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Atila M, Katselis G, Chumala P, Luo Y. Characterization of N-Succinylation of L-Lysylphosphatidylglycerol in Bacillus subtilis Using Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1606-1613. [PMID: 27506207 DOI: 10.1007/s13361-016-1455-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Phospholipids generally dominate in bacterial lipids. The negatively charged nature of phospholipids renders bacteria susceptible to cationic antibiotic peptides. In comparison with Gram-negative bacteria, Gram-positive bacteria in general have much less zwitterionic phosphatidylethanolamine. However, they are known for producing aminoacylated phosphatidylglycerol (PG), especially positively charged L-lysyl-PG, which is catalyzed by lysyl-PG synthase MprF, which appears to have a broad range of specificity for L-aminoacyl transfer RNAs. In addition, many Gram-positive bacteria also have a dlt-gene-coded D-alanylation pathway for lipoteichoic acids and wall teichoic acids covalently attached to a glycolipid or peptidoglycan. D-Alanylation also masks the dominant negative charge of the phosphate-rich polymers of teichoic acids. Using mass spectrometry, we have recently observed that precursor scans in negative mode for deprotonated amino acid fragments were most sensitive for ester-linked amino acids. Such a scan for precursors generating an m/z 145 lysyl anion revealed lysyl-PG as well as an additional species 100 m/z units greater than lysyl-PG. This unexpected species corresponded precisely to the expected mass of N-succinylated lysyl-PG. Tandem mass spectrometry revealed a precise match to the fragmentation pattern of this putative new species. PG, lysyl-PG, and N-succinyl-lysyl-PG may form a complete loop of charge reversal from -1 to +1 and then back to -1. Analogous charge reversal by N-succinylation of lysine residues in the bacterial as well as eukaryotic proteomes has been recently discovered as a major posttranslational modification. Such modification in bacterial lipids is possibly catalyzed by an enzyme homologous to the enzymes that modify lysine residues in proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Metin Atila
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - George Katselis
- Canadian Centre for Health and Safety in Agriculture/Department of Medicine, Core Mass Spectrometry Facility, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Paulos Chumala
- Canadian Centre for Health and Safety in Agriculture/Department of Medicine, Core Mass Spectrometry Facility, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yu Luo
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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202
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A Selective Cyclic Peptidic Human SIRT5 Inhibitor. Molecules 2016; 21:molecules21091217. [PMID: 27626398 PMCID: PMC6272981 DOI: 10.3390/molecules21091217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022] Open
Abstract
In the current study, we discovered that a side chain-to-side chain cyclic pentapeptide harboring a central Nε-carboxyethyl-thiocarbamoyl-lysine residue behaved as a strong and selective (versus human SIRT1/2/3/6) inhibitor against human SIRT5-catalyzed deacylation reaction. This compound was also found to be proteolytically much more stable than its linear counterpart. This compound could be a valuable lead for developing stronger, selective, metabolically stable, and cell permeable human SIRT5 inhibitors.
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203
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Imai SI, Guarente L. It takes two to tango: NAD + and sirtuins in aging/longevity control. NPJ Aging Mech Dis 2016; 2:16017. [PMID: 28721271 PMCID: PMC5514996 DOI: 10.1038/npjamd.2016.17] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 12/14/2022] Open
Abstract
The coupling of nicotinamide adenine dinucleotide (NAD+) breakdown and protein deacylation is a unique feature of the family of proteins called ‘sirtuins.’ This intimate connection between NAD+ and sirtuins has an ancient origin and provides a mechanistic foundation that translates the regulation of energy metabolism into aging and longevity control in diverse organisms. Although the field of sirtuin research went through intensive controversies, an increasing number of recent studies have put those controversies to rest and fully established the significance of sirtuins as an evolutionarily conserved aging/longevity regulator. The tight connection between NAD+ and sirtuins is regulated at several different levels, adding further complexity to their coordination in metabolic and aging/longevity control. Interestingly, it has been demonstrated that NAD+ availability decreases over age, reducing sirtuin activities and affecting the communication between the nucleus and mitochondria at a cellular level and also between the hypothalamus and adipose tissue at a systemic level. These dynamic cellular and systemic processes likely contribute to the development of age-associated functional decline and the pathogenesis of diseases of aging. To mitigate these age-associated problems, supplementation of key NAD+ intermediates is currently drawing significant attention. In this review article, we will summarize these important aspects of the intimate connection between NAD+ and sirtuins in aging/longevity control.
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Affiliation(s)
- Shin-Ichiro Imai
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Leonard Guarente
- Department of Biology and Glenn Laboratories for the Science of Aging, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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204
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Hong Y, Cao X, Han Q, Yuan C, Zhang M, Han Y, Zhu C, Lin T, Lu K, Li H, Fu Z, Lin J. Proteome-wide analysis of lysine acetylation in adult Schistosoma japonicum worm. J Proteomics 2016; 148:202-12. [PMID: 27535354 DOI: 10.1016/j.jprot.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/30/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in schistosomes, immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry, was used to comprehensively characterize the lysine-acetylated proteins in this parasite. In total, 1109 acetylated proteins and 2393 acetylation sites in S. japonicum were identified, representing the largest acetylome yet reported in a parasite. In a bioinformatic analysis showed that these acetylated proteins were mainly enriched in the biological process categories of metabolism, gene expression, translation, and transport. The classification according to molecular function revealed that the largest class involved the catalytic activity of different enzymes, including oxidoreductase, transferase, and pyrophosphatase activities. Most of the acetylated proteins in the cellular component category occurred in the cytoplasm, membrane, cytoskeleton, and nucleus. These data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. SIGNIFICANCE Schistosomiasis is one of the world's most prevalent and neglected tropical parasitic zoonotic diseases, and it causes almost 200,000 deaths annually. To control and eradicate schistosomiasis, effective vaccines are urgently required, and drug targets that are essential for schistosome survival must be identified in fundamental studies of schistosome biology. Posttranslational modifications are complex, fundamental, and important mechanisms that regulate the physiological functions of organisms. Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in S. japonicum, we employ immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry to comprehensively characterize the lysine-acetylated proteins in this parasite. The results of our data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. Meanwhile, identifying the mechanisms and proteins targeted by acetylation may also provide a promising avenue for specific drug design and the development of sophisticated therapeutic strategies.
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Affiliation(s)
- Yang Hong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Xiaodan Cao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Qian Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Chunxiu Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Min Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan Province 471023, PR China
| | - Yanhui Han
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan Province 453003, PR China
| | - Chuangang Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Tao Lin
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, United States
| | - Ke Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Hao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Zhiqiang Fu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China.
| | - Jiaojiao Lin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, PR China.
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205
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Gao X, Hong H, Li WC, Yang L, Huang J, Xiao YL, Chen XY, Chen GY. Downregulation of Rubisco Activity by Non-enzymatic Acetylation of RbcL. MOLECULAR PLANT 2016; 9:1018-27. [PMID: 27109602 DOI: 10.1016/j.molp.2016.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 05/24/2023]
Abstract
Atmospheric carbon dioxide (CO2) is assimilated by the most abundant but sluggish enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Here we show that acetylation of lysine residues of the Rubisco large subunit (RbcL), including Lys201 and Lys334 in the active sites, may be an important mechanism in the regulation of Rubisco activities. It is well known that Lys201 reacts with CO2 for carbamylation, a prerequisite for both carboxylase and oxygenase activities of Rubisco, and Lys334 contacts with ribulose-1,5-bisphosphate (RuBP). The acetylation level of RbcL in plants is lower during the day and higher at night, inversely correlating with the Rubisco carboxylation activity. A search of the chloroplast proteome database did not reveal a canonical acetyltransferase; instead, we found that a plant-derived metabolite, 7-acetoxy-4-methylcoumarin (AMC), can non-enzymatically acetylate both native Rubisco and synthesized RbcL peptides spanning Lys334 or Lys201. Furthermore, lysine residues were modified by synthesized 4-methylumbelliferone esters with different electro- and stereo-substitutes, resulting in varied Rubisco activities. 1-Chloroethyl 4-methylcoumarin-7-yl carbonate (ClMC) could transfer the chloroethyl carbamate group to lysine residues of RbcL and completely inactivate Rubisco, whereas bis(4-methylcoumarin-7-yl) carbonate (BMC) improved Rubisco activity through increasing the level of Lys201 carbamylation. Our findings indicate that RbcL acetylation negatively regulates Rubisco activity, and metabolic derivatives can be designed to dissect and improve CO2 fixation efficiency of plants through lysine modification.
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Affiliation(s)
- Xiang Gao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Hui Hong
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Wei-Chao Li
- CAS Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Lili Yang
- Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Jirong Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China
| | - You-Li Xiao
- CAS Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 200032 Shanghai, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China.
| | - Gen-Yun Chen
- Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China.
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206
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 522] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
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207
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The Metabolic Impact on Histone Acetylation and Transcription in Ageing. Trends Biochem Sci 2016; 41:700-711. [PMID: 27283514 DOI: 10.1016/j.tibs.2016.05.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/09/2016] [Accepted: 05/13/2016] [Indexed: 12/13/2022]
Abstract
Loss of cellular homeostasis during aging results in altered tissue functions and leads to a general decline in fitness and, ultimately, death. As animals age, the control of gene expression, which is orchestrated by multiple epigenetic factors, degenerates. In parallel, metabolic activity and mitochondrial protein acetylation levels also change. These two hallmarks of aging are effectively linked through the accumulating evidence that histone acetylation patterns are susceptible to alterations in key metabolites such as acetyl-CoA and NAD(+), allowing chromatin to function as a sensor of cellular metabolism. In this review we discuss experimental data supporting these connections and provide a context for the possible medical and physiological relevance.
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208
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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209
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Zheng H, Wu J, Jin Z, Yan LJ. Protein Modifications as Manifestations of Hyperglycemic Glucotoxicity in Diabetes and Its Complications. BIOCHEMISTRY INSIGHTS 2016; 9:1-9. [PMID: 27042090 PMCID: PMC4807886 DOI: 10.4137/bci.s36141] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 02/07/2023]
Abstract
Diabetes and its complications are hyperglycemic toxicity diseases. Many metabolic pathways in this array of diseases become aberrant, which is accompanied with a variety of posttranslational protein modifications that in turn reflect diabetic glucotoxicity. In this review, we summarize some of the most widely studied protein modifications in diabetes and its complications. These modifications include glycation, carbonylation, nitration, cysteine S-nitrosylation, acetylation, sumoylation, ADP-ribosylation, O-GlcNAcylation, and succination. All these posttranslational modifications can be significantly attributed to oxidative stress and/or carbon stress induced by diabetic redox imbalance that is driven by activation of pathways, such as the polyol pathway and the ADP-ribosylation pathway. Exploring the nature of these modifications should facilitate our understanding of the pathological mechanisms of diabetes and its associated complications.
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Affiliation(s)
- Hong Zheng
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, UNT Health Science Center, Fort Worth, TX, USA.; Department of Basic Theory of Traditional Chinese Medicine, College of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jinzi Wu
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, UNT Health Science Center, Fort Worth, TX, USA
| | - Zhen Jin
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, UNT Health Science Center, Fort Worth, TX, USA
| | - Liang-Jun Yan
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, UNT Health Science Center, Fort Worth, TX, USA
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210
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Abstract
Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.
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Affiliation(s)
- Wolfgang Fischle
- King Abdullah University of Science and Technology (KAUST), Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
- Max Planck Institute for Biophysical Chemistry, Laboratory of Chromatin Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty
Institute of Biochemistry (IFIB), University of Tübingen, Hoppe-Seyler-Str.
4, 72076 Tübingen, Germany
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211
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Succinate, an intermediate in metabolism, signal transduction, ROS, hypoxia, and tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1086-1101. [PMID: 26971832 DOI: 10.1016/j.bbabio.2016.03.012] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/06/2016] [Accepted: 03/07/2016] [Indexed: 12/31/2022]
Abstract
Succinate is an important metabolite at the cross-road of several metabolic pathways, also involved in the formation and elimination of reactive oxygen species. However, it is becoming increasingly apparent that its realm extends to epigenetics, tumorigenesis, signal transduction, endo- and paracrine modulation and inflammation. Here we review the pathways encompassing succinate as a metabolite or a signal and how these may interact in normal and pathological conditions.(1).
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212
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Huang Y, Liu J, Yan L, Zheng W. Simple N ε -thioacetyl-lysine-containing cyclic peptides exhibiting highly potent sirtuin inhibition. Bioorg Med Chem Lett 2016; 26:1612-1617. [DOI: 10.1016/j.bmcl.2016.01.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/26/2016] [Accepted: 01/30/2016] [Indexed: 01/05/2023]
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213
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Seidel J, Klockenbusch C, Schwarzer D. Investigating Deformylase and Deacylase Activity of Mammalian and Bacterial Sirtuins. Chembiochem 2016; 17:398-402. [DOI: 10.1002/cbic.201500611] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Cordula Klockenbusch
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
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214
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Abstract
The purpose of this review is to provide an overview of the complexity of the epigenetic target space. Chemical modifications of histones and nucleic acids constitute a key epigenetic mechanism. Whereas modifications such as methylation and acetylation are well-known, there are many additional, less explored modifications described here. The writers, readers and erasers of such diverse modifications, which constitute a major portion of the potential epigenetic target space, are discussed, in addition to the various other protein families that do not fall under these three categories. Finally, disease relevance and druggability of epigenetic targets are discussed with concluding remarks about the richness and diversity they will provide for future targeted therapies.
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Affiliation(s)
- Vineet Pande
- Discovery Sciences, Janssen-Pharmaceutical Companies of Johnson & Johnson , Turnhoutseweg 30, Beerse 2340, Belgium
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215
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Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends Biochem Sci 2016; 41:231-244. [PMID: 26822488 DOI: 10.1016/j.tibs.2015.12.006] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022]
Abstract
Reversible protein acetylation is a major regulatory mechanism for controlling protein function. Through genetic manipulations, dietary perturbations, and new proteomic technologies, the diverse functions of protein acetylation are coming into focus. Protein acetylation in mitochondria has taken center stage, revealing that 63% of mitochondrially localized proteins contain lysine acetylation sites. We summarize the field and discuss salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylation, nonenzymatic acetylation, and molecular models for regulatory acetylations that display high and low stoichiometry.
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216
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Galleano I, Schiedel M, Jung M, Madsen AS, Olsen CA. A Continuous, Fluorogenic Sirtuin 2 Deacylase Assay: Substrate Screening and Inhibitor Evaluation. J Med Chem 2016; 59:1021-31. [PMID: 26788965 DOI: 10.1021/acs.jmedchem.5b01532] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sirtuins are important regulators of lysine acylation, which is implicated in cellular metabolism and transcriptional control. This makes the sirtuin class of enzymes interesting targets for development of small molecule probes with pharmaceutical potential. To achieve detailed profiling and kinetic insight regarding sirtuin inhibitors, it is important to have access to efficient assays. In this work, we report readily synthesized fluorogenic substrates enabling enzyme-economical evaluation of SIRT2 inhibitors in a continuous assay format as well as evaluation of the properties of SIRT2 as a long chain deacylase enzyme. Novel enzymatic activities of SIRT2 were thus established in vitro, which warrant further investigation, and two known inhibitors, suramin and SirReal2, were profiled against substrates containing ε-N-acyllysine modifications of varying length.
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Affiliation(s)
- Iacopo Galleano
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Matthias Schiedel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
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217
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Valente S, Mellini P, Spallotta F, Carafa V, Nebbioso A, Polletta L, Carnevale I, Saladini S, Trisciuoglio D, Gabellini C, Tardugno M, Zwergel C, Cencioni C, Atlante S, Moniot S, Steegborn C, Budriesi R, Tafani M, Del Bufalo D, Altucci L, Gaetano C, Mai A. 1,4-Dihydropyridines Active on the SIRT1/AMPK Pathway Ameliorate Skin Repair and Mitochondrial Function and Exhibit Inhibition of Proliferation in Cancer Cells. J Med Chem 2016; 59:1471-91. [DOI: 10.1021/acs.jmedchem.5b01117] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sergio Valente
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.
le A. Moro 5, 00185 Rome, Italy
| | - Paolo Mellini
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.
le A. Moro 5, 00185 Rome, Italy
| | - Francesco Spallotta
- Division
of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Vincenzo Carafa
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Angela Nebbioso
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Lucia Polletta
- Department
of Experimental Medicine, Sapienza University of Rome, Viale Regina
Elena 324, 00161 Rome, Italy
| | - Ilaria Carnevale
- Department
of Experimental Medicine, Sapienza University of Rome, Viale Regina
Elena 324, 00161 Rome, Italy
| | - Serena Saladini
- Department
of Experimental Medicine, Sapienza University of Rome, Viale Regina
Elena 324, 00161 Rome, Italy
| | - Daniela Trisciuoglio
- Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Chiara Gabellini
- Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Maria Tardugno
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.
le A. Moro 5, 00185 Rome, Italy
| | - Clemens Zwergel
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.
le A. Moro 5, 00185 Rome, Italy
| | - Chiara Cencioni
- Division
of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Sandra Atlante
- Division
of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Sébastien Moniot
- Department
of Biochemistry, University of Bayreuth; 95447 Bayreuth, Germany
| | - Clemens Steegborn
- Department
of Biochemistry, University of Bayreuth; 95447 Bayreuth, Germany
| | - Roberta Budriesi
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Zamboni
33, 40126 Bologna, Italy
| | - Marco Tafani
- Department
of Experimental Medicine, Sapienza University of Rome, Viale Regina
Elena 324, 00161 Rome, Italy
| | - Donatella Del Bufalo
- Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Lucia Altucci
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Vico L. De Crecchio 7, 80138 Naples, Italy
- Institute of Genetics and Biophysics, IGB, Adriano Buzzati Traverso, Via P. Castellino 111, 80131 Naples, Italy
| | - Carlo Gaetano
- Division
of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.
le A. Moro 5, 00185 Rome, Italy
- Pasteur
Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
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218
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Luo X, Wu J, Jing S, Yan LJ. Hyperglycemic Stress and Carbon Stress in Diabetic Glucotoxicity. Aging Dis 2016; 7:90-110. [PMID: 26816666 DOI: 10.14336/ad.2015.0702] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/02/2015] [Indexed: 12/16/2022] Open
Abstract
Diabetes and its complications are caused by chronic glucotoxicity driven by persistent hyperglycemia. In this article, we review the mechanisms of diabetic glucotoxicity by focusing mainly on hyperglycemic stress and carbon stress. Mechanisms of hyperglycemic stress include reductive stress or pseudohypoxic stress caused by redox imbalance between NADH and NAD(+) driven by activation of both the polyol pathway and poly ADP ribose polymerase; the hexosamine pathway; the advanced glycation end products pathway; the protein kinase C activation pathway; and the enediol formation pathway. Mechanisms of carbon stress include excess production of acetyl-CoA that can over-acetylate a proteome and excess production of fumarate that can over-succinate a proteome; both of which can increase glucotoxicity in diabetes. For hyperglycemia stress, we also discuss the possible role of mitochondrial complex I in diabetes as this complex, in charge of NAD(+) regeneration, can make more reactive oxygen species (ROS) in the presence of excess NADH. For carbon stress, we also discuss the role of sirtuins in diabetes as they are deacetylases that can reverse protein acetylation thereby attenuating diabetic glucotoxicity and improving glucose metabolism. It is our belief that targeting some of the stress pathways discussed in this article may provide new therapeutic strategies for treatment of diabetes and its complications.
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Affiliation(s)
- Xiaoting Luo
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; 2 Department of Biochemistry and Molecular Biology, Gannan Medical University, Ganzhou, Jiangxi province, China, 341000
| | - Jinzi Wu
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Siqun Jing
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; 3 College of Life Sciences and Technology, Xinjiang University, Urumqi, Xinjiang, China, 830046
| | - Liang-Jun Yan
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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219
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Abstract
Six side chain-to-side chain cyclic pentapeptides (4–9) harboring a central Nε-dodecyl (or tetradecyl)-thiocarbamoyl-lysine residue all behaved as highly potent (IC50 ∼ 256–495 nM) inhibitors against human SIRT6-catalyzed deacylation reaction.
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Affiliation(s)
- Jiajia Liu
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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220
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Abstract
Proteins are acylated by a variety of metabolites that regulates many important cellular pathways in all kingdoms of life. Acyl groups in cells can vary in structure from the smallest unit, acetate, to modified long-chain fatty acids, all of which can be activated and covalently attached to diverse amino acid side chains and consequently modulate protein function. For example, acetylation of Lys residues can alter the charge state of proteins and generate new recognition elements for protein-protein interactions. Alternatively, long-chain fatty-acylation targets proteins to membranes and enables spatial control of cell signalling. To facilitate the analysis of protein acylation in biology, acyl analogues bearing alkyne or azide tags have been developed that enable fluorescent imaging and proteomic profiling of modified proteins using bioorthogonal ligation methods. Herein, we summarize the currently available acylation chemical reporters and highlight their utility to discover and quantify the roles of protein acylation in biology.
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221
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Not low hanging but still sweet: Metabolic proteomes in cardiovascular disease. J Mol Cell Cardiol 2015; 90:70-3. [PMID: 26611885 DOI: 10.1016/j.yjmcc.2015.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/22/2022]
Abstract
The application of proteomics in biology and medicine has reached a moment of truth. The demand of biologists for transformative insights into how cells work, plus the mandate of basic science research to ultimately impact clinical medicine, crystallize as a test on the rigor and reproducibility of any 'omics measurement. Studies like that by Boylston et al. indicate that proteomics can pass that test.
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222
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Griffin TM, Humphries KM, Kinter M, Lim HY, Szweda LI. Nutrient sensing and utilization: Getting to the heart of metabolic flexibility. Biochimie 2015; 124:74-83. [PMID: 26476002 DOI: 10.1016/j.biochi.2015.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/12/2015] [Indexed: 02/07/2023]
Abstract
A central feature of obesity-related cardiometabolic diseases is the impaired ability to transition between fatty acid and glucose metabolism. This impairment, referred to as "metabolic inflexibility", occurs in a number of tissues, including the heart. Although the heart normally prefers to metabolize fatty acids over glucose, the inability to upregulate glucose metabolism under energetically demanding conditions contributes to a pathological state involving energy imbalance, impaired contractility, and post-translational protein modifications. This review discusses pathophysiologic processes that contribute to cardiac metabolic inflexibility and speculates on the potential physiologic origins that lead to the current state of cardiometabolic disease in an obesogenic environment.
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Affiliation(s)
- Timothy M Griffin
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Kenneth M Humphries
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Michael Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Hui-Ying Lim
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Luke I Szweda
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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223
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Pehar M, Ball LE, Sharma DR, Harlan BA, Comte-Walters S, Neely BA, Vargas MR. Changes in Protein Expression and Lysine Acetylation Induced by Decreased Glutathione Levels in Astrocytes. Mol Cell Proteomics 2015; 15:493-505. [PMID: 26486419 DOI: 10.1074/mcp.m115.049288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 01/13/2023] Open
Abstract
Astrocytes and neurons form a highly specialized functional unit, and the loss or gain of astrocytic functions can influence the initiation and progression of different neurodegenerative diseases. Neurons depend on the antioxidant protection provided by neighboring astrocytes. Glutathione (γ-l-glutamyl-l-cysteinyl-glycine) is a major component of the antioxidant system that defends cells against the toxic effects of reactive oxygen/nitrogen species. A decline in glutathione levels has been observed in aging and neurodegenerative diseases, and it aggravates the pathology in an amyotrophic lateral sclerosis-mouse model. Using a SILAC-based quantitative proteomic approach, we analyzed changes in global protein expression and lysine acetylation in primary astrocyte cultures obtained from wild-type mice or those deficient in the glutamate-cysteine ligase modifier subunit (GCLM). GCLM knockout astrocytes display an ∼80% reduction in total glutathione levels. We identified potential molecular targets and novel sites of acetylation that are affected by the chronic decrease in glutathione levels and observed a response mediated by Nrf2 activation. In addition, sequence analysis of peptides displaying increased acetylation in GCLM knockout astrocytes revealed an enrichment of cysteine residues in the vicinity of the acetylation site, which suggests potential crosstalk between lysine-acetylation and cysteine modification. Regulation of several metabolic and antioxidant pathways was observed at the level of protein expression and lysine acetylation, revealing a coordinated response involving transcriptional and posttranslational regulation.
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Affiliation(s)
- Mariana Pehar
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425.
| | - Lauren E Ball
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425
| | - Deep R Sharma
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425
| | - Benjamin A Harlan
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425
| | - Susana Comte-Walters
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425
| | - Benjamin A Neely
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425
| | - Marcelo R Vargas
- From the ¶Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425.
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224
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He Y, Yan L, Zang W, Zheng W. Novel sirtuin inhibitory warheads derived from the N(ε)-acetyl-lysine analog L-2-amino-7-carboxamidoheptanoic acid. Org Biomol Chem 2015; 13:10442-50. [PMID: 26418815 DOI: 10.1039/c5ob01721a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Built upon the catalytic mechanism-based pan-SIRT1/2/3 inhibitory warhead L-2-amino-7-carboxamidoheptanoic acid (L-ACAH, a close structural analog of N(ε)-acetyl-lysine) that our laboratory discovered recently, in the current study, its carboxamide NH2-ethylated analog was found to be a ∼2.4-6.6-fold stronger SIRT1/2/3 inhibitory warhead than L-ACAH. Carboxamide NH2-dodecylated and carboxymethylated analogs of L-ACAH were also identified as potent SIRT6 and SIRT5 inhibitory warheads, respectively.
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Affiliation(s)
- Yanhua He
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, P. R. China.
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225
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Boylston JA, Sun J, Chen Y, Gucek M, Sack MN, Murphy E. Characterization of the cardiac succinylome and its role in ischemia-reperfusion injury. J Mol Cell Cardiol 2015; 88:73-81. [PMID: 26388266 DOI: 10.1016/j.yjmcc.2015.09.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022]
Abstract
Succinylation refers to modification of lysine residues with succinyl groups donated by succinyl-CoA. Sirtuin5 (Sirt5) is a mitochondrial NAD(+)-dependent deacylase that catalyzes the removal of succinyl groups from proteins. Sirt5 and protein succinylation are conserved across species, suggesting functional importance of the modification. Sirt5 loss impacts liver metabolism but the role of succinylation in the heart has not been explored. We combined affinity enrichment with proteomics and mass spectrometry to analyze total succinylated lysine content of mitochondria isolated from WT and Sirt5(-/-) mouse hearts. We identified 887 succinylated lysine residues in 184 proteins. 44 peptides (5 proteins) occurred uniquely in WT samples, 289 (46 proteins) in Sirt5(-/-) samples, and 554 (133 proteins) were common to both groups. The 46 unique proteins in Sirt5(-/-) heart participate in metabolic processes such as fatty acid β-oxidation (Eci2) and branched chain amino acid catabolism, and include respiratory chain proteins (Ndufa7, 12, 13, Dhsa). We performed label-free analysis of the peptides common to WT and Sirt5(-/-) hearts. 16 peptides from 9 proteins were significantly increased in Sirt5(-/-) by at least 30%. The adenine nucleotide transporter 1 showed the highest increase in succinylation in Sirt5(-/-) (108.4 fold). The data indicate that succinylation is widespread in the heart and enriched in metabolic pathways. We examined whether the loss of Sirt5 would impact ischemia-reperfusion (I/R) injury and we found an increase in infarct size in Sirt5(-/-) hearts compared to WT littermates (68.5(+)/-1.1% Sirt5(-/-) vs 39.6(+)/(-) 6.8% WT) following 20min of ischemia and 90-min reperfusion. We further demonstrate that I/R injury in Sirt5(-/-) heart is restored to WT levels by pretreatment with dimethyl malonate, a competitive inhibitor of succinate dehydrogenase (SDH), implicating alteration in SDH activity as causative of the injury.
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Affiliation(s)
| | - Junhui Sun
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Yong Chen
- Proteomics Core Facility, NHLBI, NIH, Bethesda, MD, United States
| | - Marjan Gucek
- Proteomics Core Facility, NHLBI, NIH, Bethesda, MD, United States
| | - Michael N Sack
- Center for Molecular Medicine, NHLBI, NIH, Bethesda, MD, United States
| | - Elizabeth Murphy
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States.
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226
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Affiliation(s)
- David B Lombard
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA Institute of Gerontology, University of Michigan, Ann Arbor, MI, USA
| | - Banaja P Dash
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Surinder Kumar
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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227
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Piedrafita G, Keller MA, Ralser M. The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions. Biomolecules 2015; 5:2101-22. [PMID: 26378592 PMCID: PMC4598790 DOI: 10.3390/biom5032101] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 11/16/2022] Open
Abstract
Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease—age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW1 7AA, UK.
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228
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Weinert BT, Moustafa T, Iesmantavicius V, Zechner R, Choudhary C. Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions. EMBO J 2015; 34:2620-32. [PMID: 26358839 PMCID: PMC4641529 DOI: 10.15252/embj.201591271] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
Acetylation is frequently detected on mitochondrial enzymes, and the sirtuin deacetylase SIRT3 is thought to regulate metabolism by deacetylating mitochondrial proteins. However, the stoichiometry of acetylation has not been studied and is important for understanding whether SIRT3 regulates or suppresses acetylation. Using quantitative mass spectrometry, we measured acetylation stoichiometry in mouse liver tissue and found that SIRT3 suppressed acetylation to a very low stoichiometry at its target sites. By examining acetylation changes in the liver, heart, brain, and brown adipose tissue of fasted mice, we found that SIRT3‐targeted sites were mostly unaffected by fasting, a dietary manipulation that is thought to regulate metabolism through SIRT3‐dependent deacetylation. Globally increased mitochondrial acetylation in fasted liver tissue, higher stoichiometry at mitochondrial acetylation sites, and greater sensitivity of SIRT3‐targeted sites to chemical acetylation in vitro and fasting‐induced acetylation in vivo, suggest a nonenzymatic mechanism of acetylation. Our data indicate that most mitochondrial acetylation occurs as a low‐level nonenzymatic protein lesion and that SIRT3 functions as a protein repair factor that removes acetylation lesions from lysine residues.
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Affiliation(s)
- Brian T Weinert
- The NNF Center for Protein Research, Faculty of Health Sciences University of Copenhagen, Copenhagen, Denmark
| | - Tarek Moustafa
- Division of Gastroenterology and Hepatology, Medical University Graz, Graz, Austria
| | - Vytautas Iesmantavicius
- The NNF Center for Protein Research, Faculty of Health Sciences University of Copenhagen, Copenhagen, Denmark
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Chunaram Choudhary
- The NNF Center for Protein Research, Faculty of Health Sciences University of Copenhagen, Copenhagen, Denmark
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229
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Lantier L, Williams AS, Williams IM, Yang KK, Bracy DP, Goelzer M, James FD, Gius D, Wasserman DH. SIRT3 Is Crucial for Maintaining Skeletal Muscle Insulin Action and Protects Against Severe Insulin Resistance in High-Fat-Fed Mice. Diabetes 2015; 64:3081-92. [PMID: 25948682 PMCID: PMC4542443 DOI: 10.2337/db14-1810] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
Abstract
Protein hyperacetylation is associated with glucose intolerance and insulin resistance, suggesting that the enzymes regulating the acetylome play a role in this pathological process. Sirtuin 3 (SIRT3), the primary mitochondrial deacetylase, has been linked to energy homeostasis. Thus, it is hypothesized that the dysregulation of the mitochondrial acetylation state, via genetic deletion of SIRT3, will amplify the deleterious effects of a high-fat diet (HFD). Hyperinsulinemic-euglycemic clamp experiments show, for the first time, that mice lacking SIRT3 exhibit increased insulin resistance due to defects in skeletal muscle glucose uptake. Permeabilized muscle fibers from HFD-fed SIRT3 knockout (KO) mice showed that tricarboxylic acid cycle substrate-based respiration is decreased while fatty acid-based respiration is increased, reflecting a fuel switch from glucose to fatty acids. Consistent with reduced muscle glucose uptake, hexokinase II (HKII) binding to the mitochondria is decreased in muscle from HFD-fed SIRT3 KO mice, suggesting decreased HKII activity. These results show that the absence of SIRT3 in HFD-fed mice causes profound impairments in insulin-stimulated muscle glucose uptake, creating an increased reliance on fatty acids. Insulin action was not impaired in the lean SIRT3 KO mice. This suggests that SIRT3 protects against dietary insulin resistance by facilitating glucose disposal and mitochondrial function.
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Affiliation(s)
- Louise Lantier
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN
| | - Ashley S Williams
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Ian M Williams
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Karen K Yang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Deanna P Bracy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Mickael Goelzer
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Freyja D James
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - David Gius
- Departments of Radiation Oncology and Pharmacology and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - David H Wasserman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN
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230
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McDonnell E, Peterson BS, Bomze HM, Hirschey MD. SIRT3 regulates progression and development of diseases of aging. Trends Endocrinol Metab 2015; 26:486-492. [PMID: 26138757 PMCID: PMC4558250 DOI: 10.1016/j.tem.2015.06.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
The mitochondrial sirtuin SIRT3 is a protein deacylase that influences almost every major aspect of mitochondrial biology, including nutrient oxidation, ATP generation, reactive oxygen species (ROS) detoxification, mitochondrial dynamics, and the mitochondrial unfolded protein response (UPR). Interestingly, mice lacking SIRT3 (SIRT3KO), either spontaneously or when crossed with mouse models of disease, develop several diseases of aging at an accelerated pace, such as cancer, metabolic syndrome, cardiovascular disease, and neurodegenerative diseases, and, thus, might be a valuable model of accelerated aging. In this review, we discuss functions of SIRT3 in pathways involved in diseases of aging and how the lack of SIRT3 might accelerate the aging process. We also suggest that further studies on SIRT3 will help uncover important new pathways driving the aging process.
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Affiliation(s)
- Eoin McDonnell
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Brett S Peterson
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Howard M Bomze
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
- Departments of Medicine and Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA
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231
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Affiliation(s)
- Frank K Huynh
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Deborah M Muoio
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC Sarah W. Stedman Nutrition and Metabolism Center and Departments of Medicine and Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC Sarah W. Stedman Nutrition and Metabolism Center and Departments of Medicine and Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC
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232
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Colak G, Pougovkina O, Dai L, Tan M, Te Brinke H, Huang H, Cheng Z, Park J, Wan X, Liu X, Yue WW, Wanders RJA, Locasale JW, Lombard DB, de Boer VCJ, Zhao Y. Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation. Mol Cell Proteomics 2015; 14:3056-71. [PMID: 26320211 DOI: 10.1074/mcp.m115.048850] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 11/06/2022] Open
Abstract
The protein substrates of sirtuin 5-regulated lysine malonylation (Kmal) remain unknown, hindering its functional analysis. In this study, we carried out proteomic screening, which identified 4042 Kmal sites on 1426 proteins in mouse liver and 4943 Kmal sites on 1822 proteins in human fibroblasts. Increased malonyl-CoA levels in malonyl-CoA decarboxylase (MCD)-deficient cells induces Kmal levels in substrate proteins. We identified 461 Kmal sites showing more than a 2-fold increase in response to MCD deficiency as well as 1452 Kmal sites detected only in MCD-/- fibroblast but not MCD+/+ cells, suggesting a pathogenic role of Kmal in MCD deficiency. Cells with increased lysine malonylation displayed impaired mitochondrial function and fatty acid oxidation, suggesting that lysine malonylation plays a role in pathophysiology of malonic aciduria. Our study establishes an association between Kmal and a genetic disease and offers a rich resource for elucidating the contribution of the Kmal pathway and malonyl-CoA to cellular physiology and human diseases.
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Affiliation(s)
- Gozde Colak
- From the Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois 60637
| | - Olga Pougovkina
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and
| | - Lunzhi Dai
- From the Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois 60637
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Heleen Te Brinke
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and
| | - He Huang
- From the Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois 60637
| | | | - Jeongsoon Park
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, Michigan 48109
| | - Xuelian Wan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaojing Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, and
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ronald J A Wanders
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Department of Pediatrics, Emma's Children Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Jason W Locasale
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, and
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, Michigan 48109
| | - Vincent C J de Boer
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Department of Pediatrics, Emma's Children Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands,
| | - Yingming Zhao
- From the Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois 60637, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,
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233
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Mitochondrial Impairment May Increase Cellular NAD(P)H: Resazurin Oxidoreductase Activity, Perturbing the NAD(P)H-Based Viability Assays. Cells 2015; 4:427-51. [PMID: 26308058 PMCID: PMC4588044 DOI: 10.3390/cells4030427] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 01/10/2023] Open
Abstract
Cellular NAD(P)H-dependent oxidoreductase activity with artificial dyes (NAD(P)H-OR) is an indicator of viability, as the cellular redox state is important for biosynthesis and antioxidant defense. However, high NAD(P)H due to impaired mitochondrial oxidation, known as reductive stress, should increase NAD(P)H-OR yet perturb viability. To better understand this complex behavior, we assayed NAD(P)H-OR with resazurin (Alamar Blue) in glioblastoma cell lines U87 and T98G, treated with inhibitors of central metabolism, oxythiamin, and phosphonate analogs of 2-oxo acids. Targeting the thiamin diphosphate (ThDP)-dependent enzymes, the inhibitors are known to decrease the NAD(P)H production in the pentose phosphate shuttle and/or upon mitochondrial oxidation of 2-oxo acids. Nevertheless, the inhibitors elevated NAD(P)H-OR with resazurin in a time- and concentration-dependent manner, suggesting impaired NAD(P)H oxidation rather than increased viability. In particular, inhibition of the ThDP-dependent enzymes affects metabolism of malate, which mediates mitochondrial oxidation of cytosolic NAD(P)H. We showed that oxythiamin not only inhibited mitochondrial 2-oxo acid dehydrogenases, but also induced cell-specific changes in glutamate and malate dehydrogenases and/or malic enzyme. As a result, inhibition of the 2-oxo acid dehydrogenases compromises mitochondrial metabolism, with the dysregulated electron fluxes leading to increases in cellular NAD(P)H-OR. Perturbed mitochondrial oxidation of NAD(P)H may thus complicate the NAD(P)H-based viability assay.
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234
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Zang W, Hao Y, Wang Z, Zheng W. Novel thiourea-based sirtuin inhibitory warheads. Bioorg Med Chem Lett 2015; 25:3319-24. [PMID: 26081291 PMCID: PMC4636340 DOI: 10.1016/j.bmcl.2015.05.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/12/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
N(ε)-Thiocarbamoyl-lysine was recently demonstrated by our laboratory to be a potent catalytic mechanism-based SIRT1/2/3 inhibitory warhead, in the current study, among the prepared analogs of N(ε)-thiocarbamoyl-lysine with its terminal NH2 mono-substituted with alkyl and aryl groups, we found that N(ε)-methyl-thiocarbamoyl-lysine and N(ε)-carboxyethyl-thiocarbamoyl-lysine, respectively, also behaved as strong inhibitory warheads against SIRT1/2/3 and SIRT5, typical deacetylases and deacylase in the human sirtuin family, respectively. Moreover, N(ε)-methyl-thiocarbamoyl-lysine was found in the study to be a ∼ 2.5-18.4-fold stronger SIRT1/2/3 inhibitory warhead than its lead warhead N(ε)-thiocarbamoyl-lysine.
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Affiliation(s)
- Wenwen Zang
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Yujun Hao
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Zhenghe Wang
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China.
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235
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Harris PS, Roy SR, Coughlan C, Orlicky DJ, Liang Y, Shearn CT, Roede JR, Fritz KS. Chronic ethanol consumption induces mitochondrial protein acetylation and oxidative stress in the kidney. Redox Biol 2015; 6:33-40. [PMID: 26177469 PMCID: PMC4511634 DOI: 10.1016/j.redox.2015.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/20/2022] Open
Abstract
In this study, we present the novel findings that chronic ethanol consumption induces mitochondrial protein hyperacetylation in the kidney and correlates with significantly increased renal oxidative stress. A major proteomic footprint of alcoholic liver disease (ALD) is an increase in hepatic mitochondrial protein acetylation. Protein hyperacetylation has been shown to alter enzymatic function of numerous proteins and plays a role in regulating metabolic processes. Renal mitochondrial targets of hyperacetylation include numerous metabolic and antioxidant pathways, such as lipid metabolism, oxidative phosphorylation, and amino acid metabolism, as well as glutathione and thioredoxin pathways. Disruption of protein lysine acetylation has the potential to impair renal function through metabolic dysregulation and decreased antioxidant capacity. Due to a significant elevation in ethanol-mediated renal oxidative stress, we highlight the acetylation of superoxide dismutase, peroxiredoxins, glutathione reductase, and glutathione transferase enzymes. Since oxidative stress is a known factor in ethanol-induced nephrotoxicity, we examined biochemical markers of protein hyperacetylation and oxidative stress. Our results demonstrate increased protein acetylation concurrent with depleted glutathione, altered Cys redox potential, and the presence of 4-HNE protein modifications in our 6-week model of early-stage alcoholic nephrotoxicity. These findings support the hypothesis that ethanol metabolism causes an influx of mitochondrial metabolic substrate, resulting in mitochondrial protein hyperacetylation with the potential to impact mitochondrial metabolic and antioxidant processes. Chronic ethanol metabolism induces mitochondrial protein hyperacetylation in the kidney. Ethanol-induced hyperacetylation occurs on metabolic and antioxidant proteins. The onset of renal oxidative stress correlates with mitochondrial protein hyperacetylation.
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Affiliation(s)
- Peter S Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Samantha R Roy
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Christina Coughlan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Yongliang Liang
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Colin T Shearn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - James R Roede
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
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236
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Gut P, Zweckstetter M, Banati RB. Lost in translocation: the functions of the 18-kD translocator protein. Trends Endocrinol Metab 2015; 26:349-56. [PMID: 26026242 PMCID: PMC5654500 DOI: 10.1016/j.tem.2015.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 01/29/2023]
Abstract
Research spanning nearly four decades has assigned to the translocator protein (18 kDa) (TSPO) a critical role, among others, in the mitochondrial import of cholesterol, the subsequent steps of (neuro)steroid production, and systemic endocrine regulation, with implications for the pathophysiology of immune, inflammatory, neurodegenerative, and psychiatric as well as neoplastic diseases. Recent knockout studies in mice unexpectedly report normal or latent phenotypes, raising doubts about the protein's role in steroidogenesis and other previously postulated functions and challenging the validity of earlier data on the selectivity of TSPO-binding drugs. Here we provide a synthesis of the current debate from a structural and molecular biology perspective, discuss the limits of inference in loss-of-function (gene knockout) studies, and suggest new functions of TSPO.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Bâtiment H, 1015 Lausanne, Switzerland
| | - Markus Zweckstetter
- Max-Planck-Institut für Biophysikalische Chemie, 37077 Göttingen, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37077 Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany
| | - Richard B Banati
- Life Sciences, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia; National Imaging Facility and Ramaciotti Centre for Brain Imaging, Brain and Mind Research Institute, Faculty of Health Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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237
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Fernandes J, Weddle A, Kinter CS, Humphries KM, Mather T, Szweda LI, Kinter M. Lysine Acetylation Activates Mitochondrial Aconitase in the Heart. Biochemistry 2015; 54:4008-18. [PMID: 26061789 DOI: 10.1021/acs.biochem.5b00375] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput proteomics studies have identified several thousand acetylation sites on more than 1000 proteins. Mitochondrial aconitase, the Krebs cycle enzyme that converts citrate to isocitrate, has been identified in many of these reports. Acetylated mitochondrial aconitase has also been identified as a target for sirtuin 3 (SIRT3)-catalyzed deacetylation. However, the functional significance of mitochondrial aconitase acetylation has not been determined. Using in vitro strategies, mass spectrometric analyses, and an in vivo mouse model of obesity, we found a significant acetylation-dependent activation of aconitase. Isolated heart mitochondria subjected to in vitro chemical acetylation with either acetic anhydride or acetyl-coenzyme A resulted in increased aconitase activity that was reversed with SIRT3 treatment. Quantitative mass spectrometry was used to measure acetylation at 21 lysine residues and revealed significant increases with both in vitro treatments. A high-fat diet (60% of kilocalories from fat) was used as an in vivo model and also showed significantly increased mitochondrial aconitase activity without changes in protein level. The high-fat diet also produced an increased level of aconitase acetylation at multiple sites as measured by the quantitative mass spectrometry assays. Treatment of isolated mitochondria from these mice with SIRT3 abolished the high-fat diet-induced activation of aconitase and reduced acetylation. Finally, kinetic analyses found that the increase in activity was a result of increased maximal velocity, and molecular modeling suggests the potential for acetylation at K144 to perturb the tertiary structure of the enzyme. The results of this study reveal a novel activation of mitochondrial aconitase by acetylation.
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Affiliation(s)
- Jolyn Fernandes
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States.,‡Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Alexis Weddle
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Caroline S Kinter
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Kenneth M Humphries
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States.,‡Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.,∥Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Timothy Mather
- ‡Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.,§Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Luke I Szweda
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States.,‡Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.,∥Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Michael Kinter
- †Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States.,∥Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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238
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Feldman JL, Dittenhafer-Reed KE, Kudo N, Thelen JN, Ito A, Yoshida M, Denu JM. Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation. Biochemistry 2015; 54:3037-3050. [PMID: 25897714 DOI: 10.1021/acs.biochem.5b00150] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Acylation of lysine is an important protein modification regulating diverse biological processes. It was recently demonstrated that members of the human Sirtuin family are capable of catalyzing long chain deacylation, in addition to the well-known NAD(+)-dependent deacetylation activity [Feldman, J. L., Baeza, J., and Denu, J. M. (2013) J. Biol. Chem. 288, 31350-31356]. Here we provide a detailed kinetic and structural analysis that describes the interdependence of NAD(+)-binding and acyl-group selectivity for a diverse series of human Sirtuins, SIRT1-SIRT3 and SIRT6. Steady-state and rapid-quench kinetic analyses indicated that differences in NAD(+) saturation and susceptibility to nicotinamide inhibition reflect unique kinetic behavior displayed by each Sirtuin and depend on acyl substrate chain length. Though the rate of nucleophilic attack of the 2'-hydroxyl on the C1'-O-alkylimidate intermediate varies with acyl substrate chain length, this step remains rate-determining for SIRT2 and SIRT3; however, for SIRT6, this step is no longer rate-limiting for long chain substrates. Cocrystallization of SIRT2 with myristoylated peptide and NAD(+) yielded a co-complex structure with reaction product 2'-O-myristoyl-ADP-ribose, revealing a latent hydrophobic cavity to accommodate the long chain acyl group, and suggesting a general mechanism for long chain deacylation. Comparing two separately determined co-complex structures containing either a myristoylated peptide or 2'-O-myristoyl-ADP-ribose indicates there are conformational changes at the myristoyl-ribose linkage with minimal structural differences in the enzyme active site. During the deacylation reaction, the fatty acyl group is held in a relatively fixed position. We describe a kinetic and structural model to explain how various Sirtuins display unique acyl substrate preferences and how different reaction kinetics influence NAD(+) dependence. The biological implications are discussed.
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Affiliation(s)
- Jessica L Feldman
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | | | - Norio Kudo
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Julie N Thelen
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan.,Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan.,JST, CREST Research Project, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715
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239
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Kumar S, Lombard DB. Mitochondrial sirtuins and their relationships with metabolic disease and cancer. Antioxid Redox Signal 2015; 22:1060-77. [PMID: 25545135 PMCID: PMC4389911 DOI: 10.1089/ars.2014.6213] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE Maintenance of metabolic homeostasis is critical for cellular and organismal health. Proper regulation of mitochondrial functions represents a crucial element of overall metabolic homeostasis. Mitochondrial sirtuins (SIRT3, SIRT4, and SIRT5) play pivotal roles in promoting this homeostasis by regulating numerous aspects of mitochondrial metabolism in response to environmental stressors. RECENT ADVANCES New work has illuminated multiple links between mitochondrial sirtuins and cancer. SIRT5 has been shown to regulate the recently described post-translational modifications succinyl-lysine, malonyl-lysine, and glutaryl-lysine. An understanding of these modifications is still in its infancy. Enumeration of SIRT3 and SIRT5 targets via advanced proteomic techniques promises to dramatically enhance insight into functions of these proteins. CRITICAL ISSUES In this review, we highlight the roles of mitochondrial sirtuins and their targets in cellular and organismal metabolic homeostasis. Furthermore, we discuss emerging roles for mitochondrial sirtuins in suppressing and/or promoting tumorigenesis, depending on the cellular and molecular context. FUTURE DIRECTIONS Currently, hundreds of potential SIRT3 and SIRT5 molecular targets have been identified in proteomic experiments. Future studies will need to validate the major targets of these enzymes, and elucidate how acetylation and/or acylation modulate their functionality. A great deal of interest exists in targeting sirtuins pharmacologically; this endeavor will require development of sirtuin-specific modulators (activators and inhibitors) as potential treatments for cancer and metabolic disease.
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Affiliation(s)
- Surinder Kumar
- 1 Department of Pathology, University of Michigan , Ann Arbor, Michigan
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240
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Azevedo C, Livermore T, Saiardi A. Protein Polyphosphorylation of Lysine Residues by Inorganic Polyphosphate. Mol Cell 2015; 58:71-82. [DOI: 10.1016/j.molcel.2015.02.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/02/2014] [Accepted: 02/03/2015] [Indexed: 10/23/2022]
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241
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Zhang Y, Bharathi SS, Rardin MJ, Uppala R, Verdin E, Gibson BW, Goetzman ES. SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase. PLoS One 2015; 10:e0122297. [PMID: 25811481 PMCID: PMC4374878 DOI: 10.1371/journal.pone.0122297] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/22/2015] [Indexed: 11/18/2022] Open
Abstract
SIRT3 and SIRT5 have been shown to regulate mitochondrial fatty acid oxidation but the molecular mechanisms behind the regulation are lacking. Here, we demonstrate that SIRT3 and SIRT5 both target human very long-chain acyl-CoA dehydrogenase (VLCAD), a key fatty acid oxidation enzyme. SIRT3 deacetylates and SIRT5 desuccinylates K299 which serves to stabilize the essential FAD cofactor in the active site. Further, we show that VLCAD binds strongly to cardiolipin and isolated mitochondrial membranes via a domain near the C-terminus containing lysines K482, K492, and K507. Acetylation or succinylation of these residues eliminates binding of VLCAD to cardiolipin. SIRT3 deacetylates K507 while SIRT5 desuccinylates K482, K492, and K507. Sirtuin deacylation of recombinant VLCAD rescues membrane binding. Endogenous VLCAD from SIRT3 and SIRT5 knockout mouse liver shows reduced binding to cardiolipin. Thus, SIRT3 and SIRT5 promote fatty acid oxidation by converging upon VLCAD to promote its activity and membrane localization. Regulation of cardiolipin binding by reversible lysine acylation is a novel mechanism that is predicted to extrapolate to other metabolic proteins that localize to the inner mitochondrial membrane.
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Affiliation(s)
- Yuxun Zhang
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sivakama S. Bharathi
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Matthew J. Rardin
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Radha Uppala
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eric Verdin
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Eric S. Goetzman
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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242
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Liu X, Sadhukhan S, Sun S, Wagner GR, Hirschey MD, Qi L, Lin H, Locasale JW. High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet. Mol Cell Proteomics 2015; 14:1489-500. [PMID: 25795660 DOI: 10.1074/mcp.m114.044859] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 01/09/2023] Open
Abstract
The availability of acyl-Coenzyme A (acyl-CoA) thioester compounds affects numerous cellular functions including autophagy, lipid oxidation and synthesis, and post-translational modifications. Consequently, the acyl-CoA level changes tend to be associated with other metabolic alterations that regulate these critical cellular functions. Despite their biological importance, this class of metabolites remains difficult to detect and quantify using current analytical methods. Here we show a universal method for metabolomics that allows for the detection of an expansive set of acyl-CoA compounds and hundreds of other cellular metabolites. We apply this method to profile the dynamics of acyl-CoA compounds and corresponding alterations in metabolism across the metabolic network in response to high fat feeding in mice. We identified targeted metabolites (>50) and untargeted features (>1000) with significant changes (FDR < 0.05) in response to diet. A substantial extent of this metabolic remodeling exhibited correlated changes in acyl-CoA metabolism with acyl-carnitine metabolism and other features of the metabolic network that together can lead to the discovery of biomarkers of acyl-CoA metabolism. These findings show a robust acyl-CoA profiling method and identify coordinated changes of acyl-CoA metabolism in response to nutritional stress.
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Affiliation(s)
- Xiaojing Liu
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853
| | - Sushabhan Sadhukhan
- §Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Shengyi Sun
- ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Gregory R Wagner
- ‖Duke Molecular Physiology Institute, Duke University, Medical Center, Durham, North Carolina 27710; **Department of Medicine and Department of Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - Matthew D Hirschey
- ‖Duke Molecular Physiology Institute, Duke University, Medical Center, Durham, North Carolina 27710; **Department of Medicine and Department of Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - Ling Qi
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853; ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Hening Lin
- §Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Jason W Locasale
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853; ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853;
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243
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Abstract
The mammalian sirtuins have emerged as critical regulators of cellular stress resistance, energy metabolism, and tumorigenesis. In some contexts, they delay the onset of age-related diseases and promote a healthy lifespan. The seven mammalian sirtuins, SIRT1-7, share a highly conserved NAD+-binding catalytic core domain although they exhibit distinct expression patterns, catalytic activities, and biological functions. This SnapShot provides an overview of these properties, with an emphasis on their relevance to aging.
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Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA; Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Michelle F Green
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Gregory R Wagner
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA; Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine and Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
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244
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Wright MH, Paape D, Storck EM, Serwa RA, Smith DF, Tate EW. Global analysis of protein N-myristoylation and exploration of N-myristoyltransferase as a drug target in the neglected human pathogen Leishmania donovani. ACTA ACUST UNITED AC 2015; 22:342-54. [PMID: 25728269 PMCID: PMC4372256 DOI: 10.1016/j.chembiol.2015.01.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/16/2014] [Accepted: 01/13/2015] [Indexed: 10/26/2022]
Abstract
N-Myristoyltransferase (NMT) modulates protein function through the attachment of the lipid myristate to the N terminus of target proteins, and is a promising drug target in eukaryotic parasites such as Leishmania donovani. Only a small number of NMT substrates have been characterized in Leishmania, and a global picture of N-myristoylation is lacking. Here, we use metabolic tagging with an alkyne-functionalized myristic acid mimetic in live parasites followed by downstream click chemistry and analysis to identify lipidated proteins in both the promastigote (extracellular) and amastigote (intracellular) life stages. Quantitative chemical proteomics is used to profile target engagement by NMT inhibitors, and to define the complement of N-myristoylated proteins. Our results provide new insight into the multiple pathways modulated by NMT and the pleiotropic effects of NMT inhibition. This work constitutes the first global experimental analysis of protein lipidation in Leishmania, and reveals the extent of NMT-related biology yet to be explored for this neglected human pathogen.
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Affiliation(s)
- Megan H Wright
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
| | - Daniel Paape
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | | | - Remigiusz A Serwa
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Deborah F Smith
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
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245
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Hirschey MD, Zhao Y. Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation. Mol Cell Proteomics 2015; 14:2308-15. [PMID: 25717114 DOI: 10.1074/mcp.r114.046664] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 12/14/2022] Open
Abstract
Protein acetylation is a well-studied regulatory mechanism for several cellular processes, ranging from gene expression to metabolism. Recent discoveries of new post-translational modifications, including malonylation, succinylation, and glutarylation, have expanded our understanding of the types of modifications found on proteins. These three acidic lysine modifications are structurally similar but have the potential to regulate different proteins in different pathways. The deacylase sirtuin 5 (SIRT5) catalyzes the removal of these modifications from a wide range of proteins in different subcellular compartments. Here, we review these new modifications, their regulation by SIRT5, and their emerging role in cellular regulation and diseases.
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Affiliation(s)
- Matthew D Hirschey
- From the ‡Duke Molecular Physiology Institute, Sarah W. Stedman Metabolism and Nutrition Center, §Departments of Medicine & Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, NC 27710;
| | - Yingming Zhao
- ¶Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637
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246
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Shi L, Tu BP. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Curr Opin Cell Biol 2015; 33:125-31. [PMID: 25703630 PMCID: PMC4380630 DOI: 10.1016/j.ceb.2015.02.003] [Citation(s) in RCA: 497] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/21/2015] [Accepted: 02/03/2015] [Indexed: 12/31/2022]
Abstract
Acetyl-CoA represents a key node in metabolism due to its intersection with many metabolic pathways and transformations. Emerging evidence reveals that cells monitor the levels of acetyl-CoA as a key indicator of their metabolic state, through distinctive protein acetylation modifications dependent on this metabolite. We offer the following conceptual model for understanding the role of this sentinel metabolite in metabolic regulation. High nucleocytosolic acetyl-CoA amounts are a signature of a “growth” or “fed” state and promote its utilization for lipid synthesis and histone acetylation. In contrast, under “survival” or “fasted” states, acetyl-CoA is preferentially directed into the mitochondria to promote mitochondrial-dependent activities such as the synthesis of ATP and ketone bodies. Fluctuations in acetyl-CoA within these subcellular compartments enable the substrate-level regulation of acetylation modifications, but also necessitates the function of sirtuin deacetylases to catalyze removal of spontaneous modifications that might be unintended. Thus, understanding the sources, fates, and consequences of acetyl-CoA as a carrier of two-carbon units has started to reveal its underappreciated but profound influence on the regulation of numerous life processes.
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Affiliation(s)
- Lei Shi
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, United States
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, United States.
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247
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Chemical proteomics approaches to examine novel histone posttranslational modifications. Curr Opin Chem Biol 2015; 24:80-90. [DOI: 10.1016/j.cbpa.2014.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023]
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248
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Yates LM, Fiedler D. Establishing the Stability and Reversibility of Protein Pyrophosphorylation with Synthetic Peptides. Chembiochem 2015; 16:415-23. [DOI: 10.1002/cbic.201402589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 12/24/2022]
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249
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Abstract
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Protein acetylation of lysine ε-amino
groups is abundant in cells, particularly within mitochondria. The
contribution of enzyme-catalyzed and nonenzymatic acetylation in mitochondria
remains unresolved. Here, we utilize a newly developed approach to
measure site-specific, nonenzymatic acetylation rates for 90 sites
in eight native purified proteins. Lysine reactivity (as second-order
rate constants) with acetyl-phosphate and acetyl-CoA ranged over 3
orders of magnitude, and higher chemical reactivity tracked with likelihood
of dynamic modification in vivo, providing evidence
that enzyme-catalyzed acylation might not be necessary to explain
the prevalence of acetylation in mitochondria. Structural analysis
revealed that many highly reactive sites exist within clusters of
basic residues, whereas lysines that show low reactivity are engaged
in strong attractive electrostatic interactions with acidic residues.
Lysine clusters are predicted to be high-affinity substrates of mitochondrial
deacetylase SIRT3 both in vitro and in vivo. Our analysis describing rate determination of lysine acetylation
is directly applicable to investigate targeted and proteome-wide acetylation,
whether or not the reaction is enzyme catalyzed.
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Affiliation(s)
- Josue Baeza
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - Michael J. Smallegan
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
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250
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Abstract
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Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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