mitochondrial membrane potential assays. Proinflammatory cytokines were assayed by ELISA and microglial activation was detected by immunofluorescence. MS animals showed behavioral and cognitive impairment and increased neuronal apoptosis. Supplementation with NAM or administration of honokiol, a SIRT3 activator, reversed all of the changes in behavioral and neuronal phenotypes. Administration of the SIRT3 inhibitor 3-TYP in control and NAM-treated MS rats caused behavioral and neuronal phenotypes similar to MS. In vitro, inhibition of SIRT3 activity with 3-TYP or by knockdown in HT22 cells increased ROS accumulation and caused neuronal apoptosis in a single-culture system. In co-culture systems, SIRT3 knockdown in HT22 cells activated BV2 microglia and increased levels of TNF-α, IL-6, and IL-1β. The administration of NAM blocked these alterations. Taken together, these data suggest that NAM can rescue neuronal apoptosis and microglial over-activation through the nicotinamide adenine dinucleotide (NAD+)-SIRT3-SOD2 signaling pathway, furthering our understanding of the pathogenesis of schizophrenia and providing avenues for novel treatments.
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Affiliation(s)
- Keke Hao
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Fashuai Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Henan, China
| | - Linyao Zhao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Shilin Xu
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Ying Xiong
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Rui Xu
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Xinhui Xie
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Huan Huang
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Chang Shu
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Zhongchun Liu
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Huiling Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, 430071, Wuhan, China.
| | - Gaohua Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, 430060, Wuhan, China.
- Hubei Institute of Neurology and Psychiatry Research, 430060, Wuhan, China.
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Yan K, Mousavi N, Yang XJ. Analysis of Lysine Acetylation and Acetylation-like Acylation In Vitro and In Vivo. Curr Protoc 2023; 3:e738. [PMID: 37184117 DOI: 10.1002/cpz1.738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein lysine acetylation refers to the covalent transfer of an acetyl moiety from acetyl coenzyme A to the epsilon-amino group of a lysine residue and is critical for regulating protein functions in almost all living cells or organisms. Studies in the past decade have demonstrated the unexpected finding that acetylation-like acylation, such as succinylation, propionylation, butyrylation, crotonylation, and lactylation, is also present in histones and many non-histone proteins. Acetylation and acetylation-like acylation serve as reversible on/off switches for regulating protein function while interplaying with other post-translational modifications (such as phosphorylation and methylation) in a codified manner. Lysine acetylation and acetylation-like acylation are important for regulating different cellular and developmental processes in normal and pathological states. Thus, the detection of such modifications is important for related basic research and molecular diagnostics. Traditionally, lysine acetylation is detected by autoradiography, but recent decades have seen great improvement in the quality of site-specific antibodies against acetylation (or acetylation-like acylation), thereby providing competitive alternatives to the use of radioactive acetate and acetyl-coenzyme A for in vivo and in vitro labeling, respectively. This article describes protocols for the detection of lysine acetylation and acetylation-like acylation with site-specific antibodies to complement extant autoradiography-based methods (Pelletier et al., 2017). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Acylation assays in vitro Basic Protocol 2: Determination of in vivo acylation.
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Affiliation(s)
- Kezhi Yan
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Negar Mousavi
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- McGill University Health Center, Montreal, Quebec, Canada
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Tuncay E, Gando I, Huo JY, Yepuri G, Samper N, Turan B, Yang HQ, Ramasamy R, Coetzee WA. The cardioprotective role of sirtuins is mediated in part by regulating K ATP channel surface expression. Am J Physiol Cell Physiol 2023; 324:C1017-C1027. [PMID: 36878847 PMCID: PMC10110703 DOI: 10.1152/ajpcell.00459.2022] [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: 10/12/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
Sirtuins are NAD+-dependent deacetylases with beneficial roles in conditions relevant to human health, including metabolic disease, type II diabetes, obesity, cancer, aging, neurodegenerative diseases, and cardiac ischemia. Since ATP-sensitive K+ (KATP) channels have cardioprotective roles, we investigated whether they are regulated by sirtuins. Nicotinamide mononucleotide (NMN) was used to increase cytosolic NAD+ levels and to activate sirtuins in cell lines, isolated rat and mouse cardiomyocytes or insulin-secreting INS-1 cells. KATP channels were studied with patch clamping, biochemistry techniques, and antibody uptake experiments. NMN led to an increase in intracellular NAD+ levels and an increase in the KATP channel current, without significant changes in the unitary current amplitude or open probability. An increased surface expression was confirmed using surface biotinylation approaches. The rate of KATP channel internalization was diminished by NMN, which may be a partial explanation for the increased surface expression. We show that NMN acts via sirtuins since the increased KATP channel surface expression was prevented by blockers of SIRT1 and SIRT2 (Ex527 and AGK2) and mimicked by SIRT1 activation (SRT1720). The pathophysiological relevance of this finding was studied using a cardioprotection assay with isolated ventricular myocytes, in which NMN protected against simulated ischemia or hypoxia in a KATP channel-dependent manner. Overall, our data draw a link between intracellular NAD+, sirtuin activation, KATP channel surface expression, and cardiac protection against ischemic damage.
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Affiliation(s)
- Erkan Tuncay
- Department of Biophysics, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Ivan Gando
- Department of Pathology, New York University Grossman Medical Center, New York, New York, United States
| | - Jian-Yi Huo
- Cyrus Tang Hematology Center, Soochow University, Suzhou, People's Republic of China
| | - Gautham Yepuri
- Department of Medicine, New York University Grossman Medical Center, New York, New York, United States
| | - Natalie Samper
- Department of Pathology, New York University Grossman Medical Center, New York, New York, United States
| | - Belma Turan
- Department of Biophysics, Faculty of Medicine, Lokman Hekim University, Ankara, Turkey
| | - Hua-Qian Yang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, People's Republic of China
| | - Ravichandran Ramasamy
- Department of Medicine, New York University Grossman Medical Center, New York, New York, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman Medical Center, New York, New York, United States
| | - William A Coetzee
- Department of Pathology, New York University Grossman Medical Center, New York, New York, United States
- Department of Physiology & Neuroscience, New York University Grossman Medical Center, New York, New York, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman Medical Center, New York, New York, United States
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70
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Toro TB, Bornes KE, Watt TJ. Lysine Deacetylase Substrate Selectivity: Distinct Interaction Surfaces Drive Positive and Negative Selection for Residues Following Acetyllysine. Biochemistry 2023; 62:1464-1483. [PMID: 37043688 PMCID: PMC10157890 DOI: 10.1021/acs.biochem.3c00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Lysine acetylation is a post-translational modification that is reversed by lysine deacetylases (KDACs). The goal of this work was to identify determinants of substrate specificity for KDACs, focusing on short-range interactions occurring with residues immediately following the acetyllysine. Using a fluorescence-based in vitro assay, we determined the activity for each enzyme with a limited panel of derivative substrate peptides, revealing a distinct reactivity profile for each enzyme. We mapped the interaction surface for KDAC6, KDAC8, and KDAC1 with the +1 and +2 substrate residues (with respect to acetyllysine) based on enzyme-substrate interaction pairs observed in molecular dynamics simulations. Characteristic residues in each KDAC interact preferentially with particular substrate residues and correlate with either enhanced or inhibited activity. Although nonpolar aromatic residues generally enhanced activity with all KDACs, the manner in which each enzyme interacted with these residues is distinct. Furthermore, each KDAC has distinctive interactions that correlate with lower activity, primarily ionic in nature. KDAC8 exhibited the most diverse and widest range of effects, while KDAC6 was sensitive only to the +1 position and KDAC1 selectivity was primarily driven by negative selection. The substrate preferences were validated for KDAC6 and KDAC8 using a set of peptides derived from known acetylated proteins. Overall, we determined how KDAC6, KDAC8, and KDAC1 achieve substrate specificity with residues following the acetyllysine. These new insights into KDAC specificity will be critical for identifying novel substrates of particular KDACs, designing KDAC-specific inhibitors, and demonstrate a general framework for understanding substrate specificity for other enzyme classes.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Kiara E Bornes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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71
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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72
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Carrico C, Cruz A, Walter M, Meyer J, Wehrfritz C, Shah S, Wei L, Schilling B, Verdin E. Coenzyme A binding sites induce proximal acylation across protein families. Sci Rep 2023; 13:5029. [PMID: 36977698 PMCID: PMC10050154 DOI: 10.1038/s41598-023-31900-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Lysine Nɛ-acylations, such as acetylation or succinylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic, and only a specific subset of the proteome is acylated. Coenzyme A (CoA) can act as an acyl group carrier via a thioester bond, but what controls the acylation of mitochondrial lysines remains poorly understood. Using published datasets, here we found that proteins with a CoA-binding site are more likely to be acetylated, succinylated, and glutarylated. Using computational modeling, we show that lysine residues near the CoA-binding pocket are highly acylated compared to those farther away. We hypothesized that acyl-CoA binding enhances acylation of nearby lysine residues. To test this hypothesis, we co-incubated enoyl-CoA hydratase short chain 1 (ECHS1), a CoA-binding mitochondrial protein, with succinyl-CoA and CoA. Using mass spectrometry, we found that succinyl-CoA induced widespread lysine succinylation and that CoA competitively inhibited ECHS1 succinylation. CoA-induced inhibition at a particular lysine site correlated inversely with the distance between that lysine and the CoA-binding pocket. Our study indicated that CoA acts as a competitive inhibitor of ECHS1 succinylation by binding to the CoA-binding pocket. Together, this suggests that proximal acylation at CoA-binding sites is a primary mechanism for lysine acylation in the mitochondria.
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Affiliation(s)
- Chris Carrico
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Marius Walter
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Jesse Meyer
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Lei Wei
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
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73
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Liu Y, Birsoy K. Metabolic sensing and control in mitochondria. Mol Cell 2023; 83:877-889. [PMID: 36931256 PMCID: PMC10332353 DOI: 10.1016/j.molcel.2023.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are membrane-enclosed organelles with endosymbiotic origins, harboring independent genomes and a unique biochemical reaction network. To perform their critical functions, mitochondria must maintain a distinct biochemical environment and coordinate with the cytosolic metabolic networks of the host cell. This coordination requires them to sense and control metabolites and respond to metabolic stresses. Indeed, mitochondria adopt feedback or feedforward control strategies to restrain metabolic toxicity, enable metabolic conservation, ensure stable levels of key metabolites, allow metabolic plasticity, and prevent futile cycles. A diverse panel of metabolic sensors mediates these regulatory circuits whose malfunctioning leads to inborn errors of metabolism with mild to severe clinical manifestations. In this review, we discuss the logic and molecular basis of metabolic sensing and control in mitochondria. The past research outlined recurring patterns in mitochondrial metabolic sensing and control and highlighted key knowledge gaps in this organelle that are potentially addressable with emerging technological breakthroughs.
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Affiliation(s)
- Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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74
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Pearson-Smith JN, Fulton R, Huynh CQ, Figueroa AG, Huynh GB, Liang LP, Gano LB, Michel CR, Reisdorph N, Reisdorph R, Fritz KS, Verdin E, Patel M. Neuronal SIRT3 Deletion Predisposes to Female-Specific Alterations in Cellular Metabolism, Memory, and Network Excitability. J Neurosci 2023; 43:1845-1857. [PMID: 36759193 PMCID: PMC10010453 DOI: 10.1523/jneurosci.1259-22.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/14/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Mitochondrial dysfunction is an early event in the pathogenesis of neurologic disorders and aging. Sirtuin 3 (SIRT3) regulates mitochondrial function in response to the cellular environment through the reversible deacetylation of proteins involved in metabolism and reactive oxygen species detoxification. As the primary mitochondrial deacetylase, germline, or peripheral tissue-specific deletion of SIRT3 produces mitochondrial hyperacetylation and the accelerated development of age-related diseases. Given the unique metabolic demands of neurons, the role of SIRT3 in the brain is only beginning to emerge. Using mass spectrometry-based acetylomics, high-resolution respirometry, video-EEG, and cognition testing, we report targeted deletion of SIRT3 from select neurons in the cortex and hippocampus produces altered neuronal excitability and metabolic dysfunction in female mice. Targeted deletion of SIRT3 from neuronal helix-loop-helix 1 (NEX)-expressing neurons resulted in mitochondrial hyperacetylation, female-specific superoxide dismutase-2 (SOD2) modification, increased steady-state superoxide levels, metabolic reprogramming, altered neuronal excitability, and working spatial memory deficits. Inducible neuronal deletion of SIRT3 likewise produced female-specific deficits in spatial working memory. Together, the data demonstrate that deletion of SIRT3 from forebrain neurons selectively predisposes female mice to deficits in mitochondrial and cognitive function.SIGNIFICANCE STATEMENT Mitochondrial SIRT3 is an enzyme shown to regulate energy metabolism and antioxidant function, by direct deacetylation of proteins. In this study, we show that neuronal SIRT3 deficiency renders female mice selectively vulnerable to impairment in redox and metabolic function, spatial memory, and neuronal excitability. The observed sex-specific effects on cognition and neuronal excitability in female SIRT3-deficient mice suggest that mitochondrial dysfunction may be one factor underlying comorbid neuronal diseases, such as Alzheimer's disease and epilepsy. Furthermore, the data suggest that SIRT3 dysfunction may predispose females to age-related metabolic and cognitive impairment.
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Affiliation(s)
- Jennifer N Pearson-Smith
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
- Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Ruth Fulton
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Christopher Q Huynh
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Anna G Figueroa
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Gia B Huynh
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Li-Ping Liang
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Lindsey B Gano
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Cole R Michel
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Nichole Reisdorph
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Richard Reisdorph
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Kristofer S Fritz
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Eric Verdin
- Buck Institute for Aging, Novato, California 94945
| | - Manisha Patel
- School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
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75
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Liu LW, Xie Y, Li GQ, Zhang T, Sui YH, Zhao ZJ, Zhang YY, Yang WB, Geng XL, Xue DB, Chen H, Wang YW, Lu TQ, Shang LR, Li ZB, Li L, Sun B. Gut microbiota-derived nicotinamide mononucleotide alleviates acute pancreatitis by activating pancreatic SIRT3 signalling. Br J Pharmacol 2023; 180:647-666. [PMID: 36321732 DOI: 10.1111/bph.15980] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE Gut microbiota dysbiosis induced by acute pancreatitis (AP) exacerbates pancreatic injury and systemic inflammatory responses. The alleviation of gut microbiota dysbiosis through faecal microbiota transplantation (FMT) is considered a potential strategy to reduce tissue damage and inflammation in many clinical disorders. Here, we aim to investigate the effect of gut microbiota and microbiota-derived metabolites on AP and further clarify the mechanisms associated with pancreatic damage and inflammation. EXPERIMENTAL APPROACH AP rat and mouse models were established by administration of caerulein or sodium taurocholate in vivo. Pancreatic acinar cells were exposed to caerulein and lipopolysaccharide in vitro to simulate AP. KEY RESULTS Normobiotic FMT alleviated AP-induced gut microbiota dysbiosis and ameliorated the severity of AP, including mitochondrial dysfunction, oxidative damage and inflammation. Normobiotic FMT induced higher levels of NAD+ (nicotinamide adenine dinucleotide)-associated metabolites, particularly nicotinamide mononucleotide (NMN). NMN administration mitigated AP-mediated mitochondrial dysfunction, oxidative damage and inflammation by increasing pancreatic NAD+ levels. Similarly, overexpression of the NAD+ -dependent mitochondrial deacetylase sirtuin 3 (SIRT3) alleviated the severity of AP. Furthermore, SIRT3 deacetylated peroxiredoxin 5 (PRDX5) and enhanced PRDX5 protein expression, thereby promoting its antioxidant and anti-inflammatory activities in AP. Importantly, normobiotic FMT-mediated NMN metabolism induced SIRT3-PRDX5 pathway activation during AP. CONCLUSION AND IMPLICATIONS Gut microbiota-derived NMN alleviates the severity of AP by activating the SIRT3-PRDX5 pathway. Normobiotic FMT could be served as a potential strategy for AP treatment.
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Affiliation(s)
- Li-Wei Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Yu Xie
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Guan-Qun Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Tao Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Yu-Hang Sui
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Zhong-Jie Zhao
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang-Yang Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wen-Bo Yang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xing-Long Geng
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dong-Bo Xue
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hua Chen
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yong-Wei Wang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tian-Qi Lu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li-Ren Shang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhi-Bo Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Le Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
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76
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Liu Y, Liu X, Dong X, Yin Z, Xie Z, Luo Y. Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571. Microbiol Spectr 2023; 11:e0353922. [PMID: 36475778 PMCID: PMC9927263 DOI: 10.1128/spectrum.03539-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation can quickly modify the physiology of bacteria to respond to changes in environmental or nutritional conditions, but little information on these modifications is available in rhizobia. In this study, we report the lysine acetylome of Azorhizobium caulinodans strain ORS571, a model rhizobium isolated from stem nodules of the tropical legume Sesbania rostrata that is capable of fixing nitrogen in the free-living state and during symbiosis. Antibody enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were used to characterize the acetylome. There are 2,302 acetylation sites from 982 proteins, accounting for 20.8% of the total proteins. Analysis of the acetylated motifs showed the preferences for the amino acid residues around acetylated lysines. The response regulator CheY1, previously characterized to be involved in chemotaxis in strain ORS571, was identified as an acetylated protein, and a mutation of the acetylated site of CheY1 significantly impaired the strain's motility. In addition, a Zn+-dependent deacetylase (AZC_0414) was characterized, and the construction of a deletion mutant strain showed that it played a role in chemotaxis. Our study provides the first global analysis of lysine acetylation in ORS571, suggesting that acetylation plays a role in various physiological processes. In addition, we demonstrate its involvement in the chemotaxis process. The acetylome of ORS571 provides insights to investigate the regulation mechanism of rhizobial physiology. IMPORTANCE Acetylation is an important modification that regulates protein function and has been found to regulate physiological processes in various bacteria. The physiology of rhizobium A. caulinodans ORS571 is regulated by multiple mechanisms both when free living and in symbiosis with the host; however, the regulatory role of acetylation is not yet known. Here, we took an acetylome-wide approach to identify acetylated proteins in A. caulinodans ORS571 and performed clustering analyses. Acetylation of chemotaxis proteins was preliminarily investigated, and the upstream acetylation-regulating enzyme involved in chemotaxis was characterized. These findings provide new insights to explore the physiological mechanisms of rhizobia.
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Affiliation(s)
- Yanan Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaoyan Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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77
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Capone F, Sotomayor-Flores C, Bode D, Wang R, Rodolico D, Strocchi S, Schiattarella GG. Cardiac metabolism in HFpEF: from fuel to signalling. Cardiovasc Res 2023; 118:3556-3575. [PMID: 36504368 DOI: 10.1093/cvr/cvac166] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
Heart failure (HF) is marked by distinctive changes in myocardial uptake and utilization of energy substrates. Among the different types of HF, HF with preserved ejection fraction (HFpEF) is a highly prevalent, complex, and heterogeneous condition for which metabolic derangements seem to dictate disease progression. Changes in intermediate metabolism in cardiometabolic HFpEF-among the most prevalent forms of HFpEF-have a large impact both on energy provision and on a number of signalling pathways in the heart. This dual, metabolic vs. signalling, role is played in particular by long-chain fatty acids (LCFAs) and short-chain carbon sources [namely, short-chain fatty acids (SCFAs) and ketone bodies (KBs)]. LCFAs are key fuels for the heart, but their excess can be harmful, as in the case of toxic accumulation of lipid by-products (i.e. lipotoxicity). SCFAs and KBs have been proposed as a potential major, alternative source of energy in HFpEF. At the same time, both LCFAs and short-chain carbon sources are substrate for protein post-translational modifications and other forms of direct and indirect signalling of pivotal importance in HFpEF pathogenesis. An in-depth molecular understanding of the biological functions of energy substrates and their signalling role will be instrumental in the development of novel therapeutic approaches to HFpEF. Here, we summarize the current evidence on changes in energy metabolism in HFpEF, discuss the signalling role of intermediate metabolites through, at least in part, their fate as substrates for post-translational modifications, and highlight clinical and translational challenges around metabolic therapy in HFpEF.
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Affiliation(s)
- Federico Capone
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Division of Internal Medicine, Department of Medicine, University of Padua, Padua, Italy
| | - Cristian Sotomayor-Flores
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - David Bode
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Rongling Wang
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Daniele Rodolico
- Department of Cardiovascular and Pulmonary Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Stefano Strocchi
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Gabriele G Schiattarella
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Division of Cardiology, Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
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78
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Wang X, Huang Y, Zhang K, Chen F, Nie T, Zhao Y, He F, Ni J. Changes of energy metabolism in failing heart and its regulation by SIRT3. Heart Fail Rev 2023:10.1007/s10741-023-10295-5. [PMID: 36708431 DOI: 10.1007/s10741-023-10295-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
Heart failure (HF) is the leading cause of hospitalization in elderly patients and a disease with extremely high morbidity and mortality rate worldwide. Although there are some existing treatment methods for heart failure, due to its complex pathogenesis and often accompanied by various comorbidities, there is still a lack of specific drugs to treat HF. The mortality rate of patients with HF is still high, highlighting an urgent need to elucidate the pathophysiological mechanisms of HF and seek new therapeutic approaches. The heart is an organ with a very high metabolic intensity, mainly using fatty acids, glucose, ketone bodies, and branched-chain amino acids as energy substrates to supply energy for the heart. Loss of metabolic flexibility and metabolic remodeling occurs with HF. Sirtuin3 (SIRT3) is a member of the NAD+-dependent Sirtuin family located in mitochondria, and can participate in mitochondrial physiological functions through the deacetylation of metabolic and respiratory enzymes in mitochondria. As the center of energy metabolism, mitochondria are involved in many physiological processes. Maintaining stable metabolic and physiological functions of the heart depends on normal mitochondrial function. The damage or loss of SIRT3 can lead to various cardiovascular diseases. Therefore, we summarize the recent progress of SIRT3 in cardiac mitochondrial protection and metabolic remodeling.
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Affiliation(s)
- Xiao Wang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Yuting Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, 341000, China
| | - Kai Zhang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Feng Chen
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Tong Nie
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Yun Zhao
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Feng He
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, 438000, China.
| | - Jingyu Ni
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
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79
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Beyond metabolic waste: lysine lactylation and its potential roles in cancer progression and cell fate determination. Cell Oncol (Dordr) 2023; 46:465-480. [PMID: 36656507 DOI: 10.1007/s13402-023-00775-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/21/2022] [Accepted: 11/26/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Lactate is an important metabolite derived from glycolysis under physiological and pathological conditions. The Warburg effect reveals the vital role of lactate in cancer progression. Numerous studies have reported crucial roles for lactate in cancer progression and cell fate determination. Lactylation, a novel posttranslational modification (PTM), has provided a new opportunity to investigate metabolic epigenetic regulation, and studies of this process have been initiated in a wide range of cancer cells, cancer-associated immune cells, and embryonic stem cells. CONCLUSION Lactylation is a novel and interesting mechanism of lactate metabolism linked to metabolic rewiring and epigenetic remodeling. It is a potential and hopeful target for cancer therapy. Here, we summarize the discovery of lactylation, the mechanisms of site modification, and progress in research on nonhistone lactylation. We focus on the potential roles of lactylation in cancer progression and cell fate determination and the possible therapeutic strategies for targeting lysine lactylation. Finally, we suggest some future research topics on lactylation to inspire some interesting ideas.
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80
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Kabir F, Atkinson R, Cook AL, Phipps AJ, King AE. The role of altered protein acetylation in neurodegenerative disease. Front Aging Neurosci 2023; 14:1025473. [PMID: 36688174 PMCID: PMC9845957 DOI: 10.3389/fnagi.2022.1025473] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
Acetylation is a key post-translational modification (PTM) involved in the regulation of both histone and non-histone proteins. It controls cellular processes such as DNA transcription, RNA modifications, proteostasis, aging, autophagy, regulation of cytoskeletal structures, and metabolism. Acetylation is essential to maintain neuronal plasticity and therefore essential for memory and learning. Homeostasis of acetylation is maintained through the activities of histone acetyltransferases (HAT) and histone deacetylase (HDAC) enzymes, with alterations to these tightly regulated processes reported in several neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Both hyperacetylation and hypoacetylation can impair neuronal physiological homeostasis and increase the accumulation of pathophysiological proteins such as tau, α-synuclein, and Huntingtin protein implicated in AD, PD, and HD, respectively. Additionally, dysregulation of acetylation is linked to impaired axonal transport, a key pathological mechanism in ALS. This review article will discuss the physiological roles of protein acetylation and examine the current literature that describes altered protein acetylation in neurodegenerative disorders.
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81
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Giai Gianetto Q. Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells. Methods Mol Biol 2023; 2426:267-302. [PMID: 36308693 DOI: 10.1007/978-1-0716-1967-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein post-translational modifications (PTMs) are essential elements of cellular communication. Their variations in abundance can affect cellular pathways, leading to cellular disorders and diseases. A widely used method for revealing PTM-mediated regulatory networks is their label-free quantitation (LFQ) by high-resolution mass spectrometry. The raw data resulting from such experiments are generally interpreted using specific software, such as MaxQuant, MassChroQ, or Proline for instance. They provide data matrices containing quantified intensities for each modified peptide identified. Statistical analyses are then necessary (1) to ensure that the quantified data are of good enough quality and sufficiently reproducible, (2) to highlight the modified peptides that are differentially abundant between the biological conditions under study. The objective of this chapter is therefore to provide a complete data analysis pipeline for analyzing the quantified values of modified peptides in presence of two or more biological conditions using the R software. We illustrate our pipeline starting from MaxQuant outputs dealing with the analysis of A549-ACE2 cells infected by SARS-CoV-2 at different time stamps, freely available on PRIDE (PXD020019).
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Affiliation(s)
- Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France.
- Institut Pasteur, Université Paris Cité, Proteomic Platform, Mass Spectrometry for Biology Unit, CNRS, UAR 2024, Paris, France.
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82
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Acetylation of the nuclear localization signal in Ku70 diminishes the interaction with importin-α. Biochem Biophys Rep 2022; 33:101418. [PMID: 36620088 PMCID: PMC9811216 DOI: 10.1016/j.bbrep.2022.101418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins are functionally regulated by various types of posttranslational modifications (PTMs). Ku, a heterodimer complex of Ku70 and Ku80 subunits, participates in DNA repair processes. Ku is distributed not only in the nucleus but also in the cytoplasm, suggesting that the function of Ku is regulated by its subcellular localization. Although Ku70 undergoes PTMs including phosphorylation or acetylation, it remains unknown whether the PTMs of Ku70 affect the subcellular localization of Ku. Using a cell-free pull-down assay technique, we show that Nε-acetylation of lysine residues in the synthetic peptide matched to Ku70's nuclear localization signal (NLS) reduces the peptide's interaction with the nuclear transport factor importin-α. The reduced interaction by acetylation was supported by molecular simulation analysis. In addition, when expressed in the endogenous Ku80-defective Chinese hamster ovary xrs-6 cells, some full-size human Ku70 mutants with substitutions of glutamine, a possible structural mimetic of Nε-acetyl-lysine, for lysine at the specific NLS positions exhibited no nuclear distribution. These findings imply that acetylation of particular lysine residues in the Ku70 NLS regulates nuclear localization of Ku.
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83
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Post-Translational Modifications in Tumor-Associated Antigens as a Platform for Novel Immuno-Oncology Therapies. Cancers (Basel) 2022; 15:cancers15010138. [PMID: 36612133 PMCID: PMC9817968 DOI: 10.3390/cancers15010138] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Post-translational modifications (PTMs) are generated by adding small chemical groups to amino acid residues after the translation of proteins. Many PTMs have been reported to correlate with tumor progression, growth, and survival by modifying the normal functions of the protein in tumor cells. PTMs can also elicit humoral and cellular immune responses, making them attractive targets for cancer immunotherapy. This review will discuss how the acetylation, citrullination, and phosphorylation of proteins expressed by tumor cells render the corresponding tumor-associated antigen more antigenic and affect the immune response in multiple cancers. In addition, the role of glycosylated protein mucins in anti-cancer immunotherapy will be considered. Mucin peptides in combination with stimulating adjuvants have, in fact, been utilized to produce anti-tumor antibodies and vaccines. Finally, we will also outline the results of the clinical trial exploiting glycosylated-MUC1 as a vaccine in different cancers. Overall, PTMs in TAAs could be considered in future therapies to result in lasting anti-tumor responses.
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84
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Abstract
Antibiotic resistance is increasingly becoming a challenge to public health. The regulation of bacterial metabolism by post-translational modifications (PTMs) has been widely studied. However, the mechanism underlying the regulation of acetylation in bacterial resistance to antibiotics is still unknown. Here, we performed a quantitative analysis of the acetylated proteome of a wild-type (WT) Escherichia coli (E. coli) sensitive strain and ampicillin- (Re-Amp), kanamycin- (Re-Kan), and polymyxin B-resistant (Re-Pol) strains. Based on bioinformatics analysis combined with biochemical validations, we found a common regulatory mechanism between the different resistant strains. Our results showed that protein acetylation negatively regulates bacterial metabolism to regulate antibiotic resistance and positively regulates bacterial motility. Further analyses revealed that key enzymes in various metabolic pathways were differentially acetylated. In particular, pyruvate kinase (PykF), a glycolytic enzyme that regulates bacterial metabolism, and its acetylated form were highly expressed in the three resistant strains and were identified as reversibly acetylated by the deacetylase CobB and the acetyl-transferase PatZ (peptidyl-lysine N-acetyltransferase). Results showed that PykF also could be acetylated by nonenzymatic acetyl phosphatase (AcP) in vitro. Furthermore, the deacetylation of Lys413 in PykF increased PykF enzymatic activity by changing the conformation of its ATP binding site, resulting in an increase in energy production which, in turn, increased the sensitivity of drug-resistant strains to antibiotics. This study provides novel insights for understanding bacterial resistance and lays the foundation for future research on the regulation of acetylation in antibiotic-resistant strains. IMPORTANCE The misuse of antibiotics has resulted in the emergence of many antibiotic-resistant strains which seriously threaten human health. Protein post-translational modifications, especially acetylation, tightly control bacterial metabolism. However, the comprehensive mechanism underlying the regulation of acetylation in bacterial resistance remains unexplored. Here, acetylation was found to positively regulate bacterial motility and negatively regulate energy metabolism, which was common in all antibiotic-resistant strains. Moreover, the acetylation and deacetylation process of PykF was uncovered, and deacetylation of the Lys 413 in PykF was found to contribute to bacterial sensitivity to antibiotics. This study provides a new direction for research on the development of bacterial resistance through post-translational modifications and a theoretical basis for developing antibacterial drugs.
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85
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Christopher JA, Galbada Liyanage SA, Nicholson EM, Kinney WD, Cropp TA. Genetic encoding of isobutyryl-, isovaleryl-, and β-hydroxybutryl-lysine in E. coli. RSC Adv 2022; 12:34142-34144. [PMID: 36545614 PMCID: PMC9706372 DOI: 10.1039/d2ra04898a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/19/2022] [Indexed: 11/30/2022] Open
Abstract
Here we report the synthesis and genetic encoding of the lysine post translational modifications, β-hydroxybutyryl-lysine, isobutyryl-lysine and isovaleryl-lysine. The ability to obtain a homogenous protein samples with site-specific incorporation of these acylated lysine residues can serve as a powerful tool to study the biological role of lysine post translational modifications.
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Affiliation(s)
| | | | - Eve M. Nicholson
- Department of Chemistry, Virginia Commonwealth UniversityRichmondVA 23284USA
| | - William D. Kinney
- Department of Chemistry, Virginia Commonwealth UniversityRichmondVA 23284USA
| | - T. Ashton Cropp
- Department of Chemistry, Virginia Commonwealth UniversityRichmondVA 23284USA
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86
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Ahmed S, Rahman A, Hasan MAM, Rahman J, Islam MKB, Ahmad S. predML-Site: Predicting Multiple Lysine PTM Sites With Optimal Feature Representation and Data Imbalance Minimization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3624-3634. [PMID: 34546927 DOI: 10.1109/tcbb.2021.3114349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Identifying of post-translational modifications (PTM) is crucial in the study of computational proteomics, cell biology, pathogenesis, and drug development due to its role in many bio-molecular mechanisms. Computational methods for predicting multiple PTM at the same lysine residues, often referred to as K-PTM, is still evolving. This paper presents a novel computational tool, abbreviated as predML-Site, for predicting KPTM, such as acetylation, crotonylation, methylation, succinylation from an uncategorized peptide sample involving single, multiple, or no modification. For informative feature representation, multiple sequence encoding schemes, such as the sequence-coupling, binary encoding, k-spaced amino acid pairs, amino acid factor have been used with ANOVA and incremental feature selection. As a core predictor, a cost-sensitive SVM classifier has been adopted which effectively mitigates the effect of class-label imbalance in the dataset. predML-Site predicts multi-label PTM sites with 84.18% accuracy using the top 91 features. It has also achieved 85.34% aiming and 86.58% coverage rate which are much better than the existing state-of-the-art predictors on the same rigorous validation test. This performance indicates that predML-Site can be used as a supportive tool for further K-PTM study. For the convenience of the experimental scientists, predML-Site has been deployed as a user-friendly web-server at http://103.99.176.239/predML-Site.
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87
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Qian P, Ma F, Zhang W, Cao D, Li L, Liu Z, Pei P, Zhang T, Wang S, Wu J. Chronic exercise remodels the lysine acetylome in the mouse hippocampus. Front Mol Neurosci 2022; 15:1023482. [PMID: 36385767 PMCID: PMC9650339 DOI: 10.3389/fnmol.2022.1023482] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022] Open
Abstract
Physical exercise benefits hippocampal function through various molecular mechanisms. Protein acetylation, a conserved and widespread post-translational modification, is involved in the synaptic plasticity and memory. However, whether exercise can change global acetylation and the role of acetylated proteins in the hippocampus have remained largely unknown. Herein, using healthy adult mice running for 6 weeks as exercise model and sedentary mice as control, we analyzed the hippocampal lysine acetylome and proteome by Liquid chromatography-tandem mass spectrometry. As a result, we profiled the lysine acetylation landscape for the hippocampus and identified 3,876 acetyl sites and 1,764 acetylated proteins. A total of 272 acetyl sites on 252 proteins were differentially regulated by chronic exercise, among which 18.58% acetylated proteins were annotated in mitochondria. These proteins were dominantly deacetylated and mainly associated with carbon-related metabolism, the Hippo signaling pathway, ribosomes, and protein processing. Meanwhile, 21 proteins were significantly expressed and enriched in the pathway of complement and coagulation cascades. Our findings provide a new avenue for understanding the molecular mechanisms underlying the benefits of exercise for hippocampal function and can contribute to the promotion of public health.
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Affiliation(s)
- Ping Qian
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Feifei Ma
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Wanyu Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Dingding Cao
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Luya Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Zhuo Liu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
- *Correspondence: Shan Wang,
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
- Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Jianxin Wu,
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88
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Dang F, Wei W. Targeting the acetylation signaling pathway in cancer therapy. Semin Cancer Biol 2022; 85:209-218. [PMID: 33705871 PMCID: PMC8423867 DOI: 10.1016/j.semcancer.2021.03.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Acetylation represents one of the major post-translational protein modifications, which introduces an acetyl functional group into amino acids such as the lysine residue to yield an acetate ester bond, neutralizing its positive charge. Regulation of protein functions by acetylation occurs in multiple ways, such as affecting protein stability, activity, localization, and interaction with other proteins or DNA. It has been well documented that the recruitment of histone acetyltransferases (HATs) and histone deacetylases (HDACs) to the transcriptional machinery can modulate histone acetylation status, which is directly involved in the dynamic regulation of genes controlling cell proliferation and division. Dysregulation of gene expression is involved in tumorigenesis and aberrant activation of histone deacetylases has been reported in several types of cancer. Moreover, there is growing body of evidence showing that acetylation is widely involved in non-histone proteins to impact their roles in various cellular processes including tumorigenesis. As such, small molecular compounds inhibiting HAT or HDAC enzymatic activities have been developed and investigated for therapeutic purpose. Here we review the recent progress in our understanding of protein acetylation and discuss the therapeutic potential of targeting the acetylation signaling pathway in cancer.
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Affiliation(s)
- Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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89
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [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: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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90
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Yu K, Wang Y, Zheng Y, Liu Z, Zhang Q, Wang S, Zhao Q, Zhang X, Li X, Xu RH, Liu ZX. qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. Nucleic Acids Res 2022; 51:D479-D487. [PMID: 36165955 PMCID: PMC9825568 DOI: 10.1093/nar/gkac820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 01/29/2023] Open
Abstract
Post-translational modifications (PTMs) are critical molecular mechanisms that regulate protein functions temporally and spatially in various organisms. Since most PTMs are dynamically regulated, quantifying PTM events under different states is crucial for understanding biological processes and diseases. With the rapid development of high-throughput proteomics technologies, massive quantitative PTM proteome datasets have been generated. Thus, a comprehensive one-stop data resource for surfing big data will benefit the community. Here, we updated our previous phosphorylation dynamics database qPhos to the qPTM (http://qptm.omicsbio.info). In qPTM, 11 482 553 quantification events among six types of PTMs, including phosphorylation, acetylation, glycosylation, methylation, SUMOylation and ubiquitylation in four different organisms were collected and integrated, and the matched proteome datasets were included if available. The raw mass spectrometry based false discovery rate control and the recurrences of identifications among datasets were integrated into a scoring system to assess the reliability of the PTM sites. Browse and search functions were improved to facilitate users in swiftly and accurately acquiring specific information. The results page was revised with more abundant annotations, and time-course dynamics data were visualized in trend lines. We expected the qPTM database to be a much more powerful and comprehensive data repository for the PTM research community.
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Affiliation(s)
| | | | | | | | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Siyu Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaolong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaoxing Li
- Precision Medicine Institute, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui-Hua Xu
- Correspondence may also be addressed to Rui-Hua Xu. Tel: +86 20 8734 3228; Fax: +86 20 8734 3392;
| | - Ze-Xian Liu
- To whom correspondence should be addressed. Tel: +86 20 8734 2025; Fax: +86 20 8734 2522;
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91
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Ng JWX, Chua SK, Mutwil M. Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:944992. [PMID: 36212273 PMCID: PMC9539877 DOI: 10.3389/fpls.2022.944992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522 Arabidopsis thaliana genes and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools.
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92
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Li X, Ren Z, Huang X, Yu T. LACTB, a Metabolic Therapeutic Target in Clinical Cancer Application. Cells 2022; 11:cells11172749. [PMID: 36078157 PMCID: PMC9454609 DOI: 10.3390/cells11172749] [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: 08/04/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Serine beta-lactamase-like protein (LACTB) is the only mammalian mitochondrial homolog evolved from penicillin-binding proteins and β-lactamases (PBP-βLs) in bacteria. LACTB, an active-site serine protease, polymerizes into stable filaments, which are localized to the intermembrane space (IMS) of mitochondrion and involved in the submitochondrial organization, modulating mitochondrial lipid metabolism. Cancer pathogenesis and progression are relevant to the alterations in mitochondrial metabolism. Metabolic reprogramming contributes to cancer cell behavior. This article (1) evidences the clinical implications of LACTB on neoplastic cell proliferation and migration and tumor growth and metastasis as well as LACTB’s involvement in chemotherapeutic and immunotherapeutic responses; (2) sketches the structural basis for LACTB activity and function; and (3) highlights the relevant regulatory mechanisms to LACTB. The abnormal expression of LACTB has been associated with clinicopathological features of cancer tissues and outcomes of anticancer therapies. With the current pioneer researches on the tumor-suppressed function, structural basis, and regulatory mechanism of LACTB, the perspective hints at a great appeal of enzymic property, polymerization, mutation, and epigenetic and post-translational modifications in investigating LACTB’s role in cancer pathogenesis. This perspective provides novel insights for LACTB as a metabolic regulator with potential to develop targeted cancer therapies or neoadjuvant therapeutic interventions.
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Affiliation(s)
- Xiaohua Li
- School of Basic Medical Sciences, Qingdao University, Qingdao 266071, China or
| | - Zhongkai Ren
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao 266000, China or
| | - Xiaohong Huang
- Shandong Institute of Traumatic Orthopedics, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao 266590, China
- Correspondence: (X.H.); (T.Y.)
| | - Tengbo Yu
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao 266000, China or
- Institute of Sports Medicine and Rehabilitation, Qingdao University, Qingdao 266071, China
- Correspondence: (X.H.); (T.Y.)
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93
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Bouthillette LM, Aniebok V, Colosimo DA, Brumley D, MacMillan JB. Nonenzymatic Reactions in Natural Product Formation. Chem Rev 2022; 122:14815-14841. [PMID: 36006409 DOI: 10.1021/acs.chemrev.2c00306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosynthetic mechanisms of natural products primarily depend on systems of protein catalysts. However, within the field of biosynthesis, there are cases in which the inherent chemical reactivity of metabolic intermediates and substrates evades the involvement of enzymes. These reactions are difficult to characterize based on their reactivity and occlusion within the milieu of the cellular environment. As we continue to build a strong foundation for how microbes and higher organisms produce natural products, therein lies a need for understanding how protein independent or nonenzymatic biosynthetic steps can occur. We have classified such reactions into four categories: intramolecular, multicomponent, tailoring, and light-induced reactions. Intramolecular reactions is one of the most well studied in the context of biomimetic synthesis, consisting of cyclizations and cycloadditions due to the innate reactivity of the intermediates. There are two subclasses that make up multicomponent reactions, one being homologous multicomponent reactions which results in dimeric and pseudodimeric natural products, and the other being heterologous multicomponent reactions, where two or more precursors from independent biosynthetic pathways undergo a variety of reactions to produce the mature natural product. The third type of reaction discussed are tailoring reactions, where postmodifications occur on the natural products after the biosynthetic machinery is completed. The last category consists of light-induced reactions involving ecologically relevant UV light rather than high intensity UV irradiation that is traditionally used in synthetic chemistry. This review will cover recent nonenzymatic biosynthetic mechanisms and include sources for those reviewed previously.
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Affiliation(s)
- Leah M Bouthillette
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Victor Aniebok
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Dominic A Colosimo
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
| | - David Brumley
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
| | - John B MacMillan
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
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94
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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95
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Zhang N, Zhang L, Li L, Geng J, Zhao L, Ren Y, Dong Z, Chen F. Global Profiling of 2-hydroxyisobutyrylome in Common Wheat. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:688-701. [PMID: 33581340 PMCID: PMC9880814 DOI: 10.1016/j.gpb.2020.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/17/2020] [Accepted: 08/15/2020] [Indexed: 01/31/2023]
Abstract
As a novel post-translational modification (PTM), lysine 2-hydroxyisobutyrylation (Khib) is considered to regulate gene transcriptional activities in eukaryotic cells; however, the functions of Khib-modified proteins in plants remain unknown. Here, we report that Khib is an evolutionarily-conserved PTM in wheat and its progenitors. A total of 3348 Khib sites on 1074 proteins are identified in common wheat (Triticum aestivum L.) by using affinity purification and mass spectroscopy of 2-hydroxyisobutyrylome. Bioinformatic data indicate that Khib-modified proteins participate in a wide variety of biological and metabolic pathways. Immunoprecipitation confirms that Khib-modified proteins are present endogenously. A comparison of Khib and other main PTMs shows that Khib-modified proteins are simultaneously modified by multiple PTMs. Using mutagenesis experiments and co-immunoprecipitation assays, we demonstrate that Khib on K206 of phosphoglycerate kinase (PGK) is a key regulatory modification for its enzymatic activity, and mutation on K206 affects the interactions of PGK with its substrates. Furthermore, Khib modification of low-molecular-weight proteins is a response to the deacetylase inhibitors nicotinamide and trichostatin. This study provides evidence to promote our current understanding of Khib in wheat plants, including the cooperation between Khib and its metabolic regulation.
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Affiliation(s)
- Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Lingran Zhang
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Linjie Li
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Junyou Geng
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongdong Dong
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou 450046, China.
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96
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Dubois-Deruy E, El Masri Y, Turkieh A, Amouyel P, Pinet F, Annicotte JS. Cardiac Acetylation in Metabolic Diseases. Biomedicines 2022; 10:biomedicines10081834. [PMID: 36009379 PMCID: PMC9405459 DOI: 10.3390/biomedicines10081834] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Lysine acetylation is a highly conserved mechanism that affects several biological processes such as cell growth, metabolism, enzymatic activity, subcellular localization of proteins, gene transcription or chromatin structure. This post-translational modification, mainly regulated by lysine acetyltransferase (KAT) and lysine deacetylase (KDAC) enzymes, can occur on histone or non-histone proteins. Several studies have demonstrated that dysregulated acetylation is involved in cardiac dysfunction, associated with metabolic disorder or heart failure. Since the prevalence of obesity, type 2 diabetes or heart failure rises and represents a major cause of cardiovascular morbidity and mortality worldwide, cardiac acetylation may constitute a crucial pathway that could contribute to disease development. In this review, we summarize the mechanisms involved in the regulation of cardiac acetylation and its roles in physiological conditions. In addition, we highlight the effects of cardiac acetylation in physiopathology, with a focus on obesity, type 2 diabetes and heart failure. This review sheds light on the major role of acetylation in cardiovascular diseases and emphasizes KATs and KDACs as potential therapeutic targets for heart failure.
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97
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DeepDA-Ace: A Novel Domain Adaptation Method for Species-Specific Acetylation Site Prediction. MATHEMATICS 2022. [DOI: 10.3390/math10142364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein lysine acetylation is an important type of post-translational modification (PTM), and it plays a crucial role in various cellular processes. Recently, although many researchers have focused on developing tools for acetylation site prediction based on computational methods, most of these tools are based on traditional machine learning algorithms for acetylation site prediction without species specificity, still maintained as a single prediction model. Recent studies have shown that the acetylation sites of distinct species have evident location-specific differences; however, there is currently no integrated prediction model that can effectively predict acetylation sites cross all species. Therefore, to enhance the scope of species-specific level, it is necessary to establish a framework for species-specific acetylation site prediction. In this work, we propose a domain adaptation framework DeepDA-Ace for species-specific acetylation site prediction, including Rattus norvegicus, Schistosoma japonicum, Arabidopsis thaliana, and other types of species. In DeepDA-Ace, an attention based densely connected convolutional neural network is designed to capture sequence features, and the semantic adversarial learning strategy is proposed to align features of different species so as to achieve knowledge transfer. The DeepDA-Ace outperformed both the general prediction model and fine-tuning based species-specific model across most types of species. The experiment results have demonstrated that DeepDA-Ace is superior to the general and fine-tuning methods, and its precision exceeds 0.75 on most species. In addition, our method achieves at least 5% improvement over the existing acetylation prediction tools.
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98
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Song J, Han Z, Zheng YG. Identification and Profiling of Histone Acetyltransferase Substrates by Bioorthogonal Labeling. Curr Protoc 2022; 2:e497. [PMID: 35849593 DOI: 10.1002/cpz1.497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferases (HATs, also known as lysine acetyltransferases, KATs) catalyze acetylation of their cognate protein substrates using acetyl-CoA (Ac-CoA) as a cofactor and are involved in various physiological and pathological processes. Advances in mass spectrometry-based proteomics have allowed the discovery of thousands of acetylated proteins and the specific acetylated lysine sites. However, due to the rapid dynamics and functional redundancy of HAT activities, and the limitation of using antibodies to capture acetylated lysines, it is challenging to systematically and precisely define both the substrates and sites directly acetylated by a given HAT. Here, we describe a chemoproteomic approach to identify and profile protein substrates of individual HAT enzymes on the proteomic scale. The approach involves protein engineering to enlarge the Ac-CoA binding pocket of the HAT of interest, such that a mutant form is generated that can use functionalized acyl-CoAs as a cofactor surrogate to bioorthogonally label its protein substrates. The acylated protein substrates can then be chemoselectively conjugated either with a fluorescent probe (for imaging detection) or with a biotin handle (for streptavidin pulldown and chemoproteomic identification). This modular chemical biology approach has been successfully implemented to identify protein substrates of p300, GCN5, and HAT1, and it is expected that this method can be applied to profile and identify the sub-acetylomes of many other HAT enzymes. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling HAT protein substrates with azide/alkyne-biotin Alternate Protocol: Labeling protein substrates of HATs with azide/alkyne-TAMRA for in-gel visualization Support Protocol 1: Expression and purification of HAT mutants Support Protocol 2: Synthesis of Ac-CoA surrogates Basic Protocol 2: Streptavidin enrichment of biotinylated HAT substrates Basic Protocol 3: Chemoproteomic identification of HAT substrates Basic Protocol 4: Validation of specific HAT substrates with western blotting.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
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99
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Zhao Q, Zhou J, Li F, Guo S, Zhang L, Li J, Qi Q, Shi Y. The Role and Therapeutic Perspectives of Sirtuin 3 in Cancer Metabolism Reprogramming, Metastasis, and Chemoresistance. Front Oncol 2022; 12:910963. [PMID: 35832551 PMCID: PMC9272524 DOI: 10.3389/fonc.2022.910963] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Sirtuin 3 (SIRT3), the nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, acts as a metabolic modulator mainly located in mitochondria via regulating the process of the relevant biochemical processes by targeting crucial mediators. Recently, owing to its dual role in cancer, SIRT3 has attracted extensive attention. Cancer cells have different metabolic patterns from normal cells, and SIRT3-mediated metabolism reprogramming could be critical in the cancer context, which is closely related to the mechanism of metabolism reprogramming, metastasis, and chemoresistance in tumor cells. Therefore, it is crucial to elucidate the relevant pathological mechanisms and take appropriate countermeasures for the progression of clinical strategies to inhibit the development of cancer. In this review, existing available data on the regulation of cancer metabolism reprogramming, metastasis, and chemoresistance progression of SIRT3 are detailed, as well as the status quo of SIRT3 small molecule modulators is updated in the application of cancer therapy, aiming to highlight strategies directly targeting SIRT3-mediated tumor-suppressing and tumor-promoting, and provide new approaches for therapy application. Furthermore, we offer an effective evidence-based basis for the evolvement of potential personalized therapy management strategies for SIRT3 in cancer settings.
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Affiliation(s)
- QingYi Zhao
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Zhou
- Department of Acupuncture and Moxibustion, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feng Li
- Department of Acupuncture and Moxibustion, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sen Guo
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liang Zhang
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Li
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qin Qi
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Outpatient Department, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, China
- *Correspondence: Qin Qi, ; Yin Shi,
| | - Yin Shi
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Outpatient Department, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, China
- *Correspondence: Qin Qi, ; Yin Shi,
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100
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Brunetta HS, Petrick HL, Momken I, Handy RM, Pignanelli C, Nunes EA, Piquereau J, Mericskay M, Holloway GP. Nitrate consumption preserves HFD-induced skeletal muscle mitochondrial ADP sensitivity and lysine acetylation: A potential role for SIRT1. Redox Biol 2022; 52:102307. [PMID: 35398714 PMCID: PMC9006675 DOI: 10.1016/j.redox.2022.102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Dietary nitrate supplementation, and the subsequent serial reduction to nitric oxide, has been shown to improve glucose homeostasis in several pre-clinical models of obesity and insulin resistance. While the mechanisms remain poorly defined, the beneficial effects of nitrate appear to be partially dependent on AMPK-mediated signaling events, a central regulator of metabolism and mitochondrial bioenergetics. Since AMPK can activate SIRT1, we aimed to determine if nitrate supplementation (4 mM sodium nitrate via drinking water) improved skeletal muscle mitochondrial bioenergetics and acetylation status in mice fed a high-fat diet (HFD: 60% fat). Consumption of HFD induced whole-body glucose intolerance, and within muscle attenuated insulin-induced Akt phosphorylation, mitochondrial ADP sensitivity (higher apparent Km), submaximal ADP-supported respiration, mitochondrial hydrogen peroxide (mtH2O2) production in the presence of ADP and increased cellular protein carbonylation alongside mitochondrial-specific acetylation. Consumption of nitrate partially preserved glucose tolerance and, within skeletal muscle, normalized insulin-induced Akt phosphorylation, mitochondrial ADP sensitivity, mtH2O2, protein carbonylation and global mitochondrial acetylation status. Nitrate also prevented the HFD-mediated reduction in SIRT1 protein, and interestingly, the positive effects of nitrate ingestion on glucose homeostasis and mitochondrial acetylation levels were abolished in SIRT1 inducible knock-out mice, suggesting SIRT1 is required for the beneficial effects of dietary nitrate. Altogether, dietary nitrate preserves mitochondrial ADP sensitivity and global lysine acetylation in HFD-fed mice, while in the absence of SIRT1, the effects of nitrate on glucose tolerance and mitochondrial acetylation were abrogated.
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