551
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Yi X, Guo W, Shi Q, Yang Y, Zhang W, Chen X, Kang P, Chen J, Cui T, Ma J, Wang H, Guo S, Chang Y, Liu L, Jian Z, Wang L, Xiao Q, Li S, Gao T, Li C. SIRT3-Dependent Mitochondrial Dynamics Remodeling Contributes to Oxidative Stress-Induced Melanocyte Degeneration in Vitiligo. Am J Cancer Res 2019; 9:1614-1633. [PMID: 31037127 PMCID: PMC6485185 DOI: 10.7150/thno.30398] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysregulation has been implicated in oxidative stress-induced melanocyte destruction in vitiligo. However, the molecular mechanism underlying this process is merely investigated. Given the prominent role of nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase Sirtuin3 (SIRT3) in sustaining mitochondrial dynamics and homeostasis and that SIRT3 expression and activity can be influenced by oxidative stress-related signaling, we wondered whether SIRT3 could play an important role in vitiligo melanocyte degeneration by regulating mitochondrial dynamics. Methods: We initially testified SIRT3 expression and activity in normal and vitiligo melanocytes via PCR, immunoblotting and immunofluorescence assays. Then, cell apoptosis, mitochondrial function and mitochondrial dynamics after SIRT3 intervention were analyzed by flow cytometry, immunoblotting, confocal laser microscopy, transmission electron microscopy and oxphos activity assays. Chromatin immunoprecipitation (ChIP), co-immunoprecipitation (Co-IP), immunoblotting and immunofluorescence assays were performed to clarify the upstream regulatory mechanism of SIRT3. Finally, the effect of honokiol on protecting melanocytes and the underlying mechanism were investigated via flow cytometry and immunoblotting analysis. Results: We first found that the expression and the activity of SIRT3 were significantly impaired in vitiligo melanocytes both in vitro and in vivo. Then, SIRT3 deficiency led to more melanocyte apoptosis by inducing severe mitochondrial dysfunction and cytochrome c release to cytoplasm, with Optic atrophy 1 (OPA1)-mediated mitochondrial dynamics remodeling involved in. Moreover, potentiated carbonylation and dampened peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) activation accounted for SIRT3 dysregulation in vitiligo melanocytes. Finally, we proved that honokiol could prevent melanocyte apoptosis under oxidative stress by activating SIRT3-OPA1 axis. Conclusions: Overall, we demonstrate that SIRT3-dependent mitochondrial dynamics remodeling contributes to oxidative stress-induced melanocyte degeneration in vitiligo, and honokiol is promising in preventing oxidative stress-induced vitiligo melanocyte apoptosis.
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552
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Chu GC, Pan M, Li J, Liu S, Zuo C, Tong ZB, Bai JS, Gong Q, Ai H, Fan J, Meng X, Huang YC, Shi J, Deng H, Tian C, Li YM, Liu L. Cysteine-Aminoethylation-Assisted Chemical Ubiquitination of Recombinant Histones. J Am Chem Soc 2019; 141:3654-3663. [PMID: 30758956 DOI: 10.1021/jacs.8b13213] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes through tightly regulated dynamic reversible processes. The efficient preparation of ubiquitinated histones and their analogs is important for biochemical and biophysical studies on histone ubiquitination. Here, we report the CAACU (cysteine-aminoethylation assisted chemical ubiquitination) strategy for the efficient synthesis of ubiquitinated histone analogs. The key step in the CAACU strategy is the installation of an N-alkylated 2-bromoethylamine derivative into a recombinant histone through cysteine aminoethylation, followed by native chemical ligation assisted by Seitz's auxiliary to produce mono- and diubiquitin (Ub) and small ubiquitin-like modifier (SUMO) modified histone analogs. This approach enables the rapid production of modified histones from recombinant proteins at about 1.5-6 mg/L expression. The thioether-containing isopeptide bonds in the products are chemically stable and bear only one atomic substitution in the structure, compared to their native counterparts. The ubiquitinated histone analogs prepared by CAACU can be readily reconstituted into nucleosomes and selectively recognized by relevant interacting proteins. The thioether-containing isopeptide bonds can also be recognized and hydrolyzed by deubiquitinases (DUBs). Cryo-electron microscopy (cryo-EM) of the nucleosome containing H2BKC34Ub indicated that the obtained CAACU histones were of good quality for structural studies. Collectively, this work exemplifies the utility of the CAACU strategy for the simple and efficient production of homogeneous ubiquitinated and SUMOylated histones for biochemical and biophysical studies.
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Affiliation(s)
- Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | | | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Jing-Si Bai
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | | | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | | | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
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553
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Janssen JJE, Grefte S, Keijer J, de Boer VCJ. Mito-Nuclear Communication by Mitochondrial Metabolites and Its Regulation by B-Vitamins. Front Physiol 2019; 10:78. [PMID: 30809153 PMCID: PMC6379835 DOI: 10.3389/fphys.2019.00078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are cellular organelles that control metabolic homeostasis and ATP generation, but also play an important role in other processes, like cell death decisions and immune signaling. Mitochondria produce a diverse array of metabolites that act in the mitochondria itself, but also function as signaling molecules to other parts of the cell. Communication of mitochondria with the nucleus by metabolites that are produced by the mitochondria provides the cells with a dynamic regulatory system that is able to respond to changing metabolic conditions. Dysregulation of the interplay between mitochondrial metabolites and the nucleus has been shown to play a role in disease etiology, such as cancer and type II diabetes. Multiple recent studies emphasize the crucial role of nutritional cofactors in regulating these metabolic networks. Since B-vitamins directly regulate mitochondrial metabolism, understanding the role of B-vitamins in mito-nuclear communication is relevant for therapeutic applications and optimal dietary lifestyle. In this review, we will highlight emerging concepts in mito-nuclear communication and will describe the role of B-vitamins in mitochondrial metabolite-mediated nuclear signaling.
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Affiliation(s)
| | | | | | - Vincent C. J. de Boer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
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554
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Huang H, Tang S, Ji M, Tang Z, Shimada M, Liu X, Qi S, Locasale JW, Roeder RG, Zhao Y, Li X. p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis. Mol Cell 2019; 70:663-678.e6. [PMID: 29775581 DOI: 10.1016/j.molcel.2018.04.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 12/25/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is an evolutionarily conserved and widespread histone mark like lysine acetylation (Kac). Here we report that p300 functions as a lysine 2-hyroxyisobutyryltransferase to regulate glycolysis in response to nutritional cues. We discovered that p300 differentially regulates Khib and Kac on distinct lysine sites, with only 6 of the 149 p300-targeted Khib sites overlapping with the 693 p300-targeted Kac sites. We demonstrate that diverse cellular proteins, particularly glycolytic enzymes, are targeted by p300 for Khib, but not for Kac. Specifically, deletion of p300 significantly reduces Khib levels on several p300-dependent, Khib-specific sites on key glycolytic enzymes including ENO1, decreasing their catalytic activities. Consequently, p300-deficient cells have impaired glycolysis and are hypersensitive to glucose-depletion-induced cell death. Our study reveals an p300-catalyzed, Khib-specific molecular mechanism that regulates cellular glucose metabolism and further indicate that p300 has an intrinsic ability to select short-chain acyl-CoA-dependent protein substrates.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Shuang Tang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ming Ji
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shankang Qi
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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555
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Papsdorf K, Brunet A. Linking Lipid Metabolism to Chromatin Regulation in Aging. Trends Cell Biol 2019; 29:97-116. [PMID: 30316636 PMCID: PMC6340780 DOI: 10.1016/j.tcb.2018.09.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022]
Abstract
The lifespan of an organism is strongly influenced by environmental factors (including diet) and by internal factors (notably reproductive status). Lipid metabolism is critical for adaptation to external conditions or reproduction. Interestingly, specific lipid profiles are associated with longevity, and increased uptake of certain lipids extends longevity in Caenorhabditis elegans and ameliorates disease phenotypes in humans. How lipids impact longevity, and how lipid metabolism is regulated during aging, is just beginning to be unraveled. This review describes recent advances in the regulation and role of lipids in longevity, focusing on the interaction between lipid metabolism and chromatin states in aging and age-related diseases.
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Affiliation(s)
- Katharina Papsdorf
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
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556
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Structural insights into the molecular mechanism underlying Sirt5-catalyzed desuccinylation of histone peptides. Biochem J 2019; 476:211-223. [PMID: 30523058 DOI: 10.1042/bcj20180745] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]
Abstract
Histone modification is a ubiquitous regulatory mechanism involved in a variety of biological processes, including gene expression, DNA damage repair, cell differentiation, and ontogenesis. Succinylation sites on histones have been identified and may have functional consequences. Here, we demonstrate that human sirtuin 5 (Sirt5) catalyzes the sequence-selective desuccinylation of numerous histone succinyl sites. Structural studies of Sirt5 in complex with four succinyl peptides indicate an essential role for the conserved main chain hydrogen bonds formed by the succinyl lysine (0), +1, and +3 sites for substrate-enzyme recognition. Furthermore, biochemical assays reveal that the proline residue at the +1 site of the histone succinylation substrate is unfavorable for Sirt5 interaction. Our findings illustrate the molecular mechanism underlying the sequence-selective desuccinylase activity of Sirt5 and provide insights for further studies of the biological functions associated with histone succinylation and Sirt5.
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557
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Michaelovsky E, Carmel M, Frisch A, Salmon-Divon M, Pasmanik-Chor M, Weizman A, Gothelf D. Risk gene-set and pathways in 22q11.2 deletion-related schizophrenia: a genealogical molecular approach. Transl Psychiatry 2019; 9:15. [PMID: 30710087 PMCID: PMC6358611 DOI: 10.1038/s41398-018-0354-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 11/15/2022] Open
Abstract
The 22q11.2 deletion is a strong, but insufficient, "first hit" genetic risk factor for schizophrenia (SZ). We attempted to identify "second hits" from the entire genome in a unique multiplex 22q11.2 deletion syndrome (DS) family. Bioinformatic analysis of whole-exome sequencing and comparative-genomic hybridization array identified de novo and inherited, rare and damaging variants, including copy number variations, outside the 22q11.2 region. A specific 22q11.2-haplotype was associated with psychosis. The interaction of the identified "second hits" with the 22q11.2 haploinsufficiency may affect neurodevelopmental processes, including neuron projection, cytoskeleton activity, and histone modification in 22q11.2DS-ralated psychosis. A larger load of variants, involved in neurodevelopment, in combination with additional molecular events that affect sensory perception, olfactory transduction and G-protein-coupled receptor signaling may account for the development of 22q11.2DS-related SZ. Comprehensive analysis of multiplex families is a promising approach to the elucidation of the molecular pathophysiology of 22q11.2DS-related SZ with potential relevance to treatment.
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Affiliation(s)
- Elena Michaelovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Felsenstein Medical Research Center, Petah Tikva, Israel.
| | - Miri Carmel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
| | | | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
- Geha Mental Health Center, Petah Tikva, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- The Behavioral Neurogenetics Center, Sheba Medical Center, Tel Hashomer, Israel
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558
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Hu Y, Lu Y, Zhao Y, Zhou DX. Histone Acetylation Dynamics Integrates Metabolic Activity to Regulate Plant Response to Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:1236. [PMID: 31636650 PMCID: PMC6788390 DOI: 10.3389/fpls.2019.01236] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/05/2019] [Indexed: 05/20/2023]
Abstract
Histone lysine acetylation is an essential chromatin modification for epigenetic regulation of gene expression during plant response to stress. On the other hand, enzymes involved in histone acetylation homeostasis require primary metabolites as substrates or cofactors whose levels are greatly influenced by stress and growth conditions in plants. In addition, histone lysine acylation that requires similar enzymes for deposition and removal as histone acetylation has been recently characterized in plant. Results on understanding the intrinsic relationship between histone acetylation/acylation, metabolism and stress response in plants are accumulating. In this review, we summarize recent advance in the field and propose a model of interplay between metabolism and epigenetic regulation of genes expression in plant adaptation to stress.
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Affiliation(s)
- Yongfeng Hu
- College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-sud 11, University Paris-Saclay, Orsay, France
- *Correspondence: Dao-Xiu Zhou,
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559
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Genetic Factors Affecting Sperm Chromatin Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:1-28. [PMID: 31301043 DOI: 10.1007/978-3-030-21664-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spermatozoa genome has unique features that make it a fascinating field of investigation: first, because, with oocyte genome, it can be transmitted generation after generation; second, because of genetic shuffling during meiosis, each spermatozoon is virtually unique in terms of genetic content, with consequences for species evolution; and finally, because its chromatin organization is very different from that of somatic cells or oocytes, as it is not based on nucleosomes but on nucleoprotamines which confer a higher order of packaging. Histone-to-protamine transition involves many actors, such as regulators of spermatid gene expression, components of the nuclear envelop, histone-modifying enzymes and readers, chaperones, histone variants, transition proteins, protamines, and certainly many more to be discovered.In this book chapter, we will present what is currently known about sperm chromatin structure and how it is established during spermiogenesis, with the aim to list the genetic factors that regulate its organization.
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560
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Metabolic Signaling into Chromatin Modifications in the Regulation of Gene Expression. Int J Mol Sci 2018; 19:ijms19124108. [PMID: 30567372 PMCID: PMC6321258 DOI: 10.3390/ijms19124108] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022] Open
Abstract
The regulation of cellular metabolism is coordinated through a tissue cross-talk by hormonal control. This leads to the establishment of specific transcriptional gene programs which adapt to environmental stimuli. On the other hand, recent advances suggest that metabolic pathways could directly signal into chromatin modifications and impact on specific gene programs. The key metabolites acetyl-CoA or S-adenosyl-methionine (SAM) are examples of important metabolic hubs which play in addition a role in chromatin acetylation and methylation. In this review, we will discuss how intermediary metabolism impacts on transcription regulation and the epigenome with a particular focus in metabolic disorders.
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561
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Epigenetic Modification Mechanisms Involved in Inflammation and Fibrosis in Renal Pathology. Mediators Inflamm 2018; 2018:2931049. [PMID: 30647531 PMCID: PMC6311799 DOI: 10.1155/2018/2931049] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 01/19/2023] Open
Abstract
The growing incidence of obesity, hypertension, and diabetes, coupled with the aging of the population, is increasing the prevalence of renal diseases in our society. Chronic kidney disease (CKD) is characterized by persistent inflammation, fibrosis, and loss of renal function leading to end-stage renal disease. Nowadays, CKD treatment has limited effectiveness underscoring the importance of the development of innovative therapeutic options. Recent studies have identified how epigenetic modifications participate in the susceptibility to CKD and have explained how the environment interacts with the renal cell epigenome to contribute to renal damage. Epigenetic mechanisms regulate critical processes involved in gene regulation and downstream cellular responses. The most relevant epigenetic modifications that play a critical role in renal damage include DNA methylation, histone modifications, and changes in miRNA levels. Importantly, these epigenetic modifications are reversible and, therefore, a source of potential therapeutic targets. Here, we will explain how epigenetic mechanisms may regulate essential processes involved in renal pathology and highlight some possible epigenetic therapeutic strategies for CKD treatment.
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562
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Beyond histone acetylation-writing and erasing histone acylations. Curr Opin Struct Biol 2018; 53:169-177. [PMID: 30391813 DOI: 10.1016/j.sbi.2018.10.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/13/2018] [Accepted: 10/15/2018] [Indexed: 01/01/2023]
Abstract
Histone post-translational modifications are crucial epigenetic mechanisms regulating a variety of biological events. Besides histone lysine acetylation, a repertoire of acylation types have been identified, including formylation, propionylation, butyrylation, crotonylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, succinylation, malonylation, glutarylation and benzoylation. From a structural perspective, here we summarize the writers and erasers of histone acylations and explain the molecular basis of these enzymes catalyzing non-acetyl histone acylations with a focus on histone crotonylation and β-hydroxybutyrylation. Histone acylation readout, non-histone acylations and metabolic regulation are also discussed in this review.
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563
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Brial F, Le Lay A, Dumas ME, Gauguier D. Implication of gut microbiota metabolites in cardiovascular and metabolic diseases. Cell Mol Life Sci 2018; 75:3977-3990. [PMID: 30101405 PMCID: PMC6182343 DOI: 10.1007/s00018-018-2901-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/18/2022]
Abstract
Evidence from the literature keeps highlighting the impact of mutualistic bacterial communities of the gut microbiota on human health. The gut microbita is a complex ecosystem of symbiotic bacteria which contributes to mammalian host biology by processing, otherwise, indigestible nutrients, supplying essential metabolites, and contributing to modulate its immune system. Advances in sequencing technologies have enabled structural analysis of the human gut microbiota and allowed detection of changes in gut bacterial composition in several common diseases, including cardiometabolic disorders. Biological signals sent by the gut microbiota to the host, including microbial metabolites and pro-inflammatory molecules, mediate microbiome-host genome cross-talk. This rapidly expanding line of research can identify disease-causing and disease-predictive microbial metabolite biomarkers, which can be translated into novel biodiagnostic tests, dietary supplements, and nutritional interventions for personalized therapeutic developments in common diseases. Here, we review results from the most significant studies dealing with the association of products from the gut microbial metabolism with cardiometabolic disorders. We underline the importance of these postbiotic biomarkers in the diagnosis and treatment of human disorders.
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Affiliation(s)
- Francois Brial
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France
| | - Aurélie Le Lay
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, UK
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Dominique Gauguier
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France.
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, UK.
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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564
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Chen R, Yu Z, Yin D. Multi-generational effects of lindane on nematode lipid metabolism with disturbances on insulin-like signal pathway. CHEMOSPHERE 2018; 210:607-614. [PMID: 30031344 DOI: 10.1016/j.chemosphere.2018.07.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/07/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Influences on lipid metabolism and multi-generational obesogenic effects raised new concerns on lipophilic pollutants (e.g., lindane). Yet, the mechanisms remained unanswered. The present study exposed Caenorhabditis elegans to lindane for 4 consecutive generations (F0 to F3) at 1.0 ng/L, and measured effects in the directly exposed generations (F0 to F3), indirectly exposed ones (T1 and T1') and un-exposed ones (T3 and T3'). Lindane stimulated fat storages in all generations. At the biochemical level, lindane stimulated both acetyl-CoA carboxylase (ACC) and carnitine palmitoyl-transferases (CPT) in F0, T1 and T2, while inhibited them in F3, T1' and T3', demonstrating the balance between fatty acid synthesis and its depletion toward fat accumulation over generations. Moreover, lindane caused different effects on insulin among generations. It inhibited insulin in F0 and F3 and exhibited consistent effects on the expression changes of daf-2, sgk-1 and daf-16 genes in insulin-like signal pathway. Lindane also inhibited insulin in T1 and T3 but exhibited consistent effects on the expression changes of daf-2, akt-1 and daf-16. Different roles of sgk-1 and akt-1 indicated the response strategies from tolerance (F0 and F3) to avoidance (T1 and T3). Lindane stimulated insulin in T1' and T3' and exhibited consistent effects on expression changes of daf-2, sgk-1 and daf-16 genes that were similar in F0 and F3.
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Affiliation(s)
- Rui Chen
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China; Jiaxing Tongji Institute for Environment, Jiaxing, Zhejiang, 314051, PR China
| | - Zhenyang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China; Jiaxing Tongji Institute for Environment, Jiaxing, Zhejiang, 314051, PR China.
| | - Daqiang Yin
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China.
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565
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Vaijayanthi T, Pandian GN, Sugiyama H. Chemical Control System of Epigenetics. CHEM REC 2018; 18:1833-1853. [DOI: 10.1002/tcr.201800067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/07/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Thangavel Vaijayanthi
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
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566
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Bollong MJ, Lee G, Coukos JS, Yun H, Zambaldo C, Chang JW, Chin EN, Ahmad I, Chatterjee AK, Lairson LL, Schultz PG, Moellering RE. A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling. Nature 2018; 562:600-604. [PMID: 30323285 PMCID: PMC6444936 DOI: 10.1038/s41586-018-0622-0] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 08/21/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Gihoon Lee
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - John S Coukos
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Hwayoung Yun
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.,College of Pharmacy, Pusan National University, Busan, South Korea
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Emily N Chin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Insha Ahmad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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567
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Liu Y, Lee J, Perez L, Gill AD, Hooley RJ, Zhong W. Selective Sensing of Phosphorylated Peptides and Monitoring Kinase and Phosphatase Activity with a Supramolecular Tandem Assay. J Am Chem Soc 2018; 140:13869-13877. [PMID: 30269482 DOI: 10.1021/jacs.8b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simple tuning of a host:guest pair allows selective sensing of different peptide modifications, exploiting orthogonal recognition mechanisms. Excellent selectivity for either lysine trimethylations or alcohol phosphorylations is possible by simply varying the fluorophore guest. The phosphorylation sensor can be modulated by the presence of small (μM) concentrations of metal ions, allowing array-based sensing. Phosphorylation at serine, threonine, and tyrosine can be selectively sensed via discriminant analysis. The phosphopeptide sensing is effective in the presence of small-molecule phosphates such as ATP, which in turn enables the sensor to be employed in continuous optical assays of both serine kinase and tyrosine phosphatase activity. The activity of multiple different kinases can be monitored, and the sensor is capable of detecting the phosphorylation of peptides containing multiple different modifications, including lysine methylations and acetylation. A single deep cavitand can be used as a "one size fits all" sensor that can selectively detect multiple different modifications to oligopeptides, as well as monitoring the function of their post-translational modification writer and eraser enzymes in complex systems.
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568
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Kelly RDW, Chandru A, Watson PJ, Song Y, Blades M, Robertson NS, Jamieson AG, Schwabe JWR, Cowley SM. Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo. Sci Rep 2018; 8:14690. [PMID: 30279482 PMCID: PMC6168483 DOI: 10.1038/s41598-018-32927-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/14/2018] [Indexed: 01/14/2023] Open
Abstract
Proteomic analysis of histones has shown that they are subject to a superabundance of acylations, which extend far beyond acetylation, to include: crotonylation, propionylation, butyrylation, malonylation, succinylation, β-hydroxybutyrylation and 2-hydroxyisobutyrylation. To date, much of the functional data has focussed on histone crotonylation which, similar to acetylation, has been associated with positive gene regulation and is added by the acyltransferase, p300. Although Sirtuins 1–3, along with HDAC3, have been shown to possess decrotonylase activity in vitro, there is relatively little known about the regulation of histone crotonylation in vivo. Here we show that Histone Deacetylase 1 and 2 (HDAC1/2), the catalytic core of numerous co-repressor complexes, are important histone decrotonylase enzymes. A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates. Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity. Furthermore, we mapped H3K18cr in cells using ChIP-seq, with and without HDAC1/2, and observed increased levels of crotonylation, which largely overlaps with H3K18ac in the vicinity of transcriptional start sites. Collectively, our data indicate that HDAC1/2 containing complexes are critical regulators of histone crotonylation in vivo.
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Affiliation(s)
- R D W Kelly
- Department of Molecular and Cell biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | - A Chandru
- Department of Molecular and Cell biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | - P J Watson
- Institute of Structural and Chemical biology, Henry Wellcome Building, Department of Molecular and Cell biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Y Song
- Institute of Structural and Chemical biology, Henry Wellcome Building, Department of Molecular and Cell biology, University of Leicester, Leicester, LE1 7RH, UK
| | - M Blades
- Bioinformatics and Biostatistics Analysis Support Hub (B/BASH), University of Leicester, Leicester, LE1 7RH, UK
| | - N S Robertson
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - A G Jamieson
- School of Chemistry, Joseph Black Building, University Avenue, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - J W R Schwabe
- Institute of Structural and Chemical biology, Henry Wellcome Building, Department of Molecular and Cell biology, University of Leicester, Leicester, LE1 7RH, UK
| | - S M Cowley
- Department of Molecular and Cell biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK.
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569
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Chen Y, Liu Y, Sarker MMR, Yan X, Yang C, Zhao L, Lv X, Liu B, Zhao C. Structural characterization and antidiabetic potential of a novel heteropolysaccharide from Grifola frondosa via IRS1/PI3K-JNK signaling pathways. Carbohydr Polym 2018; 198:452-461. [DOI: 10.1016/j.carbpol.2018.06.077] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/11/2018] [Accepted: 06/16/2018] [Indexed: 12/18/2022]
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570
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Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX. Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence. Genome Biol 2018; 19:144. [PMID: 30253806 PMCID: PMC6154804 DOI: 10.1186/s13059-018-1533-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 09/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone lysine acylations by short-chain fatty acids are distinct from the widely studied histone lysine acetylation in chromatin, although both modifications are regulated by primary metabolism in mammalian cells. It remains unknown whether and how histone acylation and acetylation interact to regulate gene expression in plants that have distinct regulatory pathways of primary metabolism. RESULTS We identify 4 lysine butyrylation (Kbu) sites (H3K14, H4K12, H2BK42, and H2BK134) and 45 crotonylation (Kcr) sites on rice histones by mass spectrometry. Comparative analysis of genome-wide Kbu and Kcr and H3K9ac in combination with RNA sequencing reveals 25,306 genes marked by Kbu and Kcr in rice and more than 95% of H3K9ac-marked genes are marked by both. Kbu and Kcr are enriched at the 5' region of expressed genes. In rice under starvation and submergence, Kbu and Kcr appear to be less dynamic and display changes in different sets of genes compared to H3K9ac. Furthermore, Kbu seems to preferentially poise gene activation by external stresses, rather than internal circadian rhythm which has been shown to be tightly associated with H3K9ac. In addition, we show that rice sirtuin histone deacetylase (SRT2) is involved in the removal of Kcr. CONCLUSION Kbu, Kcr, and H3K9ac redundantly mark a large number of active genes but display different responses to external and internal signals. Thus, the proportion of rice histone lysine acetylation and acylation is dynamically regulated by environmental and metabolic cues, which may represent an epigenetic mechanism to fine-tune gene expression for plant adaptation.
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Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-sud 11, University Paris-Saclay, 91405, Orsay, France.
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571
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HATs off for the Lasker awardees. Nat Rev Mol Cell Biol 2018; 19:677. [PMID: 30232395 DOI: 10.1038/s41580-018-0065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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572
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Xu H, Wang Y, Lin S, Deng W, Peng D, Cui Q, Xue Y. PTMD: A Database of Human Disease-associated Post-translational Modifications. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:244-251. [PMID: 30244175 PMCID: PMC6205080 DOI: 10.1016/j.gpb.2018.06.004] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022]
Abstract
Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.
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Affiliation(s)
- Haodong Xu
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongbo Wang
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wankun Deng
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Di Peng
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Laboratory of Molecular Cardiovascular Sciences, Center for Non-coding RNA Medicine, Peking University, Beijing 100191, China.
| | - Yu Xue
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
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573
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Huang H, Zhang D, Wang Y, Perez-Neut M, Han Z, Zheng YG, Hao Q, Zhao Y. Lysine benzoylation is a histone mark regulated by SIRT2. Nat Commun 2018; 9:3374. [PMID: 30154464 PMCID: PMC6113264 DOI: 10.1038/s41467-018-05567-w] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023] Open
Abstract
Metabolic regulation of histone marks is associated with diverse biological processes through dynamically modulating chromatin structure and functions. Here we report the identification and characterization of a histone mark, lysine benzoylation (Kbz). Our study identifies 22 Kbz sites on histones from HepG2 and RAW cells. This type of histone mark can be stimulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbz marks are associated with gene expression and have physiological relevance distinct from histone acetylation. In addition, we demonstrate that SIRT2, a NAD+-dependent protein deacetylase, removes histone Kbz both in vitro and in vivo. This study therefore reveals a new type of histone marks with potential physiological relevance and identifies possible non-canonical functions of a widely used chemical food preservative. Histone marks regulate chromatin structure and function. Here the authors identify and characterize lysine benzoylation, a histone mark that can be modulated by sodium benzoate, a widely used chemical food preservative, associated with specific regulation of gene expression.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Yi Wang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Mathew Perez-Neut
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA.
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574
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Methylglyoxal-derived posttranslational arginine modifications are abundant histone marks. Proc Natl Acad Sci U S A 2018; 115:9228-9233. [PMID: 30150385 PMCID: PMC6140490 DOI: 10.1073/pnas.1802901115] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin comprises the approximately 3 billion bases in the human genome and histone proteins. Histone posttranslational modifications (PTMs) regulate chromatin dynamics and protein transcription to expand the genetic code. Herein we describe the existence of Lys and Arg modifications on histones derived from a glycolytic by-product, methylglyoxal (MGO). These PTMs are abundant modifications, present at similar levels as those of modifications known to modulate chromatin function and leading to altered gene transcription. Using CRISPR-Cas9, we show that the deglycase DJ-1 protects histones from adduction by MGO. These findings demonstrate the existence of a previously undetected histone modification and provide a link between cellular metabolism and the histone code. Histone posttranslational modifications (PTMs) regulate chromatin dynamics, DNA accessibility, and transcription to expand the genetic code. Many of these PTMs are produced through cellular metabolism to offer both feedback and feedforward regulation. Herein we describe the existence of Lys and Arg modifications on histones by a glycolytic by-product, methylglyoxal (MGO). Our data demonstrate that adduction of histones by MGO is an abundant modification, present at the same order of magnitude as Arg methylation. These modifications were detected on all four core histones at critical residues involved in both nucleosome stability and reader domain binding. In addition, MGO treatment of cells lacking the major detoxifying enzyme, glyoxalase 1, results in marked disruption of H2B acetylation and ubiquitylation without affecting H2A, H3, and H4 modifications. Using RNA sequencing, we show that MGO is capable of altering gene transcription, most notably in cells lacking GLO1. Finally, we show that the deglycase DJ-1 protects histones from adduction by MGO. Collectively, our findings demonstrate the existence of a previously undetected histone modification derived from glycolysis, which may have far-reaching implications for the control of gene expression and protein transcription linked to metabolism.
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575
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Zhang Q, Bai B, Mei X, Wan C, Cao H, Dan Li, Wang S, Zhang M, Wang Z, Wu J, Wang H, Huo J, Ding G, Zhao J, Xie Q, Wang L, Qiu Z, Zhao S, Zhang T. Elevated H3K79 homocysteinylation causes abnormal gene expression during neural development and subsequent neural tube defects. Nat Commun 2018; 9:3436. [PMID: 30143612 PMCID: PMC6109101 DOI: 10.1038/s41467-018-05451-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/06/2018] [Indexed: 11/08/2022] Open
Abstract
Neural tube defects (NTDs) are serious congenital malformations. Excessive maternal homocysteine (Hcy) increases the risk of NTDs, while its mechanism remains elusive. Here we report the role of histone homocysteinylation in neural tube closure (NTC). A total of 39 histone homocysteinylation sites are identified in samples from human embryonic brain tissue using mass spectrometry. Elevated levels of histone KHcy and H3K79Hcy are detected at increased cellular Hcy levels in human fetal brains. Using ChIP-seq and RNA-seq assays, we demonstrate that an increase in H3K79Hcy level down-regulates the expression of selected NTC-related genes including Cecr2, Smarca4, and Dnmt3b. In human NTDs brain tissues, decrease in expression of CECR2, SMARCA4, and DNMT3B is also detected along with high levels of Hcy and H3K79Hcy. Our results suggest that higher levels of Hcy contribute to the onset of NTDs through up-regulation of histone H3K79Hcy, leading to abnormal expressions of selected NTC-related genes.
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Affiliation(s)
- Qin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Baoling Bai
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Xinyu Mei
- Obstetrics & Gynecology Hospital of Fudan University, State Key Lab of Genetic, Engineering and Institutes of Biomedical Sciences, 200433, Shanghai, China
| | - Chunlei Wan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Haiyan Cao
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Dan Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
- Weifang Medical University, 261053, Weifang, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Min Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Zhigang Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, 100005, Beijing, China
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Hongyan Wang
- Obstetrics & Gynecology Hospital of Fudan University, State Key Lab of Genetic, Engineering and Institutes of Biomedical Sciences, 200433, Shanghai, China
| | - Junsheng Huo
- Key Laboratory of Trace Element Nutrition of National Health and Family Planning Commission of the People's Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 102206, Beijing, China
| | - Gangqiang Ding
- Key Laboratory of Trace Element Nutrition of National Health and Family Planning Commission of the People's Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 102206, Beijing, China
| | - Jianyuan Zhao
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Qiu Xie
- Chinese Academy of Medical Sciences & Peking Union Medical College, 100005, Beijing, China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Shiming Zhao
- Obstetrics & Gynecology Hospital of Fudan University, State Key Lab of Genetic, Engineering and Institutes of Biomedical Sciences, 200433, Shanghai, China.
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China.
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576
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Wu Q, Ke L, Wang C, Fan P, Wu Z, Xu X. Global Analysis of Lysine 2-Hydroxyisobutyrylome upon SAHA Treatment and Its Relationship with Acetylation and Crotonylation. J Proteome Res 2018; 17:3176-3183. [PMID: 30109935 DOI: 10.1021/acs.jproteome.8b00289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine 2-hydroxyisobutyrylation is a newly discovered protein acylation and was reported to share acyltransferases and deacylases with the widely studied lysine acetylation. The well-known acetyltransferase Tip60 and histone deacetylases HDAC 2 and HDAC 3 were discovered to be "writer" and "eraser" of this new PTM on histones. However, the acyltransferases and deacylases for nonhistone proteins are still unclear. In this work, lysine 2-hydroxyisobutyrylome on both histones and nonhistone proteins upon SAHA treatment were intensively studied and 8765 lysine 2-hydroxyisobutyrylation sites on 2484 proteins were identified in A549 cells. This is the largest data set of lysine 2-hydroxyisobutyrylome in mammalian cells to date. It was found that lysine 2-hydroxyisobutyrylation participates in varieties of biological functions and processes including ribosome, glycolysis/gluconeogenesis, and transcription. More importantly, it was found that most quantified sites on core histones were up-regulated upon SAHA treatment for all 2-hydroxyisobutyrylation, crotonylation, and acetylation and the fold changes upon SAHA of 2-hydroxyisobutyrylation and crotonylation on nonhistone proteins were highly correlated, while their fold changes have little correlations with acetylation on nonhistone proteins.
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Affiliation(s)
- Quan Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China.,Department of Microbiology and Immunobiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Li Ke
- Department of Thoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Chi Wang
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Pingsheng Fan
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Zhiwei Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Xiaoling Xu
- Department of Respiration, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
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577
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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578
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Nieborak A, Schneider R. Metabolic intermediates - Cellular messengers talking to chromatin modifiers. Mol Metab 2018; 14:39-52. [PMID: 29397344 PMCID: PMC6034042 DOI: 10.1016/j.molmet.2018.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To maintain homeostasis, cells need to coordinate the expression of their genes. Epigenetic mechanisms controlling transcription activation and repression include DNA methylation and post-translational modifications of histones, which can affect the architecture of chromatin and/or create 'docking platforms' for multiple binding proteins. These modifications can be dynamically set and removed by various enzymes that depend on the availability of key metabolites derived from different intracellular pathways. Therefore, small metabolites generated in anabolic and catabolic processes can integrate multiple external and internal stimuli and transfer information on the energetic state of a cell to the transcriptional machinery by regulating the activity of chromatin-modifying enzymes. SCOPE OF REVIEW This review provides an overview of the current literature and concepts on the connections and crosstalk between key cellular metabolites, enzymes responsible for their synthesis, recycling, and conversion and chromatin marks controlling gene expression. MAJOR CONCLUSIONS Whereas current evidence indicates that many chromatin-modifying enzymes respond to alterations in the levels of their cofactors, cosubstrates, and inhibitors, the detailed molecular mechanisms and functional consequences of such processes are largely unresolved. A deeper investigation of mechanisms responsible for altering the total cellular concentration of particular metabolites, as well as their nuclear abundance and accessibility for chromatin-modifying enzymes, will be necessary to better understand the crosstalk between metabolism, chromatin marks, and gene expression.
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Affiliation(s)
- Anna Nieborak
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Faculty of Biology, LMU, 82152 Martinsried, Germany.
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579
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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580
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Huang H, Wang DL, Zhao Y. Quantitative Crotonylome Analysis Expands the Roles of p300 in the Regulation of Lysine Crotonylation Pathway. Proteomics 2018; 18:e1700230. [PMID: 29932303 PMCID: PMC6420807 DOI: 10.1002/pmic.201700230] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 06/10/2018] [Indexed: 01/24/2023]
Abstract
Lysine crotonylation (Kcr) is a recently identified post-translational modification (PTM) that is regulated by an acetyltransferase, p300. The p300-catalyzed histone Kcr is able to stimulate transcription to a greater degree than the well-studied histone lysine acetylation (Kac). Despite these progresses, the global Kcr substrates regulated by p300 remain largely unknown, hindering efforts to establish mechanistic links between Kcr and p300-mediated phenotypes. Here, a quantitative proteomics study to characterize the p300-regulated lysine crotonylome is reported. A total of 816 unique endogenous crotonylation sites are identified across 392 proteins, with 88 sites from 69 proteins being decreased by more than 0.7-fold (log2 < 0.5) and 31 sites from 17 proteins being increased by more than 1.4-fold (log2 > 0.5) in response to p300 knockout (KO). The most downregulated crotonylome alterations under p300 deficiency concern components of the nonsense-mediated decay, infectious disease, and viral/eukaryotic translation pathways. Moreover, some p300-targeted Kcr substrates are potentially linked to diseases such as cancer. Taken together, this study reveals the lysine crotonylome in response to p300, which sheds light on the role for lysine crotonylation in regulation of diverse cellular processes and provides new insights into mechanisms of p300 functions.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, 60637 Chicago, IL, USA,
| | - Dan-Li Wang
- School of Marine Sciences, Ningbo University, 315211 Ningbo, China
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, 60637 Chicago, IL, USA,
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581
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Epigenetic chromatin modification by amber suppression technology. Curr Opin Chem Biol 2018; 45:1-9. [DOI: 10.1016/j.cbpa.2018.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/28/2018] [Indexed: 01/10/2023]
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582
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Fellows R, Varga-Weisz P. In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones. Bio Protoc 2018; 8:e2924. [PMID: 30283810 PMCID: PMC6166789 DOI: 10.21769/bioprotoc.2924] [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: 11/02/2022] Open
Abstract
Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the effect of inhibitors and estimate kinetic constants.
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Affiliation(s)
| | - Patrick Varga-Weisz
- Babraham Institute, Cambridge, UK.,School of Biological Sciences, University of Essex, Colchester, UK
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583
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Chen B, Sun Y, Niu J, Jarugumilli GK, Wu X. Protein Lipidation in Cell Signaling and Diseases: Function, Regulation, and Therapeutic Opportunities. Cell Chem Biol 2018; 25:817-831. [PMID: 29861273 PMCID: PMC6054547 DOI: 10.1016/j.chembiol.2018.05.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/06/2017] [Accepted: 05/01/2018] [Indexed: 01/08/2023]
Abstract
Protein lipidation is an important co- or posttranslational modification in which lipid moieties are covalently attached to proteins. Lipidation markedly increases the hydrophobicity of proteins, resulting in changes to their conformation, stability, membrane association, localization, trafficking, and binding affinity to their co-factors. Various lipids and lipid metabolites serve as protein lipidation moieties. The intracellular concentrations of these lipids and their derivatives are tightly regulated by cellular metabolism. Therefore, protein lipidation links the output of cellular metabolism to the regulation of protein function. Importantly, deregulation of protein lipidation has been linked to various diseases, including neurological disorders, metabolic diseases, and cancers. In this review, we highlight recent progress in our understanding of protein lipidation, in particular, S-palmitoylation and lysine fatty acylation, and we describe the importance of these modifications for protein regulation, cell signaling, and diseases. We further highlight opportunities and new strategies for targeting protein lipidation for therapeutic applications.
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Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Yang Sun
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA.
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584
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SIRT7 has a critical role in bone formation by regulating lysine acylation of SP7/Osterix. Nat Commun 2018; 9:2833. [PMID: 30026585 PMCID: PMC6053369 DOI: 10.1038/s41467-018-05187-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 06/18/2018] [Indexed: 12/02/2022] Open
Abstract
SP7/Osterix (OSX) is a master regulatory transcription factor that activates a variety of genes during differentiation of osteoblasts. However, the influence of post-translational modifications on the regulation of its transactivation activity is largely unknown. Here, we report that sirtuins, which are NAD(+)-dependent deacylases, regulate lysine deacylation-mediated transactivation of OSX. Germline Sirt7 knockout mice develop severe osteopenia characterized by decreased bone formation and an increase of osteoclasts. Similarly, osteoblast-specific Sirt7 knockout mice showed attenuated bone formation. Interaction of SIRT7 with OSX leads to the activation of transactivation by OSX without altering its protein expression. Deacylation of lysine (K) 368 in the C-terminal region of OSX by SIRT7 promote its N-terminal transactivation activity. In addition, SIRT7-mediated deacylation of K368 also facilitates depropionylation of OSX by SIRT1, thereby increasing OSX transactivation activity. In conclusion, our findings suggest that SIRT7 has a critical role in bone formation by regulating acylation of OSX. SP7/Osterix is a transcription factor involved in osteoblast differentiation. Here, the authors show that Sirtuin 7 activates Osterix posttranslationally by regulating its lysine acylation, and that mice lacking Sirtuin 7 in osteoblasts show reduced bone formation.
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585
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586
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Candida glabrata Med3 Plays a Role in Altering Cell Size and Budding Index To Coordinate Cell Growth. Appl Environ Microbiol 2018; 84:AEM.00781-18. [PMID: 29776932 DOI: 10.1128/aem.00781-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/14/2018] [Indexed: 12/11/2022] Open
Abstract
Candida glabrata is a promising microorganism for the production of organic acids. Here, we report deletion and quantitative-expression approaches to elucidate the role of C. glabrata Med3AB (CgMed3AB), a subunit of the mediator transcriptional coactivator, in regulating cell growth. Deletion of CgMed3AB caused an 8.6% decrease in final biomass based on growth curve plots and 10.5% lower cell viability. Based on transcriptomics data, the reason for this growth defect was attributable to changes in expression of genes involved in pyruvate and acetyl-coenzyme A (CoA)-related metabolism in a Cgmed3abΔ strain. Furthermore, the mRNA level of acetyl-CoA synthetase was downregulated after deleting Cgmed3ab, resulting in 22.8% and 21% lower activity of acetyl-CoA synthetase and cellular acetyl-CoA, respectively. Additionally, the mRNA level of CgCln3, whose expression depends on acetyl-CoA, was 34% lower in this strain. As a consequence, the cell size and budding index in the Cgmed3abΔ strain were both reduced. Conversely, overexpression of Cgmed3ab led to 16.8% more acetyl-CoA and 120% higher CgCln3 mRNA levels, as well as 19.1% larger cell size and a 13.3% higher budding index than in wild-type cells. Taken together, these results suggest that CgMed3AB regulates cell growth in C. glabrata by coordinating homeostasis between cellular acetyl-CoA and CgCln3.IMPORTANCE This study demonstrates that CgMed3AB can regulate cell growth in C. glabrata by coordinating the homeostasis of cellular acetyl-CoA metabolism and the cell cycle cyclin CgCln3. Specifically, we report that CgMed3AB regulates the cellular acetyl-CoA level, which induces the transcription of Cgcln3, finally resulting in alterations to the cell size and budding index. In conclusion, we report that CgMed3AB functions as a wheel responsible for driving cellular acetyl-CoA metabolism, indirectly inducing the transcription of Cgcln3 and coordinating cell growth. We propose that Mediator subunits may represent a vital regulatory target modulating cell growth in C. glabrata.
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587
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Ryall JG, Lynch GS. The molecular signature of muscle stem cells is driven by nutrient availability and innate cell metabolism. Curr Opin Clin Nutr Metab Care 2018; 21:240-245. [PMID: 29697538 DOI: 10.1097/mco.0000000000000472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW To discuss how innate muscle stem-cell metabolism and nutrient availability can provide temporal regulation of chromatin accessibility and transcription. RECENT FINDINGS Fluorescence-activated cell sorting coupled with whole transcriptome sequencing revealed for the first time that quiescent and proliferating skeletal muscle stem cells exhibit a process of metabolic reprogramming, from fatty-acid oxidation during quiescence to glycolysis during proliferation. Using a combination of immunofluorescence and chromatin immunoprecipitation sequencing, this shift in metabolism has been linked to altered availability of key metabolites essential for histone (de)acetylation and (de)methylation, including acetyl-CoA, s-adenosylmethionine and α-ketoglutarate. Importantly, these changes in metabolite availability have been linked to muscle stem-cell function. SUMMARY Together, these results provide greater insight into how muscle stem cells interact with their local environment, with important implications for metabolic diseases, skeletal muscle regeneration and cell-transplantation therapies.
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Affiliation(s)
- James G Ryall
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
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588
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Abstract
PURPOSE OF REVIEW Ketone body metabolism is a dynamic and integrated metabolic node in human physiology, whose roles include but extend beyond alternative fuel provision during carbohydrate restriction. Here we discuss the most recent observations suggesting that ketosis coordinates cellular function via epigenomic regulation. RECENT FINDINGS Ketosis has been linked to covalent modifications, including lysine acetylation, methylation, and hydroxybutyrylation, to key histones that serve as dynamic regulators of chromatin architecture and gene transcription. Although it remains to be fully established whether these changes to the epigenome are attributable to ketone bodies themselves or other aspects of ketotic states, the regulated genes mediate classical responses to carbohydrate restriction. SUMMARY Direct regulation of gene expression may occur in-vivo via through ketone body-mediated histone modifications during adherence to low-carbohydrate diets, fasting ketosis, exogenous ketone body therapy, and diabetic ketoacidosis. Additional convergent functional genomics, metabolomics, and proteomics studies are required in both animal models and in humans to identify the molecular mechanisms through which ketosis regulates nuclear signaling events in a myriad of conditions relevant to disease, and the contexts in which the benefits of ketosis might outweigh the risks.
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Affiliation(s)
- Hai-Bin Ruan
- Department of Integrative Biology and Physiology
| | - Peter A Crawford
- Division of Molecular Medicine, Department of Medicine
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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589
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Rahman J, Rahman S. Mitochondrial medicine in the omics era. Lancet 2018; 391:2560-2574. [PMID: 29903433 DOI: 10.1016/s0140-6736(18)30727-x] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/28/2018] [Accepted: 03/14/2018] [Indexed: 12/16/2022]
Abstract
Mitochondria are dynamic bioenergetic organelles whose maintenance requires around 1500 proteins from two genomes. Mutations in either the mitochondrial or nuclear genome can disrupt a plethora of cellular metabolic and homoeostatic functions. Mitochondrial diseases represent one of the most common and severe groups of inherited genetic disorders, characterised by clinical, biochemical, and genetic heterogeneity, diagnostic odysseys, and absence of disease-modifying curative therapies. This Review aims to discuss recent advances in mitochondrial biology and medicine arising from widespread use of high-throughput omics technologies, and also includes a broad discussion of emerging therapies for mitochondrial disease. New insights into both bioenergetic and biosynthetic mitochondrial functionalities have expedited the genetic diagnosis of primary mitochondrial disorders, and identified novel mitochondrial pathomechanisms and new targets for therapeutic intervention. As we enter this new era of mitochondrial medicine, underpinned by global unbiased approaches and multifaceted investigation of mitochondrial function, omics technologies will continue to shed light on unresolved mitochondrial questions, paving the way for improved outcomes for patients with mitochondrial diseases.
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Affiliation(s)
- Joyeeta Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK; Metabolic Unit, Great Ormond Street Hospital NHS Foundation Trust, London, UK.
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590
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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591
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Liu Z, Zhang QB, Bu C, Wang D, Yu K, Gan Z, Chang J, Cheng Z, Liu Z. Quantitative Dynamics of Proteome, Acetylome, and Succinylome during Stem-Cell Differentiation into Hepatocyte-like Cells. J Proteome Res 2018; 17:2491-2498. [PMID: 29882676 DOI: 10.1021/acs.jproteome.8b00238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Stem-cell differentiation is a complex biological process controlled by a series of functional protein clusters and signaling transductions, especially metabolism-related pathways. Although previous studies have quantified the proteome and phosphoproteome for stem-cell differentiation, the investigation of acylation-mediated regulation is still absent. In this study, we quantitatively profiled the proteome, acetylome, and succinylome in pluripotent human embryonic stem cells (hESCs) and differentiated hepatocyte-like cells (HLCs). In total, 3843 proteins, 185 acetylation sites in 103 proteins, and 602 succinylation sites in 391 proteins were quantified. The quantitative proteome showed that in differentiated HLCs the TGF-β, JAK-STAT, and RAS signaling pathways were activated, whereas ECM-related processes such as sulfates and leucine degradation were depressed. Interestingly, it was observed that the acetylation and succinylation were more intensive in hESCs, whereas protein processing in endoplasmic reticulum and the carbon metabolic pathways were especially highly succinylated. Because the metabolism patterns in pluripotent hESCs and the differentiated HLCs were different, we proposed that the dynamic acylations, especially succinylation, might regulate the Warburg-like effect and TCA cycle during differentiation. Taken together, we systematically profiled the protein and acylation levels of regulation in pluripotent hESCs and differentiated HLCs, and the results indicated the important roles of acylation in pluripotency maintenance and differentiation.
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Affiliation(s)
- Zekun Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China , Collaborative Innovation Center for Cancer Medicine , Guangzhou 510060 , China
| | - Qing-Bin Zhang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease , Stomatology Hospital of Guangzhou Medical University , Guangzhou 510140 , China
| | - Chen Bu
- Jingjie PTM BioLabs (Hangzhou), Co. Ltd. , Hangzhou 310018 , China
| | - Dawei Wang
- Department of Thoracic Surgery , China Meitan General Hospital , Beijing 100028 , China
| | - Kai Yu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China , Collaborative Innovation Center for Cancer Medicine , Guangzhou 510060 , China
| | - Zhixue Gan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology , Tongji University , Shanghai 200092 , China
| | - Jianfeng Chang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology , Tongji University , Shanghai 200092 , China
| | - Zhongyi Cheng
- Jingjie PTM BioLabs (Hangzhou), Co. Ltd. , Hangzhou 310018 , China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China , Collaborative Innovation Center for Cancer Medicine , Guangzhou 510060 , China
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592
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Xu JY, Zhao L, Liu X, Hu H, Liu P, Tan M, Ye BC. Characterization of the Lysine Acylomes and the Substrates Regulated by Protein Acyltransferase in Mycobacterium smegmatis. ACS Chem Biol 2018; 13:1588-1597. [PMID: 29799716 DOI: 10.1021/acschembio.8b00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein acylation plays important roles in bacterial pathogenesis through regulation of enzymatic activity, protein stability, nucleic acid binding ability, and protein-protein interactions. Mycobacteria, a genus including invasive pathogens known to cause serious diseases, shapes its pathogenicity through adaptation of its energy metabolism to microenvironments encountered within mammalian hosts. In this process, acetyl-CoA and propionyl-CoA function as important intermediates. However, the function of acetyl-CoA/propionyl-CoA driven protein acylation remains to be elucidated. Herein, we systematically investigated protein acetylome/propionylome in the nonpathogenic Mycobacterium smegmatis through antibody-enrichment-based proteomic analysis in which 146 acetylated sites on 121 proteins and 26 propionylated sites on 25 proteins were identified. After that, characteristic differences of the two acylomes were elucidated through such bioinformatic methods as motif analysis, protein-protein analysis, Gene Ontology analysis, and KEGG analysis. In addition, quantitative mass spectrometric method was used to evaluate the site-specific and motif-biased catalytic mechanism mediated by the cAMP-dependent acetyltransferase MsKat in M. smegmatis. Furthermore, we raised the possibility that both O-serine and Nε-lysine acetylation might coregulate the propionyl-CoA synthetase. This study described the landscape of acetylome and propionylome in the M. smegmatis, showing an unexpected role of protein acylation regulation in mycobacteria.
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Affiliation(s)
- Jun-Yu Xu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lei Zhao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - XinXin Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ping Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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593
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Xu JY, Xu Y, Xu Z, Zhai LH, Ye Y, Zhao Y, Chu X, Tan M, Ye BC. Protein Acylation is a General Regulatory Mechanism in Biosynthetic Pathway of Acyl-CoA-Derived Natural Products. Cell Chem Biol 2018; 25:984-995.e6. [PMID: 29887264 DOI: 10.1016/j.chembiol.2018.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/25/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022]
Abstract
Coenzyme A (CoA) esters of short fatty acids (acyl-CoAs) function as key precursors for the biosynthesis of various natural products and the dominant donors for lysine acylation. Herein, we investigated the functional interplay between beneficial and adverse effects of acyl-CoA supplements on the production of acyl-CoA-derived natural products in microorganisms by using erythromycin-biosynthesized Saccharopolyspora erythraea as a model: accumulation of propionyl-CoA benefited erythromycin biosynthesis, but lysine propionylation inhibited the activities of important enzymes involved in biosynthetic pathways of erythromycin. The results showed that the overexpression of NAD+-dependent deacylase could circumvent the inhibitory effects of high acyl-CoA concentrations. In addition, we demonstrated the similar lysine acylation mechanism in other acyl-CoA-derived natural product biosynthesis, such as malonyl-CoA-derived alkaloid and butyryl-CoA-derived bioalcohol. These observations systematically uncovered the important role of protein acylation on interaction between the accumulation of high concentrations of acyl-CoAs and the efficiency of their use in metabolic pathways.
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Affiliation(s)
- Jun-Yu Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yingming Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
| | - Bang-Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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594
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Chakraborty J, Nemeria NS, Farinas E, Jordan F. Catalysis of transthiolacylation in the active centers of dihydrolipoamide acyltransacetylase components of 2-oxo acid dehydrogenase complexes. FEBS Open Bio 2018; 8:880-896. [PMID: 29928569 PMCID: PMC5986005 DOI: 10.1002/2211-5463.12431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli 2‐oxoglutarate dehydrogenase complex (OGDHc) comprises multiple copies of three enzymes—E1o, E2o, and E3—and transthioesterification takes place within the catalytic domain of E2o. The succinyl group from the thiol ester of S8‐succinyldihydrolipoyl‐E2o is transferred to the thiol group of coenzyme A (CoA), forming the all‐important succinyl‐CoA. Here, we report mechanistic studies of enzymatic transthioesterification on OGDHc. Evidence is provided for the importance of His375 and Asp374 in E2o for the succinyl transfer reaction. The magnitude of the rate acceleration provided by these residues (54‐fold from each with alanine substitution) suggests a role in stabilization of the symmetrical tetrahedral oxyanionic intermediate by formation of two hydrogen bonds, rather than in acid–base catalysis. Further evidence ruling out a role in acid–base catalysis is provided by site‐saturation mutagenesis studies at His375 (His375Trp substitution with little penalty) and substitutions to other potential hydrogen bond participants at Asp374. Taking into account that the rate constant for reductive succinylation of the E2o lipoyl domain (LDo) by E1o and 2‐oxoglutarate (99 s−1) was approximately twofold larger than the rate constant for kcat of 48 s−1 for the overall reaction (NADH production), it could be concluded that succinyl transfer to CoA and release of succinyl‐CoA, rather than reductive succinylation, is the rate‐limiting step. The results suggest a revised mechanism of catalysis for acyl transfer in the superfamily of 2‐oxo acid dehydrogenase complexes, thus provide fundamental information regarding acyl‐CoA formation, so important for several biological processes including post‐translational succinylation of protein lysines. Enzymes 2‐oxoglutarate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/2.html); dihydrolipoamide succinyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/61.html); dihydrolipoamide dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/8/1/4.html); pyruvate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/1.html); dihydrolipoamide acetyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/12.html).
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Affiliation(s)
- Joydeep Chakraborty
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | | | - Edgardo Farinas
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | - Frank Jordan
- Department of Chemistry Rutgers University Newark NJ USA
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595
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Xu JY, Xu Y, Chu X, Tan M, Ye BC. Protein Acylation Affects the Artificial Biosynthetic Pathway for Pinosylvin Production in Engineered E. coli. ACS Chem Biol 2018; 13:1200-1208. [PMID: 29690763 DOI: 10.1021/acschembio.7b01068] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of regulatory system on the engineered biosynthetic pathway in chassis cells remains incompletely understood in microorganisms. Acyl-CoAs function as key precursors for the biosynthesis of various natural products and the dominant donors for protein acylation. The polyphenol pinosylvin, with high antimicrobial and antifungal activities, is biosynthesized with malonyl-CoA as its direct precursors. But correlation between lysine malonylation and pinosylvin biosynthesis remains unknown. Herein, we found that the malonyl-CoA-driven lysine malonylation plays an important role in interaction between the engineered pathway of pinosylvin synthesis and E. coli chassis cell. Oversupply of malonyl-CoA leads to an increase in malonylation level of global proteome as well as the enzymes in the artificial pathway, thereby decreasing yield of pinosylvin. The results revealed that the intricate balance of cellular acyl-CoA concentrations is critical for the yields of acyl-CoA-derived natural products. We next modified the enzymes in the biosynthetic pathway to adjust their acylation level and successfully improved the yield of pinosylvin. Our study uncovers the effect of protein acylation on the biosynthetic pathway, helps optimization of synthetic constructs, and provides new strategies in metabolic engineering and synthetic biology at the protein post-translational level.
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Affiliation(s)
- Jun-Yu Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Xu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bang-Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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596
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Malonylation of histone H2A at lysine 119 inhibits Bub1-dependent H2A phosphorylation and chromosomal localization of shugoshin proteins. Sci Rep 2018; 8:7671. [PMID: 29769606 PMCID: PMC5956101 DOI: 10.1038/s41598-018-26114-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/04/2018] [Indexed: 11/17/2022] Open
Abstract
Post-translational modifications of histones, such as acetylation and phosphorylation, are highly conserved in eukaryotes and their combination enables precise regulation of many cellular functions. Recent studies using mass spectrometry have revealed various non-acetyl acylations in histones, including malonylation and succinylation, which change the positive charge of lysine into a negative one. However, the molecular function of histone malonylation or succinylation is poorly understood. Here, we discovered the functions of malonylation in histone H2A at lysine 119 (H2A-K119) in chromosome segregation during mitosis and meiosis. Analyses of H2A-K119 mutants in Saccharomyces cerevisiae and Schizosaccharomyces pombe showed that anionic mutations, specifically to aspartate (K119D) and glutamate (K119E), showed mis-segregation of the chromosomes and sensitivity to microtubule-destabilizing reagents in mitosis and meiosis. We found that the chromosomal localization of shugoshin proteins, which depends on Bub1-catalyzed phosphorylation of H2A at serine 121 (H2A-S121), was significantly reduced in the H2A-K119D and the H2A-K119E mutants. Biochemical analyses using K119-unmodified or -malonylated H2A-C-tail peptides showed that H2A-K119 malonylation inhibited the interaction between Bub1 and H2A, leading to a decrease in Bub1-dependent H2A-S121 phosphorylation. Our results indicate a novel crosstalk between lysine malonylation and serine/threonine phosphorylation, which may be important for fine-tuning chromatin functions such as chromosome segregation.
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597
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Schvartzman JM, Thompson CB, Finley LWS. Metabolic regulation of chromatin modifications and gene expression. J Cell Biol 2018; 217:2247-2259. [PMID: 29760106 PMCID: PMC6028552 DOI: 10.1083/jcb.201803061] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Schvartzman et al. review how alterations in the levels of specific metabolites in mammalian cells result in chromatin modifications that influence gene expression. Dynamic regulation of gene expression in response to changing local conditions is critical for the survival of all organisms. In metazoans, coherent regulation of gene expression programs underlies the development of functionally distinct cell lineages. The cooperation between transcription factors and the chromatin landscape enables precise control of gene expression in response to cell-intrinsic and cell-extrinsic signals. Many of the chemical modifications that decorate DNA and histones are adducts derived from intermediates of cellular metabolic pathways. In addition, several of the enzymes that can remove these marks use metabolites as part of their enzymatic reaction. These observations have led to the hypothesis that fluctuations in metabolite levels influence the deposition and removal of chromatin modifications. In this review, we consider the emerging evidence that cellular metabolic activity contributes to gene expression and cell fate decisions through metabolite-dependent effects on chromatin organization.
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Affiliation(s)
- Juan Manuel Schvartzman
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY .,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
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598
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Yu P, Wu G, Lee HW, Simons M. Endothelial Metabolic Control of Lymphangiogenesis. Bioessays 2018; 40:e1700245. [PMID: 29750374 DOI: 10.1002/bies.201700245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/12/2018] [Indexed: 12/11/2022]
Abstract
Lymphangiogenesis is an important developmental process that is critical to regulation of fluid homeostasis, immune surveillance and response as well as pathogenesis of a number of diseases, among them cancer, inflammation, and heart failure. Specification, formation, and maturation of lymphatic blood vessels involves an interplay between a series of events orchestrated by various transcription factors that determine expression of key genes involved in lymphangiogenesis. These are traditionally thought to be under control of several key growth factors including vascular growth factor-C (VEGF-C) and fibroblast growth factors (FGFs). Recent insights into VEGF and FGF signaling point to their role in control of endothelial metabolic processes such as glycolysis and fatty acid oxidation that, in turn, play a major role in regulation of lymphangiogenesis. These advances have significantly increased our understanding of lymphatic biology and opened new therapeutic vistas. Here we review our current understanding of metabolic controls in the lymphatic vasculature.
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Affiliation(s)
- Pengchun Yu
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Guosheng Wu
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, 06511, USA.,Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Heon-Woo Lee
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Michael Simons
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, 06511, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
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599
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Zhang H, Menzies KJ, Auwerx J. The role of mitochondria in stem cell fate and aging. Development 2018; 145:145/8/dev143420. [PMID: 29654217 DOI: 10.1242/dev.143420] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The importance of mitochondria in energy metabolism, signal transduction and aging in post-mitotic tissues has been well established. Recently, the crucial role of mitochondrial-linked signaling in stem cell function has come to light and the importance of mitochondria in mediating stem cell activity is becoming increasingly recognized. Despite the fact that many stem cells exhibit low mitochondrial content and a reliance on mitochondrial-independent glycolytic metabolism for energy, accumulating evidence has implicated the importance of mitochondrial function in stem cell activation, fate decisions and defense against senescence. In this Review, we discuss the recent advances that link mitochondrial metabolism, homeostasis, stress responses, and dynamics to stem cell function, particularly in the context of disease and aging. This Review will also highlight some recent progress in mitochondrial therapeutics that may present attractive strategies for improving stem cell function as a basis for regenerative medicine and healthy aging.
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Affiliation(s)
- Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun-Yat Sen University, 510080, Guangzhou, China.,Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, CH-1015, Switzerland
| | - Keir J Menzies
- Interdisciplinary School of Health Sciences, University of Ottawa Brain and Mind Research Institute and Centre for Neuromuscular Disease, Ottawa, Canada, K1H 8M5
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, CH-1015, Switzerland
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600
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Kumar S, Lombard DB. Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology. Crit Rev Biochem Mol Biol 2018; 53:311-334. [PMID: 29637793 DOI: 10.1080/10409238.2018.1458071] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sirtuins are NAD+-dependent protein deacylases/ADP-ribosyltransferases that have emerged as candidate targets for new therapeutics to treat metabolic disorders and other diseases, including cancer. The sirtuin SIRT5 resides primarily in the mitochondrial matrix and catalyzes the removal of negatively charged lysine acyl modifications; succinyl, malonyl, and glutaryl groups. Evidence has now accumulated to document the roles of SIRT5 as a significant regulator of cellular homeostasis, in a context- and cell-type specific manner, as has been observed previously for other sirtuin family members. SIRT5 regulates protein substrates involved in glycolysis, the TCA cycle, fatty acid oxidation, electron transport chain, ketone body formation, nitrogenous waste management, and ROS detoxification, among other processes. SIRT5 plays pivotal roles in cardiac physiology and stress responses and is involved in the regulation of numerous aspects of myocardial energy metabolism. SIRT5 is implicated in neoplasia, as both a tumor promoter and suppressor in a context-specific manner, and may serve a protective function in the setting of neurodegenerative disorders. Here, we review the current understanding of functional impacts of SIRT5 on its metabolic targets, and its molecular functions in both normal and pathological conditions. Finally, we will discuss the potential utility of SIRT5 as a drug target and also summarize the current status, progress, and challenges in developing small molecule compounds to modulate SIRT5 activity with high potency and specificity.
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Affiliation(s)
- Surinder Kumar
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA
| | - David B Lombard
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA.,b Institute of Gerontology , University of Michigan , Ann Arbor , MI , USA
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