301
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Martin J, Balmer ML, Rajendran S, Maurhofer O, Dufour JF, St-Pierre MV. Nutritional stress exacerbates hepatic steatosis induced by deletion of the histidine nucleotide-binding (Hint2) mitochondrial protein. Am J Physiol Gastrointest Liver Physiol 2016; 310:G497-509. [PMID: 26767982 DOI: 10.1152/ajpgi.00178.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/07/2016] [Indexed: 01/31/2023]
Abstract
The histidine nucleotide-binding protein, Hint2, is a mitochondrial phosphoramidase expressed in liver, brown fat, pancreas, and muscle. The livers of Hint2 knockout (Hint2(-/-)) mice accumulate triglycerides and show a pattern of mitochondrial protein lysine hyperacetylation. The extent and nature of the lysine acetylation changes and the response of Hint2(-/-) mice to nutritional challenges that elicit a modification of protein acetylation have not been investigated. To compare the adaptation of Hint2(-/-) and control (Hint2(+/+)) mice with episodes of fasting and high-fat diet (HFD), we subjected animals to either feeding ad libitum or fasting for 24 h, and to either a HFD or control diet for 8 wk. Triglyceride content was higher in Hint2(-/-) than in Hint2(+/+) livers, whereas plasma triglycerides were fourfold lower. Malonyl-CoA levels were increased twofold in Hint2(-/-) livers. After 24 h fasting, Hint2(-/-) displayed a decrease in body temperature, commensurate with a decrease in mass of brown fat and downregulation of uncoupling protein 1. HFD-treated Hint2(-/-) livers showed more steatosis, and plasma insulin and cholesterol were higher than in Hint(+/+) mice. Several proteins identified as substrates of sirtuin 3 and 5 and active in intermediary and ketone metabolism were hyperacetylated in liver and brown fat mitochondria after both HFD and fasting regimens. Glutamate dehydrogenase activity was downregulated in fed and fasted livers, and this was attributed to an increase in acetylation and ADP-ribosylation. The absence of Hint2 deregulates the posttranslational modification of several mitochondrial proteins, which impedes the adaptation to episodes of nutritional stress.
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Affiliation(s)
- Juliette Martin
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and
| | - Maria L Balmer
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and
| | - Saranya Rajendran
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and
| | - Olivier Maurhofer
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and
| | - Jean-François Dufour
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and Visceral Surgery, University Hospital, Inselspital, Bern, Switzerland
| | - Marie V St-Pierre
- Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and
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302
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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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303
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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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304
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Schuster S, Roessler C, Meleshin M, Zimmermann P, Simic Z, Kambach C, Schiene-Fischer C, Steegborn C, Hottiger MO, Schutkowski M. A continuous sirtuin activity assay without any coupling to enzymatic or chemical reactions. Sci Rep 2016; 6:22643. [PMID: 26940860 PMCID: PMC4778124 DOI: 10.1038/srep22643] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 02/16/2016] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are NAD(+) dependent lysine deacylases involved in many regulatory processes such as control of metabolic pathways, DNA repair and stress response. Modulators of sirtuin activity are required as tools for uncovering the biological function of these enzymes and as potential therapeutic agents. Systematic discovery of such modulators is hampered by the lack of direct and continuous activity assays. The present study describes a novel continuous assay based on the increase of a fluorescence signal subsequent to sirtuin mediated removal of a fluorescent acyl chain from a modified TNFα-derived peptide. This substrate is well recognized by human sirtuins 1-6 and represents the best sirtuin 2 substrate described so far with a kcat/KM-value of 176 000 M(-1)s(-1). These extraordinary substrate properties allow the first determination of Ki-values for the specific Sirt2 inhibitory peptide S2iL5 (600 nM) and for the quasi-universal sirtuin inhibitor peptide thioxo myristoyl TNFα (80 nM).
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Affiliation(s)
- Sabine Schuster
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Claudia Roessler
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Philipp Zimmermann
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Christian Kambach
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, joint research project gFP5, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Michael O Hottiger
- IVBMB, University of Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
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305
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Horton JL, Martin OJ, Lai L, Riley NM, Richards AL, Vega RB, Leone TC, Pagliarini DJ, Muoio DM, Bedi KC, Margulies KB, Coon JJ, Kelly DP. Mitochondrial protein hyperacetylation in the failing heart. JCI Insight 2016; 2. [PMID: 26998524 DOI: 10.1172/jci.insight.84897] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Myocardial fuel and energy metabolic derangements contribute to the pathogenesis of heart failure. Recent evidence implicates posttranslational mechanisms in the energy metabolic disturbances that contribute to the pathogenesis of heart failure. We hypothesized that accumulation of metabolite intermediates of fuel oxidation pathways drives posttranslational modifications of mitochondrial proteins during the development of heart failure. Myocardial acetylproteomics demonstrated extensive mitochondrial protein lysine hyperacetylation in the early stages of heart failure in well-defined mouse models and the in end-stage failing human heart. To determine the functional impact of increased mitochondrial protein acetylation, we focused on succinate dehydrogenase A (SDHA), a critical component of both the tricarboxylic acid (TCA) cycle and respiratory complex II. An acetyl-mimetic mutation targeting an SDHA lysine residue shown to be hyperacetylated in the failing human heart reduced catalytic function and reduced complex II-driven respiration. These results identify alterations in mitochondrial acetyl-CoA homeostasis as a potential driver of the development of energy metabolic derangements that contribute to heart failure.
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Affiliation(s)
- Julie L Horton
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Ola J Martin
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Ling Lai
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA; Genome Center of Wisconsin, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Alicia L Richards
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA; Genome Center of Wisconsin, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Rick B Vega
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Teresa C Leone
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Deborah M Muoio
- Departments of Medicine, Pharmacology, and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Kenneth C Bedi
- Cardiovascular Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenneth B Margulies
- Cardiovascular Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA; Genome Center of Wisconsin, University of Wisconsin - Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Daniel P Kelly
- Cardiovascular Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
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306
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Inhibition of histone deacetylases in cancer therapy: lessons from leukaemia. Br J Cancer 2016; 114:605-11. [PMID: 26908329 PMCID: PMC4800301 DOI: 10.1038/bjc.2016.36] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 12/13/2022] Open
Abstract
Histone deacetylases (HDACs) are a key component of the epigenetic machinery regulating gene expression, and behave as oncogenes in several cancer types, spurring the development of HDAC inhibitors (HDACi) as anticancer drugs. This review discusses new results regarding the role of HDACs in cancer and the effect of HDACi on tumour cells, focusing on haematological malignancies, particularly acute myeloid leukaemia. Histone deacetylases may have opposite roles at different stages of tumour progression and in different tumour cell sub-populations (cancer stem cells), highlighting the importance of investigating these aspects for further improving the clinical use of HDACi in treating cancer.
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307
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Schölz C, Lyon D, Refsgaard JC, Jensen LJ, Choudhary C, Weinert BT. Avoiding abundance bias in the functional annotation of post-translationally modified proteins. Nat Methods 2016; 12:1003-4. [PMID: 26513550 DOI: 10.1038/nmeth.3621] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christian Schölz
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Department of Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jan C Refsgaard
- Department of Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Department of Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Brian T Weinert
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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308
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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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309
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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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310
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Abstract
Reversible acetylation was initially described as an epigenetic mechanism regulating DNA accessibility. Since then, this process has emerged as a controller of histone and nonhistone acetylation that integrates key physiological processes such as metabolism, circadian rhythm and cell cycle, along with gene regulation in various organisms. The widespread and reversible nature of acetylation also revitalized interest in the mechanisms that regulate lysine acetyltransferases (KATs) and deacetylases (KDACs) in health and disease. Changes in protein or histone acetylation are especially relevant for many common diseases including obesity, diabetes mellitus, neurodegenerative diseases and cancer, as well as for some rare diseases such as mitochondrial diseases and lipodystrophies. In this Review, we examine the role of reversible acetylation in metabolic control and how changes in levels of metabolites or cofactors, including nicotinamide adenine dinucleotide, nicotinamide, coenzyme A, acetyl coenzyme A, zinc and butyrate and/or β-hydroxybutyrate, directly alter KAT or KDAC activity to link energy status to adaptive cellular and organismal homeostasis.
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Affiliation(s)
- Keir J Menzies
- Interdisciplinary School of Health Sciences, University of Ottawa, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Hongbo Zhang
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Elena Katsyuba
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Station 15, 1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Station 15, 1015 Lausanne, Switzerland
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311
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Suenkel B, Steegborn C. Recombinant Preparation, Biochemical Analysis, and Structure Determination of Sirtuin Family Histone/Protein Deacylases. Methods Enzymol 2016; 573:183-208. [DOI: 10.1016/bs.mie.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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312
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Davies MN, Kjalarsdottir L, Thompson JW, Dubois LG, Stevens RD, Ilkayeva OR, Brosnan MJ, Rolph TP, Grimsrud PA, Muoio DM. The Acetyl Group Buffering Action of Carnitine Acetyltransferase Offsets Macronutrient-Induced Lysine Acetylation of Mitochondrial Proteins. Cell Rep 2015; 14:243-54. [PMID: 26748706 DOI: 10.1016/j.celrep.2015.12.030] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/26/2015] [Accepted: 12/03/2015] [Indexed: 11/25/2022] Open
Abstract
Lysine acetylation (AcK), a posttranslational modification wherein a two-carbon acetyl group binds covalently to a lysine residue, occurs prominently on mitochondrial proteins and has been linked to metabolic dysfunction. An emergent theory suggests mitochondrial AcK occurs via mass action rather than targeted catalysis. To test this hypothesis, we performed mass spectrometry-based acetylproteomic analyses of quadriceps muscles from mice with skeletal muscle-specific deficiency of carnitine acetyltransferase (CrAT), an enzyme that buffers the mitochondrial acetyl-CoA pool by converting short-chain acyl-CoAs to their membrane permeant acylcarnitine counterparts. CrAT deficiency increased tissue acetyl-CoA levels and susceptibility to diet-induced AcK of broad-ranging mitochondrial proteins, coincident with diminished whole body glucose control. Sub-compartment acetylproteome analyses of muscles from obese mice and humans showed remarkable overrepresentation of mitochondrial matrix proteins. These findings reveal roles for CrAT and L-carnitine in modulating the muscle acetylproteome and provide strong experimental evidence favoring the nonenzymatic carbon pressure model of mitochondrial AcK.
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Affiliation(s)
- Michael N Davies
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Lilja Kjalarsdottir
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27701, USA; Proteomics and Metabolomics Shared Resource, Duke University, Durham, NC 27701, USA
| | - Laura G Dubois
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, NC 27701, USA
| | - Robert D Stevens
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Olga R Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - M Julia Brosnan
- CV and Metabolic Diseases (CVMED), a Pfizer Research Unit, Cambridge, MA 02139, USA
| | - Timothy P Rolph
- CV and Metabolic Diseases (CVMED), a Pfizer Research Unit, Cambridge, MA 02139, USA
| | - Paul A Grimsrud
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Deborah M Muoio
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27701, USA.
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313
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Bacterial protein acetylation: new discoveries unanswered questions. Curr Genet 2015; 62:335-41. [PMID: 26660885 DOI: 10.1007/s00294-015-0552-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022]
Abstract
Nε-acetylation is emerging as an abundant post-translational modification of bacterial proteins. Two mechanisms have been identified: one is enzymatic, dependent on an acetyltransferase and acetyl-coenzyme A; the other is non-enzymatic and depends on the reactivity of acetyl phosphate. Some, but not most, of those acetylations are reversed by deacetylases. This review will briefly describe the current status of the field and raise questions that need answering.
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314
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Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S. Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction. Microbiologyopen 2015; 5:152-73. [PMID: 26663479 PMCID: PMC4767432 DOI: 10.1002/mbo3.320] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/23/2015] [Accepted: 11/03/2015] [Indexed: 11/06/2022] Open
Abstract
The bacterium Corynebacterium glutamicum is utilized during industrial fermentation to produce amino acids such as L-glutamate. During L-glutamate fermentation, C. glutamicum changes the flux of central carbon metabolism to favor L-glutamate production, but the molecular mechanisms that explain these flux changes remain largely unknown. Here, we found that the profiles of two major lysine acyl modifications were significantly altered upon glutamate overproduction in C. glutamicum; acetylation decreased, whereas succinylation increased. A label-free semi-quantitative proteomic analysis identified 604 acetylated proteins with 1328 unique acetylation sites and 288 succinylated proteins with 651 unique succinylation sites. Acetylation and succinylation targeted enzymes in central carbon metabolic pathways that are directly related to glutamate production, including the 2-oxoglutarate dehydrogenase complex (ODHC), a key enzyme regulating glutamate overproduction. Structural mapping revealed that several critical lysine residues in the ODHC components were susceptible to acetylation and succinylation. Furthermore, induction of glutamate production was associated with changes in the extent of acetylation and succinylation of lysine, suggesting that these modifications may affect the activity of enzymes involved in glutamate production. Deletion of phosphotransacetylase decreased the extent of protein acetylation in nonproducing condition, suggesting that acetyl phosphate-dependent acetylation is active in C. glutamicum. However, no effect was observed on the profiles of acetylation and succinylation in glutamate-producing condition upon disruption of acetyl phosphate metabolism or deacetylase homologs. It was considered likely that the reduced acetylation in glutamate-producing condition may reflect metabolic states where the flux through acid-producing pathways is very low, and substrates for acetylation do not accumulate in the cell. Succinylation would occur more easily than acetylation in such conditions where the substrates for both acetylation and succinylation are limited. This is the first study investigating the acetylome and succinylome of C. glutamicum, and it provides new insight into the roles of acyl modifications in C. glutamicum biology.
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Affiliation(s)
- Yuta Mizuno
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Kyowa Hakko Bio Co., Ltd., Tokyo, Japan
| | - Megumi Nagano-Shoji
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Kyowa Hakko Bio Co., Ltd., Tokyo, Japan
| | - Shosei Kubo
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Department of Environmental Materials Science, Tokyo Denki University, Tokyo, Japan
| | - Yumi Kawamura
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kawasaki
- Department of Environmental Materials Science, Tokyo Denki University, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,RIKEN Center for Sustainable Resource Science, Saitama, Japan
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315
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Interplay between oxidant species and energy metabolism. Redox Biol 2015; 8:28-42. [PMID: 26741399 PMCID: PMC4710798 DOI: 10.1016/j.redox.2015.11.010] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 02/07/2023] Open
Abstract
It has long been recognized that energy metabolism is linked to the production of reactive oxygen species (ROS) and critical enzymes allied to metabolic pathways can be affected by redox reactions. This interplay between energy metabolism and ROS becomes most apparent during the aging process and in the onset and progression of many age-related diseases (i.e. diabetes, metabolic syndrome, atherosclerosis, neurodegenerative diseases). As such, the capacity to identify metabolic pathways involved in ROS formation, as well as specific targets and oxidative modifications is crucial to our understanding of the molecular basis of age-related diseases and for the design of novel therapeutic strategies. Herein we review oxidant formation associated with the cell's energetic metabolism, key antioxidants involved in ROS detoxification, and the principal targets of oxidant species in metabolic routes and discuss their relevance in cell signaling and age-related diseases. Energy metabolism is both a source and target of oxidant species. Reactive oxygen species are formed in redox reactions in catabolic pathways. Sensitive targets of oxidant species regulate the flux of metabolic pathways. Metabolic pathways and antioxidant systems are regulated coordinately.
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316
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Su X, Wellen KE, Rabinowitz JD. Metabolic control of methylation and acetylation. Curr Opin Chem Biol 2015; 30:52-60. [PMID: 26629854 DOI: 10.1016/j.cbpa.2015.10.030] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Methylation and acetylation of DNA and histone proteins are the chemical basis for epigenetics. From bacteria to humans, methylation and acetylation are sensitive to cellular metabolic status. Modification rates depend on the availability of one-carbon and two-carbon substrates (S-adenosylmethionine, acetyl-CoA, and in bacteria also acetyl-phosphate). In addition, they are sensitive to demodification enzyme cofactors (α-ketoglutarate, NAD(+)) and structural analog metabolites that function as epigenetic enzyme inhibitors (e.g., S-adenosylhomocysteine, 2-hydroxyglutarate). Methylation and acetylation likely initially evolved to tailor protein activities in microbes to their metabolic milieu. While the extracellular environment of mammals is more tightly controlled, the combined impact of nutrient abundance and metabolic enzyme expression impacts epigenetics in mammals sufficiently to drive important biological outcomes such as stem cell fate and cancer.
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Affiliation(s)
- Xiaoyang Su
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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317
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Li F, He X, Ye D, Lin Y, Yu H, Yao C, Huang L, Zhang J, Wang F, Xu S, Wu X, Liu L, Yang C, Shi J, He X, Liu J, Qu Y, Guo F, Zhao J, Xu W, Zhao S. NADP(+)-IDH Mutations Promote Hypersuccinylation that Impairs Mitochondria Respiration and Induces Apoptosis Resistance. Mol Cell 2015; 60:661-75. [PMID: 26585387 DOI: 10.1016/j.molcel.2015.10.017] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/07/2015] [Accepted: 10/09/2015] [Indexed: 02/05/2023]
Abstract
Elucidating the tumorigenic mechanism of R-2-hydroxyglutarate (R-2HG) is critical for determining how NADP(+)-IDH mutations cause cancer. Here we report that R-2HG induces cancerous metabolism and apoptosis resistance through promoting hypersuccinylation. By competitive inhibition of the mitochondrial tricarboxylic acid cycle enzyme succinate dehydrogenase (SDH), R-2HG preferentially induced succinyl-CoA accumulation and hypersuccinylation in the mitochondria. IDH1 mutation-bearing glioma samples and cells were hypersuccinylated in the mitochondria. IDH1 mutation or SDH inactivation resulted in hypersuccinylation, causing respiration inhibition and inducing cancerous metabolism and mitochondrial depolarization. These mitochondrial dysfunctions induced BCL-2 accumulation at the mitochondrial membrane, leading to apoptosis resistance of hypersuccinylated cells. Relief of hypersuccinylation by overexpressing the desuccinylase SIRT5 or supplementing glycine rescued mitochondrial dysfunctions, reversed BCL-2 accumulation, and slowed the oncogenic growth of hypersuccinylated IDH1(R132C)-harboring HT1080 cells. Thus, R-2HG-induced hypersuccinylation contributes to the tumorigenicity of NADP(+)-IDH mutations, suggesting the potential of hypersuccinylation inhibition as an intervention for hypersuccinylation-related tumors.
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Affiliation(s)
- Feng Li
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Xiadi He
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yan Lin
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Hongxiu Yu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Cuifang Yao
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Lei Huang
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China
| | - Jianong Zhang
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China
| | - Fang Wang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Sha Xu
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Xiaohui Wu
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200032, P.R. China
| | - Lixia Liu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Chen Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Jiaqi Shi
- Department of Urology, Affiliated Hospital of Guiyang Medical College, Guiyang 550004, P.R. China
| | - Xiaoyang He
- Guizhou Cancer Hospital, Guiyang 550001, P.R. China
| | - Jie Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; Institute of Digestive Medicine, Affiliated Huashan Hospital, Fudan University, Shanghai 200032, P.R. China; Department of Urology, Affiliated Hospital of Guiyang Medical College, Guiyang 550004, P.R. China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Fushen Guo
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China
| | - Jianyuan Zhao
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China
| | - Wei Xu
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China.
| | - Shimin Zhao
- State Key Lab of Genetic Engineering and the Obstetrics & Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, P.R. China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; School of Life Sciences and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, P.R. China; Institute of Digestive Medicine, Affiliated Huashan Hospital, Fudan University, Shanghai 200032, P.R. China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China.
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318
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Knyphausen P, Kuhlmann N, de Boor S, Lammers M. Lysine-acetylation as a fundamental regulator of Ran function: Implications for signaling of proteins of the Ras-superfamily. Small GTPases 2015; 6:189-95. [PMID: 26507377 PMCID: PMC4905271 DOI: 10.1080/21541248.2015.1103399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The small GTP-binding protein Ran is involved in the regulation of essential cellular processes in interphase but also in mitotic cells: Ran controls the nucleocytoplasmic transport of proteins and RNA, it regulates mitotic spindle formation and nuclear envelope assembly. Deregulations in Ran dependent processes were implicated in the development of severe diseases such as cancer and neurodegenerative disorders. To understand how Ran-function is regulated is therefore of highest importance. Recently, several lysine-acetylation sites in Ran were identified by quantitative mass-spectrometry, some being located in highly important regions such as the P-loop, switch I, switch II and the G5/SAK motif. We recently reported that lysine-acetylation regulates nearly all aspects of Ran-function such as RCC1 catalyzed nucleotide exchange, intrinsic nucleotide hydrolysis, its interaction with NTF2 and the formation of import- and export-complexes. As a hint for its biological importance, we identified Ran-specific lysine-deacetylases (KDACs) and -acetyltransferases (KATs). Also for other small GTPases such as Ras, Rho, Cdc42, and for many effectors and regulators thereof, lysine-acetylation sites were discovered. However, the functional impact of lysine-acetylation as a regulator of protein function has only been marginally investigated so far. We will discuss recent findings of lysine-acetylation as a novel modification to regulate Ras-protein signaling.
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Affiliation(s)
- Philipp Knyphausen
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Nora Kuhlmann
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Susanne de Boor
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Michael Lammers
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
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319
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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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320
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Azevedo C, Saiardi A. Why always lysine? The ongoing tale of one of the most modified amino acids. Adv Biol Regul 2015; 60:144-150. [PMID: 26482291 DOI: 10.1016/j.jbior.2015.09.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022]
Abstract
The complex physiology of living organisms must be finely-tuned to permit the flexibility required to respond to the changing environment. Evolution has provided an interconnected and intricate array of regulatory mechanisms to facilitate this fine-tuning. The number of genes cannot alone explain the complexity of these mechanisms. Rather, signalling is regulated at multiple levels, from genomic to transcriptional, translational and post-translational. Post-translational modification (PTM) of proteins offers an additional level of regulation after protein synthesis that allows a rapid, controlled and reversible response to environmental cues. Many amino acid side chains are post-translationally modified. These modifications can either be enzymatic, such as the phosphorylation of serine, threonine and tyrosine residues, or non-enzymatic, such as the nitrosylation of cysteine residues. Strikingly, lysine residues are targeted by a particularly high number of PTMs including acetylation, methylation, ubiquitination and sumoylation. Additionally, lysines have recently been identified as the target of the non-enzymatic PTM polyphosphorylation. This novel PTM sees linear chains of inorganic polyphosphates (polyP) covalently attached to lysine residues. Interestingly, polyphosphorylation is indirectly dependent on inositol pyrophosphates, a class of cellular messengers. The attachment of polyP to lysine occurs through the phosphoramidate bond, which, unlike the phosphester bond, is unstable under the conditions used in common mass spectroscopy. This characteristic, together with the diversity of lysine PTMs, suggests that many other lysine modifications may still remain unidentified, raising the intriguing possibility that lysine PTMs may be the major means by which signalling pathways modify protein behaviour.
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Affiliation(s)
- Cristina Azevedo
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
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321
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Olia AS, Barker K, McCullough CE, Tang HY, Speicher DW, Qiu J, LaBaer J, Marmorstein R. Nonenzymatic Protein Acetylation Detected by NAPPA Protein Arrays. ACS Chem Biol 2015; 10:2034-47. [PMID: 26083674 DOI: 10.1021/acschembio.5b00342] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acetylation is a post-translational modification that occurs on thousands of proteins located in many cellular organelles. This process mediates many protein functions and modulates diverse biological processes. In mammalian cells, where acetyl-CoA is the primary acetyl donor, acetylation in the mitochondria is thought to occur by chemical means due to the relatively high concentration of acetyl-CoA located in this organelle. In contrast, acetylation outside of the mitochondria is thought to be mediated predominantly by acetyltransferase enzymes. Here, we address the possibility that nonenzymatic chemical acetylation outside of the mitochondria may be more common than previously appreciated. We employed the Nucleic Acid Programmable Protein Array platform to perform an unbiased screen for human proteins that undergo chemical acetylation, which resulted in the identification of a multitude of proteins with diverse functions and cellular localization. Mass spectrometry analysis revealed that basic residues typically precede the acetylated lysine in the -7 to -3 position, and we show by mutagenesis that these basic residues contribute to chemical acetylation capacity. We propose that these basic residues lower the pKa of the substrate lysine for efficient chemical acetylation. Many of the identified proteins reside outside of the mitochondria and have been previously demonstrated to be acetylated in vivo. As such, our studies demonstrate that chemical acetylation occurs more broadly throughout the eukaryotic cell than previously appreciated and suggests that this post-translational protein modification may have more diverse roles in protein function and pathway regulation.
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Affiliation(s)
- Adam S. Olia
- Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Program
in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, United States
| | - Kristi Barker
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States
| | - Cheryl E. McCullough
- Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Program
in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, United States
| | - Hsin-Yao Tang
- Program
in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania, United States
| | - David W. Speicher
- Program
in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania, United States
| | - Ji Qiu
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States
| | - Joshua LaBaer
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Program
in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, United States
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322
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Simic Z, Weiwad M, Schierhorn A, Steegborn C, Schutkowski M. The ɛ-Amino Group of Protein Lysine Residues Is Highly Susceptible to Nonenzymatic Acylation by Several Physiological Acyl-CoA Thioesters. Chembiochem 2015; 16:2337-47. [PMID: 26382620 DOI: 10.1002/cbic.201500364] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 01/04/2023]
Abstract
Mitochondrial enzymes implicated in the pathophysiology of diabetes, cancer, and metabolic syndrome are highly regulated by acetylation. However, mitochondrial acetyltransferases have not been identified. Here, we show that acetylation and also other acylations are spontaneous processes that depend on pH value, acyl-CoA concentration and the chemical nature of the acyl residue. In the case of a peptide derived from carbamoyl phosphate synthetase 1, the rates of succinylation and glutarylation were up to 150 times than for acetylation. These results were confirmed by using the protein substrate cyclophilin A (CypA). Deacylation experiments revealed that SIRT3 exhibits deacetylase activity but is not able to remove any of the succinyl groups from CypA, whereas SIRT5 is an effective protein desuccinylase. Thus, the acylation landscape on lysine residues might largely depend on the enzymatic activity of specific sirtuins, and the availability and reactivity of acyl-CoA compounds.
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Affiliation(s)
- Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Matthias Weiwad
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany.
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323
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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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324
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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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325
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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326
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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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327
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Roessler C, Tüting C, Meleshin M, Steegborn C, Schutkowski M. A Novel Continuous Assay for the Deacylase Sirtuin 5 and Other Deacetylases. J Med Chem 2015; 58:7217-23. [PMID: 26308971 DOI: 10.1021/acs.jmedchem.5b00293] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sirtuins are NAD(+) dependent lysine deacylases involved in many regulatory processes like control of metabolic pathways, DNA repair, and stress response. Modulators of sirtuin activity are needed as tools for uncovering the biological function of these enzymes and as potential therapeutics. Systematic discovery of such modulators is hampered by the lack of efficient and simple continuous activity assays running at low sirtuin concentrations in microtiter plates. Here we describe an improved continuous sirtuin 5 assay based on the coupling of the sirtuin reaction to a proteolytic cleavage using internally fluorescence-quenched substrates. Systematic optimization of a carbamoyl phosphate synthetase 1 derived, glutarylated peptide yielded a Sirt5 substrate with k(cat)/K(M) value of 337,000 M(-1) s(-1), which represents the best sirtuin substrate described so far. These extraordinary substrate properties allowed reliable determination of Ki values for different inhibitors in the presence of only 10 nM sirtuin in microtiter plate format. Assay conditions could be transferred effectively to other lysine deacetylases, like sirtuin 2 and sirtuin 3, which now enables more efficient development of sirtuin targeting drugs.
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Affiliation(s)
- Claudia Roessler
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Christian Tüting
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Marat Meleshin
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth , Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Mike Schutkowski
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
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328
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Singhal A, Arora G, Virmani R, Kundu P, Khanna T, Sajid A, Misra R, Joshi J, Yadav V, Samanta S, Saini N, Pandey AK, Visweswariah SS, Hentschker C, Becher D, Gerth U, Singh Y. Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase. J Biol Chem 2015; 290:26218-34. [PMID: 26350458 DOI: 10.1074/jbc.m115.687269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 02/02/2023] Open
Abstract
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.
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Affiliation(s)
- Anshika Singhal
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Gunjan Arora
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India, the Translational Health Science and Technology Institute, Faridabad 121001, India
| | - Richa Virmani
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Parijat Kundu
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Tanya Khanna
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Andaleeb Sajid
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Jayadev Joshi
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vikas Yadav
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Sintu Samanta
- the Indian Institute of Science, Bangalore 560012, India, and
| | - Neeru Saini
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Amit K Pandey
- the Translational Health Science and Technology Institute, Faridabad 121001, India,
| | | | - Christian Hentschker
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Dörte Becher
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Ulf Gerth
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Yogendra Singh
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India,
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329
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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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330
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de Diego Puente T, Gallego-Jara J, Castaño-Cerezo S, Bernal Sánchez V, Fernández Espín V, García de la Torre J, Manjón Rubio A, Cánovas Díaz M. The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization. J Biol Chem 2015; 290:23077-93. [PMID: 26251518 DOI: 10.1074/jbc.m115.649806] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/31/2023] Open
Abstract
Lysine acetylation is an important post-translational modification in the metabolic regulation of both prokaryotes and eukaryotes. In Escherichia coli, PatZ (formerly YfiQ) is the only known acetyltransferase protein and is responsible for acetyl-CoA synthetase acetylation. In this study, we demonstrated PatZ-positive cooperativity in response to acetyl-CoA and the regulation of acetyl-CoA synthetase activity by the acetylation level. Furthermore, functional analysis of an E809A mutant showed that the conserved glutamate residue is not relevant for the PatZ catalytic mechanism. Biophysical studies demonstrated that PatZ is a stable tetramer in solution and is transformed to its octameric form by autoacetylation. Moreover, this modification is reversed by the sirtuin CobB. Finally, an in silico PatZ tetramerization model based on hydrophobic and electrostatic interactions is proposed and validated by three-dimensional hydrodynamic analysis. These data reveal, for the first time, the structural regulation of an acetyltransferase by autoacetylation in a prokaryotic organism.
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Affiliation(s)
| | - Julia Gallego-Jara
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Sara Castaño-Cerezo
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | | | - Vanesa Fernández Espín
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - José García de la Torre
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - Arturo Manjón Rubio
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Manuel Cánovas Díaz
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
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331
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Abstract
Heart failure is a leading cause of death worldwide. Despite medical advances, the dismal prognosis of heart failure has not been improved. The heart is a high energy-demanding organ. Impairments of cardiac energy metabolism and mitochondrial function are intricately linked to cardiac dysfunction. Mitochondrial dysfunction contributes to impaired myocardial energetics and increased oxidative stress in heart failure, and the opening of mitochondrial permeability transition pore triggers cell death and myocardial remodeling. Therefore, there has been growing interest in targeting mitochondria and metabolism for heart failure therapy. Recent developments suggest that mitochondrial protein lysine acetylation modulates the sensitivity of the heart to stress and hence the propensity to heart failure. This article reviews the role of mitochondrial dysfunction in heart failure, with a special emphasis on the regulation of the nicotinamide adenine dinucleotide (NAD(+)/NADH) ratio and sirtuin-dependent lysine acetylation by mitochondrial function. Strategies for targeting NAD(+)-sensitive mechanisms in order to intervene in protein lysine acetylation and, thereby, improve stress tolerance, are described, and their usefulness in heart failure therapy is discussed.
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Affiliation(s)
- Chi Fung Lee
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington
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332
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Lu J, Cheng K, Zhang B, Xu H, Cao Y, Guo F, Feng X, Xia Q. Novel mechanisms for superoxide-scavenging activity of human manganese superoxide dismutase determined by the K68 key acetylation site. Free Radic Biol Med 2015; 85:114-26. [PMID: 25908444 DOI: 10.1016/j.freeradbiomed.2015.04.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 03/22/2015] [Accepted: 04/09/2015] [Indexed: 01/29/2023]
Abstract
Superoxide is the primary reactive oxygen species generated in the mitochondria. Manganese superoxide dismutase (SOD2) is the major enzymatic superoxide scavenger present in the mitochondrial matrix and one of the most crucial reactive oxygen species-scavenging enzymes in the cell. SOD2 is activated by sirtuin 3 (SIRT3) through NAD(+)-dependent deacetylation. However, the exact acetylation sites of SOD2 are ambiguous and the mechanisms underlying the deacetylation-mediated SOD2 activation largely remain unknown. We are the first to characterize SOD2 mutants of the acetylation sites by investigating the relative enzymatic activity, structures, and electrostatic potential of SOD2 in this study. These SOD2 mutations affected the superoxide-scavenging activity in vitro and in HEK293T cells. The lysine 68 (K68) site is the most important acetylation site contributing to SOD2 activation and plays a role in cell survival after paraquat treatment. The molecular basis underlying the regulation of SOD2 activity by K68 was investigated in detail. Molecular dynamics simulations revealed that K68 mutations induced a conformational shift of residues located in the active center of SOD2 and altered the charge distribution on the SOD2 surface. Thus, the entry of the superoxide anion into the coordinated core of SOD2 was inhibited. Our results provide a novel mechanistic insight, whereby SOD2 acetylation affects the structure and charge distribution of SOD2, its tetramerization, and p53-SOD2 interactions of SOD2 in the mitochondria, which may play a role in nuclear-mitochondrial communication during aging.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Kuoyuan Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Huan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Yuanzhao Cao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Fei Guo
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China
| | - Xudong Feng
- Department of Medicine, Children׳s Hospital Boston, Harvard Medical School, Boston, MA 02445, USA.
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, People׳s Republic of China.
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333
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Chen B, Wang J, Huang Y, Zheng W. Human SIRT3 tripeptidic inhibitors containing N(ε)-thioacetyl-lysine. Bioorg Med Chem Lett 2015. [PMID: 26220157 DOI: 10.1016/j.bmcl.2015.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Built upon our lead pan-SIRT1/2/3 tripeptidic inhibitors that contain the catalytic mechanism-based sirtuin inhibitory warhead N(ε)-thioacetyl-lysine, three of their analogs (i.e., 7, 9, and 19) were discovered in the current study to exhibit a significantly enhanced SIRT3 inhibitory selectivity while maintaining the SIRT3 inhibitory potency. These compounds represent novel lead compounds for developing more potent and selective SIRT3 inhibitors of the catalytic mechanism-based type.
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Affiliation(s)
- Bing Chen
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Juan Wang
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Yajun Huang
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China.
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334
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Kosono S, Tamura M, Suzuki S, Kawamura Y, Yoshida A, Nishiyama M, Yoshida M. Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source. PLoS One 2015; 10:e0131169. [PMID: 26098117 PMCID: PMC4476798 DOI: 10.1371/journal.pone.0131169] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/29/2015] [Indexed: 11/19/2022] Open
Abstract
Lysine residues can be post-translationally modified by various acyl modifications in bacteria and eukarya. Here, we showed that two major acyl modifications, acetylation and succinylation, were changed in response to the carbon source in the Gram-positive model bacterium Bacillus subtilis. Acetylation was more common when the cells were grown on glucose, glycerol, or pyruvate, whereas succinylation was upregulated when the cells were grown on citrate, reflecting the metabolic states that preferentially produce acetyl-CoA and succinyl-CoA, respectively. To identify and quantify changes in acetylation and succinylation in response to the carbon source, we performed a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate. We identified 629 acetylated proteins with 1355 unique acetylation sites and 204 succinylated proteins with 327 unique succinylation sites. Acetylation targeted different metabolic pathways under the two growth conditions: branched-chain amino acid biosynthesis and purine metabolism in glucose and the citrate cycle in citrate. Succinylation preferentially targeted the citrate cycle in citrate. Acetylation and succinylation mostly targeted different lysine residues and showed a preference for different residues surrounding the modification sites, suggesting that the two modifications may depend on different factors such as characteristics of acyl-group donors, molecular environment of the lysine substrate, and/or the modifying enzymes. Changes in acetylation and succinylation were observed in proteins involved in central carbon metabolism and in components of the transcription and translation machineries, such as RNA polymerase and the ribosome. Mutations that modulate protein acylation affected B. subtilis growth. A mutation in acetate kinase (ackA) increased the global acetylation level, suggesting that acetyl phosphate-dependent acetylation is common in B. subtilis, just as it is in Escherichia coli. Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.
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Affiliation(s)
- Saori Kosono
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- * E-mail:
| | - Masaru Tamura
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shota Suzuki
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yumi Kawamura
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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335
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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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336
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Nishida Y, Rardin MJ, Carrico C, He W, Sahu AK, Gut P, Najjar R, Fitch M, Hellerstein M, Gibson BW, Verdin E. SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target. Mol Cell 2015; 59:321-32. [PMID: 26073543 DOI: 10.1016/j.molcel.2015.05.022] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 03/27/2015] [Accepted: 05/11/2015] [Indexed: 02/01/2023]
Abstract
Protein acylation links energetic substrate flux with cellular adaptive responses. SIRT5 is a NAD(+)-dependent lysine deacylase and removes both succinyl and malonyl groups. Using affinity enrichment and label free quantitative proteomics, we characterized the SIRT5-regulated lysine malonylome in wild-type (WT) and Sirt5(-/-) mice. 1,137 malonyllysine sites were identified across 430 proteins, with 183 sites (from 120 proteins) significantly increased in Sirt5(-/-) animals. Pathway analysis identified glycolysis as the top SIRT5-regulated pathway. Importantly, glycolytic flux was diminished in primary hepatocytes from Sirt5(-/-) compared to WT mice. Substitution of malonylated lysine residue 184 in glyceraldehyde 3-phosphate dehydrogenase with glutamic acid, a malonyllysine mimic, suppressed its enzymatic activity. Comparison with our previous reports on acylation reveals that malonylation targets a different set of proteins than acetylation and succinylation. These data demonstrate that SIRT5 is a global regulator of lysine malonylation and provide a mechanism for regulation of energetic flux through glycolysis.
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Affiliation(s)
- Yuya Nishida
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew J Rardin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Chris Carrico
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wenjuan He
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexandria K Sahu
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Philipp Gut
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rami Najjar
- Cell Signaling Technology, Inc, 3 Trask Lane, Danvers, MA 01923, USA
| | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; KineMed, Inc., Emeryville, CA 94608, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
| | - Eric Verdin
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA.
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337
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Abstract
Molecular, catalytic and structural properties of glyoxalase pathway enzymes of many species are now known. Current research has focused on the regulation of activity and expression of Glo1 (glyoxalase I) and Glo2 (glyoxalase II) and their role in health and disease. Human GLO1 has MRE (metal-response element), IRE (insulin-response element), E2F4 (early gene 2 factor isoform 4), AP-2α (activating enhancer-binding protein 2α) and ARE (antioxidant response-element) regulatory elements and is a hotspot for copy number variation. The human Glo2 gene, HAGH (hydroxyacylglutathione hydrolase), has a regulatory p53-response element. Glo1 is linked to healthy aging, obesity, diabetes and diabetic complications, chronic renal disease, cardiovascular disease, other disorders and multidrug resistance in cancer chemotherapy. Mathematical modelling of the glyoxalase pathway predicts that pharmacological levels of increased Glo1 activity markedly decrease cellular methylglyoxal and related glycation, and pharmacological Glo1 inhibition markedly increases cellular methylglyoxal and related glycation. Glo1 inducers are in development to sustain healthy aging and for treatment of vascular complications of diabetes and other disorders, and cell-permeant Glo1 inhibitors are in development for treatment of multidrug-resistant tumours, malaria and potentially pathogenic bacteria and fungi.
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338
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Kochanowski K, Sauer U, Noor E. Posttranslational regulation of microbial metabolism. Curr Opin Microbiol 2015; 27:10-7. [PMID: 26048423 DOI: 10.1016/j.mib.2015.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/04/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Fluxes in microbial metabolism are controlled by various regulatory layers that alter abundance or activity of metabolic enzymes. Recent studies suggest a division of labor between these layers: transcriptional regulation mostly controls the allocation of protein resources, passive flux regulation by enzyme saturation and thermodynamics allows rapid responses at the expense of higher protein cost, and posttranslational regulation is utilized by cells to directly take control of metabolic decisions. We present recent advances in elucidating the role of these regulatory layers, focusing on posttranslational modifications and allosteric interactions. As the systematic mapping of posttranslational regulatory events has now become possible, the next challenge is to identify those regulatory events that are functionally relevant under a given condition.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland; Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland.
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
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339
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Pietrocola F, Galluzzi L, Bravo-San Pedro JM, Madeo F, Kroemer G. Acetyl coenzyme A: a central metabolite and second messenger. Cell Metab 2015; 21:805-21. [PMID: 26039447 DOI: 10.1016/j.cmet.2015.05.014] [Citation(s) in RCA: 866] [Impact Index Per Article: 96.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acetyl-coenzyme A (acetyl-CoA) is a central metabolic intermediate. The abundance of acetyl-CoA in distinct subcellular compartments reflects the general energetic state of the cell. Moreover, acetyl-CoA concentrations influence the activity or specificity of multiple enzymes, either in an allosteric manner or by altering substrate availability. Finally, by influencing the acetylation profile of several proteins, including histones, acetyl-CoA controls key cellular processes, including energy metabolism, mitosis, and autophagy, both directly and via the epigenetic regulation of gene expression. Thus, acetyl-CoA determines the balance between cellular catabolism and anabolism by simultaneously operating as a metabolic intermediate and as a second messenger.
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Affiliation(s)
- Federico Pietrocola
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - Lorenzo Galluzzi
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - José Manuel Bravo-San Pedro
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| | - Guido Kroemer
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France.
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340
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Lorendeau D, Christen S, Rinaldi G, Fendt SM. Metabolic control of signalling pathways and metabolic auto-regulation. Biol Cell 2015; 107:251-72. [DOI: 10.1111/boc.201500015] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Doriane Lorendeau
- Vesalius Research Center; VIB; Leuven 3000 Belgium
- Department of Oncology; KU Leuven; Leuven 3000 Belgium
| | - Stefan Christen
- Vesalius Research Center; VIB; Leuven 3000 Belgium
- Department of Oncology; KU Leuven; Leuven 3000 Belgium
| | - Gianmarco Rinaldi
- Vesalius Research Center; VIB; Leuven 3000 Belgium
- Department of Oncology; KU Leuven; Leuven 3000 Belgium
| | - Sarah-Maria Fendt
- Vesalius Research Center; VIB; Leuven 3000 Belgium
- Department of Oncology; KU Leuven; Leuven 3000 Belgium
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341
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Protein acetylation as a means to regulate protein function in tune with metabolic state. Biochem Soc Trans 2015; 42:1037-42. [PMID: 25109999 DOI: 10.1042/bst20140135] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein acetylation has emerged as a prominent post-translational modification that can occur on a wide variety of proteins. The metabolite acetyl-CoA is a key intermediate in energy metabolism that also serves as the acetyl group donor in protein acetylation modifications. Therefore such acetylation modifications might be coupled to the intracellular availability of acetyl-CoA. In the present article, we summarize recent evidence suggesting that the particular protein acetylation modifications enable the regulation of protein function in tune with acetyl-CoA availability and thus the metabolic state of the cell.
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342
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Palmieri EM, Spera I, Menga A, Infantino V, Porcelli V, Iacobazzi V, Pierri CL, Hooper DC, Palmieri F, Castegna A. Acetylation of human mitochondrial citrate carrier modulates mitochondrial citrate/malate exchange activity to sustain NADPH production during macrophage activation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:729-38. [PMID: 25917893 DOI: 10.1016/j.bbabio.2015.04.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/27/2015] [Accepted: 04/18/2015] [Indexed: 01/22/2023]
Abstract
The mitochondrial citrate-malate exchanger (CIC), a known target of acetylation, is up-regulated in activated immune cells and plays a key role in the production of inflammatory mediators. However, the role of acetylation in CIC activity is elusive. We show that CIC is acetylated in activated primary human macrophages and U937 cells and the level of acetylation is higher in glucose-deprived compared to normal glucose medium. Acetylation enhances CIC transport activity, leading to a higher citrate efflux from mitochondria in exchange with malate. Cytosolic citrate levels do not increase upon activation of cells grown in deprived compared to normal glucose media, indicating that citrate, transported from mitochondria at higher rates from acetylated CIC, is consumed at higher rates. Malate levels in the cytosol are lower in activated cells grown in glucose-deprived compared to normal glucose medium, indicating that this TCA intermediate is rapidly recycled back into the cytosol where it is used by the malic enzyme. Additionally, in activated cells CIC inhibition increases the NADP+/NADPH ratio in glucose-deprived cells; this ratio is unchanged in glucose-rich grown cells due to the activity of the pentose phosphate pathway. Consistently, the NADPH-producing isocitrate dehydrogenase level is higher in activated glucose-deprived as compared to glucose rich cells. These results demonstrate that, in the absence of glucose, activated macrophages increase CIC acetylation to enhance citrate efflux from mitochondria not only to produce inflammatory mediators but also to meet the NADPH demand through the actions of isocitrate dehydrogenase and malic enzyme.
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Affiliation(s)
- Erika M Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Iolanda Spera
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Alessio Menga
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | | | - Vito Porcelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Vito Iacobazzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari "Aldo Moro", Bari, Italy; CNR Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Douglas C Hooper
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, USA; Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, USA
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari "Aldo Moro", Bari, Italy.
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari "Aldo Moro", Bari, Italy.
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343
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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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344
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Gibson GE, Xu H, Chen HL, Chen W, Denton TT, Zhang S. Alpha-ketoglutarate dehydrogenase complex-dependent succinylation of proteins in neurons and neuronal cell lines. J Neurochem 2015; 134:86-96. [PMID: 25772995 DOI: 10.1111/jnc.13096] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/13/2015] [Accepted: 03/04/2015] [Indexed: 01/13/2023]
Abstract
Reversible post-translation modifications of proteins are common in all cells and appear to regulate many processes. Nevertheless, the enzyme(s) responsible for the alterations and the significance of the modification are largely unknown. Succinylation of proteins occurs and causes large changes in the structure of proteins; however, the source of the succinyl groups, the targets, and the consequences of these modifications on other proteins remain unknown. These studies focused on succinylation of mitochondrial proteins. The results demonstrate that the α-ketoglutarate dehydrogenase complex (KGDHC) can serve as a trans-succinylase that mediates succinylation in an α-ketoglutarate-dependent manner. Inhibition of KGDHC reduced succinylation of both cytosolic and mitochondrial proteins in cultured neurons and in a neuronal cell line. Purified KGDHC can succinylate multiple proteins including other enzymes of the tricarboxylic acid cycle leading to modification of their activity. Inhibition of KGDHC also modifies acetylation by modifying the pyruvate dehydrogenase complex. The much greater effectiveness of KGDHC than succinyl-CoA suggests that the catalysis owing to the E2k succinyltransferase is important. Succinylation appears to be a major signaling system and it can be mediated by KGDHC. Reversible post-translation modifications of proteins are common and may regulate many processes. Succinylation of proteins occurs and causes large changes in the structure of proteins. However, the source of the succinyl groups, the targets, and the consequences of these modifications on other proteins remains unknown. The results demonstrate that the mitochondrial α-ketoglutarate dehydrogenase complex (KGDHC) can succinylate multiple mitochondrial proteins and alter their function. Succinylation appears to be a major signaling system and it can be mediated by KGDHC.
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Affiliation(s)
- Gary E Gibson
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Hui Xu
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Huan-Lian Chen
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Wei Chen
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Travis T Denton
- College of Pharmacy, Washington State University, Spokane, Washington, USA
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
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345
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Rousseaux S, Khochbin S. Histone Acylation beyond Acetylation: Terra Incognita in Chromatin Biology. CELL JOURNAL 2015; 17:1-6. [PMID: 25870829 PMCID: PMC4393657 DOI: 10.22074/cellj.2015.506] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 12/24/2014] [Indexed: 12/16/2022]
Abstract
Histone acetylation, one of the first and best studied histone post-translational modifications (PTMs), as well as the factors involved in its deposition (writers), binding (readers) and removal (erasers), have been shown to act at the heart of regulatory circuits controlling essential cellular functions. The identification of a variety of competing histone lysine-modifying acyl groups including propionyl, butyryl, 2-hydroxyisobutyryl, crotonyl, malonyl, succinyl and glutaryl, raises numerous questions on their functional significance, the molecular systems that manage their establishment, removal and interplay with the well-known acetylation-based mechanisms. Detailed and large-scale investigations of two of these new histone PTMs, crotonylation and 2-hydroxyisobutyrylation, along with histone acetylation, in the context of male genome programming, where stage-specific gene expression programs are switched on and off in turn, have shed light on their functional contribution to the epigenome for the first time. These initial investigations fired many additional questions, which remain to be explored. This review surveys the major results taken from these two new histone acylations and discusses the new biology that is emerging based on the diversity of histone lysine acylations.
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Affiliation(s)
| | - Saadi Khochbin
- INSERMU823University Grenoble-AlpesInstitute Albert BonniotGrenobleF-38700France
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346
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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347
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Overmyer KA, Evans CR, Qi NR, Minogue CE, Carson JJ, Chermside-Scabbo CJ, Koch LG, Britton SL, Pagliarini DJ, Coon JJ, Burant CF. Maximal oxidative capacity during exercise is associated with skeletal muscle fuel selection and dynamic changes in mitochondrial protein acetylation. Cell Metab 2015; 21:468-78. [PMID: 25738461 PMCID: PMC4350023 DOI: 10.1016/j.cmet.2015.02.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/16/2014] [Accepted: 02/06/2015] [Indexed: 01/24/2023]
Abstract
Maximal exercise-associated oxidative capacity is strongly correlated with health and longevity in humans. Rats selectively bred for high running capacity (HCR) have improved metabolic health and are longer-lived than their low-capacity counterparts (LCR). Using metabolomic and proteomic profiling, we show that HCR efficiently oxidize fatty acids (FAs) and branched-chain amino acids (BCAAs), sparing glycogen and reducing accumulation of short- and medium-chain acylcarnitines. HCR mitochondria have reduced acetylation of mitochondrial proteins within oxidative pathways at rest, and there is rapid protein deacetylation with exercise, which is greater in HCR than LCR. Fluxomic analysis of valine degradation with exercise demonstrates a functional role of differential protein acetylation in HCR and LCR. Our data suggest that efficient FA and BCAA utilization contribute to high intrinsic exercise capacity and the health and longevity benefits associated with enhanced fitness.
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Affiliation(s)
- Katherine A Overmyer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles R Evans
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nathan R Qi
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Joshua J Carson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Lauren G Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steven L Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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348
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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: 302] [Impact Index Per Article: 33.6] [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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349
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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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350
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Muoio DM. Metabolic inflexibility: when mitochondrial indecision leads to metabolic gridlock. Cell 2015; 159:1253-62. [PMID: 25480291 DOI: 10.1016/j.cell.2014.11.034] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 12/18/2022]
Abstract
Normal energy metabolism is characterized by periodic shifts in glucose and fat oxidation, as the mitochondrial machinery responsible for carbon combustion switches freely between alternative fuels according to physiological and nutritional circumstances. These transitions in fuel choice are orchestrated by an intricate network of metabolic and cell signaling events that enable exquisite crosstalk and cooperation between competing substrates to maintain energy and glucose homeostasis. By contrast, obesity-related cardiometabolic diseases are increasingly recognized as disorders of metabolic inflexibility, in which nutrient overload and heightened substrate competition result in mitochondrial indecision, impaired fuel switching, and energy dysregulation. This Perspective offers a speculative view on the molecular origins and pathophysiological consequences of metabolic inflexibility.
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Affiliation(s)
- Deborah M Muoio
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA.
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