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Thiagarajan D, Vedantham S, Ananthakrishnan R, Schmidt AM, Ramasamy R. Mechanisms of transcription factor acetylation and consequences in hearts. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1862:2221-2231. [PMID: 27543804 PMCID: PMC5159280 DOI: 10.1016/j.bbadis.2016.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/12/2016] [Accepted: 08/14/2016] [Indexed: 01/06/2023]
Abstract
Acetylation of proteins as a post-translational modification is gaining rapid acceptance as a cellular control mechanism on par with other protein modification mechanisms such as phosphorylation and ubiquitination. Through genetic manipulations and evolving proteomic technologies, identification and consequences of transcription factor acetylation is beginning to emerge. In this review, we summarize the field and discuss newly unfolding mechanisms and consequences of transcription factor acetylation in normal and stressed hearts. This article is part of a Special Issue entitled: The role of post-translational protein modifications on heart and vascular metabolism edited by Jason R.B. Dyck & Jan F.C. Glatz.
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Affiliation(s)
- Devi Thiagarajan
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, NY, New York 10016, United States
| | | | - Radha Ananthakrishnan
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, NY, New York 10016, United States
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, NY, New York 10016, United States
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, NY, New York 10016, United States.
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Meyer JG, D'Souza AK, Sorensen DJ, Rardin MJ, Wolfe AJ, Gibson BW, Schilling B. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1758-1771. [PMID: 27590315 PMCID: PMC5059418 DOI: 10.1007/s13361-016-1476-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/28/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Post-translational modification of lysine residues by NƐ-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods can overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy. Graphical Abstract ᅟ.
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Affiliation(s)
- Jesse G Meyer
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | | | | | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94143, USA.
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Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Mol Cell 2016; 63:621-632. [PMID: 27499296 DOI: 10.1016/j.molcel.2016.06.033] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 03/25/2016] [Accepted: 06/21/2016] [Indexed: 12/23/2022]
Abstract
Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function.
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Gertz M, Steegborn C. Using mitochondrial sirtuins as drug targets: disease implications and available compounds. Cell Mol Life Sci 2016; 73:2871-96. [PMID: 27007507 PMCID: PMC11108305 DOI: 10.1007/s00018-016-2180-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/15/2016] [Accepted: 03/11/2016] [Indexed: 02/06/2023]
Abstract
Sirtuins are an evolutionary conserved family of NAD(+)-dependent protein lysine deacylases. Mammals have seven Sirtuin isoforms, Sirt1-7. They contribute to regulation of metabolism, stress responses, and aging processes, and are considered therapeutic targets for metabolic and aging-related diseases. While initial studies were focused on Sirt1 and 2, recent progress on the mitochondrial Sirtuins Sirt3, 4, and 5 has stimulated research and drug development for these isoforms. Here we review the roles of Sirtuins in regulating mitochondrial functions, with a focus on the mitochondrially located isoforms, and on their contributions to disease pathologies. We further summarize the compounds available for modulating the activity of these Sirtuins, again with a focus on mitochondrial isoforms, and we describe recent results important for the further improvement of compounds. This overview illustrates the potential of mitochondrial Sirtuins as drug targets and summarizes the status, progress, and challenges in developing small molecule compounds modulating their activity.
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Affiliation(s)
- Melanie Gertz
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
- Bayer Pharma AG, Apratherweg 18a, 42096, Wuppertal, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany.
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55
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Song HY, Park SH, Kang HJ, Vassilopoulos A. Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates. J Vis Exp 2016:53563. [PMID: 26966987 DOI: 10.3791/53563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Acetylation has emerged as an important post-translational modification (PTM) regulating a plethora of cellular processes and functions. This is further supported by recent findings in high-resolution mass spectrometry based proteomics showing that many new proteins and sites within these proteins can be acetylated. However the identity of the enzymes regulating these proteins and sites is often unknown. Among these enzymes, sirtuins, which belong to the class III histone lysine deacetylases, have attracted great interest as enzymes regulating the acetylome under different physiological or pathophysiological conditions. Here we describe methods to link SIRT2, the cytoplasmic sirtuin, with its substrates including both in vitro and in vivo deacetylation assays. These assays can be applied in studies focused on other members of the sirtuin family to unravel the specific role of sirtuins and are necessary in order to establish the regulatory interplay of specific deacetylases with their substrates as a first step to better understand the role of protein acetylation. Furthermore, such assays can be used to distinguish functional acetylation sites on a protein from what may be non-regulatory acetylated lysines, as well as to examine the interplay between a deacetylase and its substrate in a physiological context.
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Affiliation(s)
- Ha Yong Song
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Seong-Hoon Park
- Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Hong-Jun Kang
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Athanassios Vassilopoulos
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University;
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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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57
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Cheng Y, Hou T, Ping J, Chen G, Chen J. Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model. Proteome Sci 2016; 14:3. [PMID: 26843850 PMCID: PMC4739109 DOI: 10.1186/s12953-016-0092-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/26/2016] [Indexed: 02/07/2023] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is a clinical frequent disease. However, its pathogenesis still needs further study, especially the mechanism at the molecular level. The recent identified novel protein post-translational modification, lysine succinylation was reported involved in diverse metabolism and cellular processes. In this study, we performed the quantitative succinylome analysis in the liver of NAFLD model to elucidate the regulatory role of lysine succinylation in NAFLD progression. Methods Firstly, experimental model of NAFLD was induced by carbon tetrachloride injection and supplementary high-lipid and low-protein diet. Then series histochemical and biochemical variables were determined. For the quantitative succinylome analysis, tandem mass tags (TMT)-labeling, highly sensitive immune-affinity purification, liquid chromatography-tandem mass spectrometry techniques were applied. Bioinformatics analysis including gene ontology annotation based classification; Wolfpsort based subcellular prediction; function enrichment; protein-protein interaction network construction and conserved succinylation site motifs extraction were performed to decipher the differentially changed succinylated proteins and sites and p-value < 0.05 was selected as threshold. Results Totally, 815 succinylation sites on 407 proteins were identified, of which 243 succinylation acetylation sites on 178 proteins showed changed succinylation level with the threshold fold change > 1.5. Theses differentially changed succinylated proteins were involved in diverse metabolism pathways and cellular processes including carbon metabolism, amino acid metabolism, fat acid metabolism, binding and catalyzing, anti-oxidation and xenobiotics metabolism. Besides, these differentially changed succinylated proteins were prominently localized to cytoplasm and mitochondria. Moreover, 8 conserved succinylation site motifs were extracted around the succinylation sites. Conclusions Protein succinylation was an extensive post-translation modification in rat. The changed succinylation level in diverse proteins may disturb multiple metabolism pathways and promote non-alcoholic fatty liver disease development. This study provided a basis for further characterization of the pathophysiological role of lysine succinylation in NAFLD progression, which laid a foundation for the innovation of novel NAFLD drugs and therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0092-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Cheng
- Department of liver disease, Hospital for Infectious Diseases of Pudong New Area, Shanghai, 201299 P. R. China ; Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Tianlu Hou
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Jian Ping
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Gaofeng Chen
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Jianjie Chen
- Department of liver disease, Hospital for Infectious Diseases of Pudong New Area, Shanghai, 201299 P. R. China ; Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
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58
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Suski M, Olszanecki R, Chmura Ł, Stachowicz A, Madej J, Okoń K, Adamek D, Korbut R. Influence of metformin on mitochondrial subproteome in the brain of apoE knockout mice. Eur J Pharmacol 2016; 772:99-107. [DOI: 10.1016/j.ejphar.2015.12.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
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59
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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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60
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Xie L, Fang W, Deng W, Yu Z, Li J, Chen M, Liao W, Xie J, Pan W. Global profiling of lysine acetylation in human histoplasmosis pathogen Histoplasma capsulatum. Int J Biochem Cell Biol 2016; 73:1-10. [PMID: 26806293 DOI: 10.1016/j.biocel.2016.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/29/2015] [Accepted: 01/15/2016] [Indexed: 11/16/2022]
Abstract
Histoplasma capsulatum is the causative agent of human histoplasmosis, which can cause respiratory and systemic mycosis in immune-compromised individuals. Lysine acetylation, a protein posttranslational protein modification, is widespread in both eukaryotes and prokaryotes. Although increasing evidence suggests that lysine acetylation may play critical roles in fungus physiology, very little is known about its extent and function in H. capsulatum. To comprehensively profile protein lysine acetylation in H. capsulatum, we performed a global acetylome analysis through peptide prefractionation, antibody enrichment, and LC-MS/MS analysis, identifying 775 acetylation sites on 456 acetylated proteins; and functionally analysis showing their involvement in different biological processes. We defined six types of acetylation site motifs, and the results imply that lysine residue of polypeptide with tyrosine at the -1 and +1 positions, histidine at the +1 position, and phenylalanine (F) at the +1 and +2 position is a preferred substrate of lysine acetyltransferase. Moreover, some virulence factors candidates including calmodulin and DnaK are acetylated. In conclusion, our data set may serve as an important resource for the elucidation of associations between functional protein lysine acetylation and virulence in H. capsulatum.
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Affiliation(s)
- Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Juan Li
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China.
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
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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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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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63
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Wende AR. Post-translational modifications of the cardiac proteome in diabetes and heart failure. Proteomics Clin Appl 2015; 10:25-38. [PMID: 26140508 PMCID: PMC4698356 DOI: 10.1002/prca.201500052] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/03/2015] [Accepted: 06/29/2015] [Indexed: 12/19/2022]
Abstract
Cardiovascular complications are the leading cause of death in diabetic patients. Decades of research has focused on altered gene expression, altered cellular signaling, and altered metabolism. This work has led to better understanding of disease progression and treatments aimed at reversing or stopping this deadly process. However, one of the pieces needed to complete the puzzle and bridge the gap between altered gene expression and changes in signaling/metabolism is the proteome and its host of modifications. Defining the mechanisms of regulation includes examining protein levels, localization, and activity of the functional component of cellular machinery. Excess or misutilization of nutrients in obesity and diabetes may lead to PTMs contributing to cardiovascular disease progression. PTMs link regulation of metabolic changes in the healthy and diseased heart with regulation of gene expression itself (e.g. epigenetics), protein enzymatic activity (e.g. mitochondrial oxidative capacity), and function (e.g. contractile machinery). Although a number of PTMs are involved in each of these pathways, we will highlight the role of the serine and threonine O‐linked addition of β‐N‐acetyl‐glucosamine or O‐GlcNAcylation. This nexus of nutrient supply, utilization, and storage allows for the modification and translation of mitochondrial function to many other aspects of the cell.
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Affiliation(s)
- Adam R Wende
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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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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65
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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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66
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Thompson D, Regev A, Roy S. Comparative analysis of gene regulatory networks: from network reconstruction to evolution. Annu Rev Cell Dev Biol 2015; 31:399-428. [PMID: 26355593 DOI: 10.1146/annurev-cellbio-100913-012908] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequence to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.
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Affiliation(s)
- Dawn Thompson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
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67
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McDonnell E, Peterson BS, Bomze HM, Hirschey MD. SIRT3 regulates progression and development of diseases of aging. Trends Endocrinol Metab 2015; 26:486-492. [PMID: 26138757 PMCID: PMC4558250 DOI: 10.1016/j.tem.2015.06.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
The mitochondrial sirtuin SIRT3 is a protein deacylase that influences almost every major aspect of mitochondrial biology, including nutrient oxidation, ATP generation, reactive oxygen species (ROS) detoxification, mitochondrial dynamics, and the mitochondrial unfolded protein response (UPR). Interestingly, mice lacking SIRT3 (SIRT3KO), either spontaneously or when crossed with mouse models of disease, develop several diseases of aging at an accelerated pace, such as cancer, metabolic syndrome, cardiovascular disease, and neurodegenerative diseases, and, thus, might be a valuable model of accelerated aging. In this review, we discuss functions of SIRT3 in pathways involved in diseases of aging and how the lack of SIRT3 might accelerate the aging process. We also suggest that further studies on SIRT3 will help uncover important new pathways driving the aging process.
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Affiliation(s)
- Eoin McDonnell
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Brett S Peterson
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Howard M Bomze
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC 27701, USA
- Departments of Medicine and Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA
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68
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Song BJ, Akbar M, Abdelmegeed MA, Byun K, Lee B, Yoon SK, Hardwick JP. Mitochondrial dysfunction and tissue injury by alcohol, high fat, nonalcoholic substances and pathological conditions through post-translational protein modifications. Redox Biol 2015; 3:109-23. [PMID: 25465468 PMCID: PMC4297931 DOI: 10.1016/j.redox.2014.10.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are critically important in providing cellular energy ATP as well as their involvement in anti-oxidant defense, fat oxidation, intermediary metabolism and cell death processes. It is well-established that mitochondrial functions are suppressed when living cells or organisms are exposed to potentially toxic agents including alcohol, high fat diets, smoking and certain drugs or in many pathophysiological states through increased levels of oxidative/nitrative stress. Under elevated nitroxidative stress, cellular macromolecules proteins, DNA, and lipids can undergo different oxidative modifications, leading to disruption of their normal, sometimes critical, physiological functions. Recent reports also indicated that many mitochondrial proteins are modified via various post-translation modifications (PTMs) and primarily inactivated. Because of the recently-emerging information, in this review, we specifically focus on the mechanisms and roles of five major PTMs (namely oxidation, nitration, phosphorylation, acetylation, and adduct formation with lipid-peroxides, reactive metabolites, or advanced glycation end products) in experimental models of alcoholic and nonalcoholic fatty liver disease as well as acute hepatic injury caused by toxic compounds. We also highlight the role of the ethanol-inducible cytochrome P450-2E1 (CYP2E1) in some of these PTM changes. Finally, we discuss translational research opportunities with natural and/or synthetic anti-oxidants, which can prevent or delay the onset of mitochondrial dysfunction, fat accumulation and tissue injury. Hepatotoxic agents including alcohol and high fat elevate nitroxidative stress. Increased nitroxidative stress promotes post-translational protein modifications. Post-translational protein modifications of many proteins lead to their inactivation. Inactivation of mitochondrial proteins contributes to mitochondrial dysfunction. Mitochondrial dysfunction contributes to necrotic or apoptotic tissue injury.
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69
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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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70
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Larance M, Lamond AI. Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 2015; 16:269-80. [DOI: 10.1038/nrm3970] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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71
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Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Fotuhi Siahpirani A, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM. SIRT3 mediates multi-tissue coupling for metabolic fuel switching. Cell Metab 2015; 21:637-46. [PMID: 25863253 PMCID: PMC4393847 DOI: 10.1016/j.cmet.2015.03.007] [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: 08/21/2014] [Revised: 12/17/2014] [Accepted: 03/09/2015] [Indexed: 02/07/2023]
Abstract
SIRT3 is a member of the Sirtuin family of NAD(+)-dependent deacylases and plays a critical role in metabolic regulation. Organism-wide SIRT3 loss manifests in metabolic alterations; however, the coordinating role of SIRT3 among metabolically distinct tissues is unknown. Using multi-tissue quantitative proteomics comparing fasted wild-type mice to mice lacking SIRT3, innovative bioinformatic analysis, and biochemical validation, we provide a comprehensive view of mitochondrial acetylation and SIRT3 function. We find SIRT3 regulates the acetyl-proteome in core mitochondrial processes common to brain, heart, kidney, liver, and skeletal muscle, but differentially regulates metabolic pathways in fuel-producing and fuel-utilizing tissues. We propose an additional maintenance function for SIRT3 in liver and kidney where SIRT3 expression is elevated to reduce the acetate load on mitochondrial proteins. We provide evidence that SIRT3 impacts ketone body utilization in the brain and reveal a pivotal role for SIRT3 in the coordination between tissues required for metabolic homeostasis.
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Affiliation(s)
| | - Alicia L Richards
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Jing Fan
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Michael J Smallegan
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | | | - Zachary A Kemmerer
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Tomas A Prolla
- Department of Genetics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA.
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72
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Zhang Y, Bharathi SS, Rardin MJ, Uppala R, Verdin E, Gibson BW, Goetzman ES. SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase. PLoS One 2015; 10:e0122297. [PMID: 25811481 PMCID: PMC4374878 DOI: 10.1371/journal.pone.0122297] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/22/2015] [Indexed: 11/18/2022] Open
Abstract
SIRT3 and SIRT5 have been shown to regulate mitochondrial fatty acid oxidation but the molecular mechanisms behind the regulation are lacking. Here, we demonstrate that SIRT3 and SIRT5 both target human very long-chain acyl-CoA dehydrogenase (VLCAD), a key fatty acid oxidation enzyme. SIRT3 deacetylates and SIRT5 desuccinylates K299 which serves to stabilize the essential FAD cofactor in the active site. Further, we show that VLCAD binds strongly to cardiolipin and isolated mitochondrial membranes via a domain near the C-terminus containing lysines K482, K492, and K507. Acetylation or succinylation of these residues eliminates binding of VLCAD to cardiolipin. SIRT3 deacetylates K507 while SIRT5 desuccinylates K482, K492, and K507. Sirtuin deacylation of recombinant VLCAD rescues membrane binding. Endogenous VLCAD from SIRT3 and SIRT5 knockout mouse liver shows reduced binding to cardiolipin. Thus, SIRT3 and SIRT5 promote fatty acid oxidation by converging upon VLCAD to promote its activity and membrane localization. Regulation of cardiolipin binding by reversible lysine acylation is a novel mechanism that is predicted to extrapolate to other metabolic proteins that localize to the inner mitochondrial membrane.
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Affiliation(s)
- Yuxun Zhang
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sivakama S. Bharathi
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Matthew J. Rardin
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Radha Uppala
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eric Verdin
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Eric S. Goetzman
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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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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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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Abstract
![]()
Protein acetylation of lysine ε-amino
groups is abundant in cells, particularly within mitochondria. The
contribution of enzyme-catalyzed and nonenzymatic acetylation in mitochondria
remains unresolved. Here, we utilize a newly developed approach to
measure site-specific, nonenzymatic acetylation rates for 90 sites
in eight native purified proteins. Lysine reactivity (as second-order
rate constants) with acetyl-phosphate and acetyl-CoA ranged over 3
orders of magnitude, and higher chemical reactivity tracked with likelihood
of dynamic modification in vivo, providing evidence
that enzyme-catalyzed acylation might not be necessary to explain
the prevalence of acetylation in mitochondria. Structural analysis
revealed that many highly reactive sites exist within clusters of
basic residues, whereas lysines that show low reactivity are engaged
in strong attractive electrostatic interactions with acidic residues.
Lysine clusters are predicted to be high-affinity substrates of mitochondrial
deacetylase SIRT3 both in vitro and in vivo. Our analysis describing rate determination of lysine acetylation
is directly applicable to investigate targeted and proteome-wide acetylation,
whether or not the reaction is enzyme catalyzed.
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Affiliation(s)
- Josue Baeza
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - Michael J. Smallegan
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department of Biomolecular Chemistry and ‡Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
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Hölper S, Nolte H, Bober E, Braun T, Krüger M. Dissection of metabolic pathways in the Db/Db mouse model by integrative proteome and acetylome analysis. MOLECULAR BIOSYSTEMS 2015; 11:908-22. [DOI: 10.1039/c4mb00490f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An in vivo SILAC-based quantitative proteomics approach to analyse protein abundances and acetylation levels under diabetic conditions.
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Affiliation(s)
- Soraya Hölper
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Hendrik Nolte
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Eva Bober
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
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77
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Fang X, Chen W, Zhao Y, Ruan S, Zhang H, Yan C, Jin L, Cao L, Zhu J, Ma H, Cheng Z. Global analysis of lysine acetylation in strawberry leaves. FRONTIERS IN PLANT SCIENCE 2015; 6:739. [PMID: 26442052 PMCID: PMC4569977 DOI: 10.3389/fpls.2015.00739] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/31/2015] [Indexed: 05/08/2023]
Abstract
Protein lysine acetylation is a reversible and dynamic post-translational modification. It plays an important role in regulating diverse cellular processes including chromatin dynamic, metabolic pathways, and transcription in both prokaryotes and eukaryotes. Although studies of lysine acetylome in plants have been reported, the throughput was not high enough, hindering the deep understanding of lysine acetylation in plant physiology and pathology. In this study, taking advantages of anti-acetyllysine-based enrichment and high-sensitive-mass spectrometer, we applied an integrated proteomic approach to comprehensively investigate lysine acetylome in strawberry. In total, we identified 1392 acetylation sites in 684 proteins, representing the largest dataset of acetylome in plants to date. To reveal the functional impacts of lysine acetylation in strawberry, intensive bioinformatic analysis was performed. The results significantly expanded our current understanding of plant acetylome and demonstrated that lysine acetylation is involved in multiple cellular metabolism and cellular processes. More interestingly, nearly 50% of all acetylated proteins identified in this work were localized in chloroplast and the vital role of lysine acetylation in photosynthesis was also revealed. Taken together, this study not only established the most extensive lysine acetylome in plants to date, but also systematically suggests the significant and unique roles of lysine acetylation in plants.
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Affiliation(s)
- Xianping Fang
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Wenyue Chen
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Yun Zhao
- Experiment Center, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Songlin Ruan
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Hengmu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Chengqi Yan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Liang Jin
- Research and Development Center of Flower, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | | | - Jun Zhu
- Jingjie PTM BiolabsHangzhou, China
| | - Huasheng Ma
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
- *Correspondence: Huasheng Ma, Hangzhou Academy of Agricultural Sciences, Institute of Biology, East Hangxin Road 1, Hangzhou 310024, China
| | - Zhongyi Cheng
- Institute for Advanced Study of Translational Medicine, Tongji UniversityShanghai, China
- Zhongyi Cheng, Institute for Advanced Study of Translational Medicine, Tongji University, Siping Road 1239, Shanghai 200092, China
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78
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Effect of lysine to alanine mutations on the phosphate activation and BPTES inhibition of glutaminase. Neurochem Int 2014; 88:10-4. [PMID: 25510640 DOI: 10.1016/j.neuint.2014.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/24/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022]
Abstract
The GLS1 gene encodes a mitochondrial glutaminase that is highly expressed in brain, kidney, small intestine and many transformed cells. Recent studies have identified multiple lysine residues in glutaminase that are sites of N-acetylation. Interestingly, these sites are located within either a loop segment that regulates access of glutamine to the active site or the dimer:dimer interface that participates in the phosphate-dependent oligomerization and activation of the enzyme. These two segments also contain the binding sites for bis-2[5-phenylacetamido-1,2,4-thiadiazol-2-yl]ethylsulfide (BPTES), a highly specific and potent uncompetitive inhibitor of this glutaminase. BPTES is also the lead compound for development of novel cancer chemotherapeutic agents. To provide a preliminary assessment of the potential effects of N-acetylation, the corresponding lysine to alanine mutations were constructed in the hGACΔ1 plasmid. The wild type and mutated proteins were purified by Ni(+)-affinity chromatography and their phosphate activation and BPTES inhibition profiles were analyzed. Two of the alanine substitutions in the loop segment (K311A and K328A) and the one in the dimer:dimer interface (K396A) form enzymes that require greater concentrations of phosphate to produce half-maximal activation and exhibit greater sensitivity to BPTES inhibition. By contrast, the K320A mutation results in a glutaminase that exhibits near maximal activity in the absence of phosphate and is not inhibited by BPTES. Thus, lysine N-acetylation may contribute to the acute regulation of glutaminase activity in various tissues and alter the efficacy of BPTES-type inhibitors.
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79
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Lysine acetylproteome analysis suggests its roles in primary and secondary metabolism in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2014; 99:1399-413. [PMID: 25487885 DOI: 10.1007/s00253-014-6144-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 01/19/2023]
Abstract
Lysine acetylation is a dynamic, reversible posttranslational modification that is known to play an important role in regulating the activity of many key enzymes in bacteria. Acetylproteome studies have been performed on some bacteria. However, until now, there have been no data on Actinomycetes, which are the major producers of therapeutic antibiotics. In this study, we investigated the first acetylproteome of the erythromycin-producing actinomycete Saccharopolyspora erythraea using a high-resolution mass spectrometry-based proteomics approach. Using immune-affinity isolation of acetyl-peptides with an anti-acetyllysine antibody followed by nano ultra performance liquid chromatography tandem mass spectroscopy (nanoUPLC-MS/MS) analysis, we identified 664 unique lysine-acetylated sites on 363 proteins. Acetylated proteins are involved in many biological processes such as protein synthesis, glycolysis/gluconeogenesis, citric acid (TCA) cycle, fatty acid metabolism, secondary metabolism, and the feeder metabolic pathways of erythromycin synthesis. We characterized the acetylproteome and analyzed in detail the impact of acetylation on diverse cellular functions according to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Four motif sequences surrounding the acetylation sites (K(AC)H, K(AC)Y, K(AC)XXXXR, and K(AC)XXXXK) were found in the S. erythraea acetylproteome. These findings suggest that abundant lysine acetylation occurs in Actinomycetes, expand our current knowledge of the bacterial acetylproteome, and provide insight into the regulatory function of acetylation in primary and secondary metabolism.
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80
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Lu YF, Xu YY, Jin F, Wu Q, Shi JS, Liu J. Icariin is a PPARα activator inducing lipid metabolic gene expression in mice. Molecules 2014; 19:18179-91. [PMID: 25383754 PMCID: PMC6270773 DOI: 10.3390/molecules191118179] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/12/2014] [Accepted: 10/13/2014] [Indexed: 01/06/2023] Open
Abstract
Icariin is effective in the treatment of hyperlipidemia. To understand the effect of icariin on lipid metabolism, effects of icariin on PPARα and its target genes were investigated. Mice were treated orally with icariin at doses of 0, 100, 200, and 400 mg/kg, or clofibrate (500 mg/kg) for five days. Liver total RNA was isolated and the expressions of PPARα and lipid metabolism genes were examined. PPARα and its marker genes Cyp4a10 and Cyp4a14 were induced 2-4 fold by icariin, and 4-8 fold by clofibrate. The fatty acid (FA) binding and co-activator proteins Fabp1, Fabp4 and Acsl1 were increased 2-fold. The mRNAs of mitochondrial FA β-oxidation enzymes (Cpt1a, Acat1, Acad1 and Hmgcs2) were increased 2-3 fold. The mRNAs of proximal β-oxidation enzymes (Acox1, Ech1, and Ehhadh) were also increased by icariin and clofibrate. The expression of mRNAs for sterol regulatory element-binding factor-1 (Srebf1) and FA synthetase (Fasn) were unaltered by icariin. The lipid lysis genes Lipe and Pnpla2 were increased by icariin and clofibrate. These results indicate that icariin is a novel PPARα agonist, activates lipid metabolism gene expressions in liver, which could be a basis for its lipid-lowering effects and its beneficial effects against diabetes.
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Affiliation(s)
- Yuan-Fu Lu
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
| | - Yun-Yan Xu
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
| | - Feng Jin
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
| | - Qin Wu
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
| | - Jing-Shan Shi
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
| | - Jie Liu
- Key Lab for Pharmacology of Ministry of Education, Department of Pharmacology, Zunyi Medical College, Zunyi 563003, China.
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81
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Smith-Hammond CL, Hoyos E, Miernyk JA. The pea seedling mitochondrial Nε-lysine acetylome. Mitochondrion 2014; 19 Pt B:154-65. [PMID: 24780491 DOI: 10.1016/j.mito.2014.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022]
Abstract
Posttranslational lysine acetylation is believed to occur in all taxa and to affect thousands of proteins. In contrast to the hundreds of mitochondrial proteins reported to be lysine-acetylated in non-plant species, only a handful have been reported from the plant taxa previously examined. To investigate whether this reflects a biologically significant difference or merely a peculiarity of the samples thus far examined, we immunoenriched and analyzed acetylated peptides from highly purified pea seedling mitochondria using mass spectrometry. Our results indicate that a multitude of mitochondrial proteins, involved in a variety of processes, are acetylated in pea seedlings.
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Affiliation(s)
- Colin L Smith-Hammond
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Elizabeth Hoyos
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Ján A Miernyk
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA.
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82
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Peinado JR, Diaz-Ruiz A, Frühbeck G, Malagon MM. Mitochondria in metabolic disease: getting clues from proteomic studies. Proteomics 2014; 14:452-66. [PMID: 24339000 DOI: 10.1002/pmic.201300376] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/08/2013] [Accepted: 11/21/2013] [Indexed: 01/11/2023]
Abstract
Mitochondria play a key role as major regulators of cellular energy homeostasis, but in the context of mitochondrial dysfunction, mitochondria may generate reactive oxidative species and induce cellular apoptosis. Indeed, altered mitochondrial status has been linked to the pathogenesis of several metabolic disorders and specially disorders related to insulin resistance, such as obesity, type 2 diabetes, and other comorbidities comprising the metabolic syndrome. In the present review, we summarize information from various mitochondrial proteomic studies of insulin-sensitive tissues under different metabolic states. To that end, we first focus our attention on the pancreas, as mitochondrial malfunction has been shown to contribute to beta cell failure and impaired insulin release. Furthermore, proteomic studies of mitochondria obtained from liver, muscle, and adipose tissue are summarized, as these tissues constitute the primary insulin target metabolic tissues. Since recent advances in proteomic techniques have exposed the importance of PTMs in the development of metabolic disease, we also present information on specific PTMs that may directly affect mitochondria during the pathogenesis of metabolic disease. Specifically, mitochondrial protein acetylation, phosphorylation, and other PTMs related to oxidative damage, such as nitrosylation and carbonylation, are discussed.
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Affiliation(s)
- Juan R Peinado
- Department of Medical Sciences, Faculty of Medicine, Ciudad Real, Spain
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83
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The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 2014; 15:536-50. [PMID: 25053359 DOI: 10.1038/nrm3841] [Citation(s) in RCA: 966] [Impact Index Per Article: 96.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling. Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many biological processes through the regulation of protein interactions, activity and localization. In addition, proteins are frequently modified by other types of acylations, such as formylation, butyrylation, propionylation, succinylation, malonylation, myristoylation, glutarylation and crotonylation. The intricate link between lysine acylation and cellular metabolism has been clarified by the occurrence of several such metabolite-sensitive acylations and their selective removal by sirtuin deacylases. These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes.
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84
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Wang Y, Kavran JM, Chen Z, Karukurichi KR, Leahy DJ, Cole PA. Regulation of S-adenosylhomocysteine hydrolase by lysine acetylation. J Biol Chem 2014; 289:31361-72. [PMID: 25248746 DOI: 10.1074/jbc.m114.597153] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S-Adenosylhomocysteine hydrolase (SAHH) is an NAD(+)-dependent tetrameric enzyme that catalyzes the breakdown of S-adenosylhomocysteine to adenosine and homocysteine and is important in cell growth and the regulation of gene expression. Loss of SAHH function can result in global inhibition of cellular methyltransferase enzymes because of high levels of S-adenosylhomocysteine. Prior proteomics studies have identified two SAHH acetylation sites at Lys(401) and Lys(408) but the impact of these post-translational modifications has not yet been determined. Here we use expressed protein ligation to produce semisynthetic SAHH acetylated at Lys(401) and Lys(408) and show that modification of either position negatively impacts the catalytic activity of SAHH. X-ray crystal structures of 408-acetylated SAHH and dually acetylated SAHH have been determined and reveal perturbations in the C-terminal hydrogen bonding patterns, a region of the protein important for NAD(+) binding. These crystal structures along with mutagenesis data suggest that such hydrogen bond perturbations are responsible for SAHH catalytic inhibition by acetylation. These results suggest how increased acetylation of SAHH may globally influence cellular methylation patterns.
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Affiliation(s)
- Yun Wang
- From the Deptartments of Pharmacology and Molecular Sciences and
| | - Jennifer M Kavran
- Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Zan Chen
- From the Deptartments of Pharmacology and Molecular Sciences and
| | | | - Daniel J Leahy
- From the Deptartments of Pharmacology and Molecular Sciences and Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Philip A Cole
- From the Deptartments of Pharmacology and Molecular Sciences and
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85
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Philp A, Rowland T, Perez-Schindler J, Schenk S. Understanding the acetylome: translating targeted proteomics into meaningful physiology. Am J Physiol Cell Physiol 2014; 307:C763-73. [PMID: 25186010 PMCID: PMC4216940 DOI: 10.1152/ajpcell.00399.2013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is well established that exercise elicits a finely tuned adaptive response in skeletal muscle, with contraction frequency, duration, and recovery shaping skeletal muscle plasticity. Given the power of physical activity to regulate metabolic health, numerous research groups have focused on the molecular mechanisms that sense, interpret, and translate this contractile signal into postexercise adaptation. While our current understanding is that contraction-sensitive allosteric factors (e.g., Ca2+, AMP, NAD+, and acetyl-CoA) initiate signaling changes, how the muscle translates changes in these factors into the appropriate adaptive response remains poorly understood. During the past decade, systems biology approaches, utilizing “omics” screening techniques, have allowed researchers to define global processes of regulation with incredible sensitivity and specificity. As a result, physiologists are now able to study substrate flux with stable isotope tracers in combination with metabolomic approaches and to coordinate these functional changes with proteomic and transcriptomic analysis. In this review, we highlight lysine acetylation as an important posttranslational modification in skeletal muscle. We discuss the evolution of acetylation research and detail how large proteomic screens in diverse metabolic systems have led to the current hypothesis that acetylation may be a fundamental mechanism to fine-tune metabolic adaptation in skeletal muscle.
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Affiliation(s)
- Andrew Philp
- School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Thomas Rowland
- School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Joaquin Perez-Schindler
- School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
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86
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Papanicolaou KN, O'Rourke B, Foster DB. Metabolism leaves its mark on the powerhouse: recent progress in post-translational modifications of lysine in mitochondria. Front Physiol 2014; 5:301. [PMID: 25228883 PMCID: PMC4151196 DOI: 10.3389/fphys.2014.00301] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/23/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine modifications have been studied extensively in the nucleus, where they play pivotal roles in gene regulation and constitute one of the pillars of epigenetics. In the cytoplasm, they are critical to proteostasis. However, in the last decade we have also witnessed the emergence of mitochondria as a prime locus for post-translational modification (PTM) of lysine thanks, in large measure, to evolving proteomic techniques. Here, we review recent work on evolving set of PTM that arise from the direct reaction of lysine residues with energized metabolic thioester-coenzyme A intermediates, including acetylation, succinylation, malonylation, and glutarylation. We highlight the evolutionary conservation, kinetics, stoichiometry, and cross-talk between members of this emerging family of PTMs. We examine the impact on target protein function and regulation by mitochondrial sirtuins. Finally, we spotlight work in the heart and cardiac mitochondria, and consider the roles acetylation and other newly-found modifications may play in heart disease.
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Affiliation(s)
- Kyriakos N Papanicolaou
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - D Brian Foster
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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87
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Villeneuve LM, Stauch KL, Fox HS. Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands. J Proteomics 2014; 109:228-39. [PMID: 25046836 DOI: 10.1016/j.jprot.2014.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 06/02/2014] [Accepted: 07/10/2014] [Indexed: 12/31/2022]
Abstract
UNLABELLED Many biological processes converge on the mitochondria. In such systems, where many pathways converge, manipulation of the components can produce varied and far-reaching effects. Due to the centrality of the mitochondria in many cellular pathways, we decided to investigate the brain mitochondrial proteome during early development. Using a SWATH mass spectrometry-based technique, we were able to identify vast proteomic alterations between whole brain mitochondria from rats at embryonic day 18 compared to postnatal day 7. These findings include statistically significant alterations in proteins involved in glycolysis and mitochondrial trafficking/dynamics. Additionally, bioinformatic analysis enabled the identification of HIF1A and XBP1 as upstream transcriptional regulators of many of the differentially expressed proteins. These data suggest that the cell is rearranging the mitochondria to accommodate special energy demands and that cytosolic proteins exert mitochondrial effects through dynamic interactions with the mitochondria. BIOLOGICAL SIGNIFICANCE Although mitochondria play critical roles in many cellular pathways, our understanding of how these organelles change over time is limited. The changes occurring in the mitochondria at early time points are especially important as many mitochondrial disorders produce neurological dysfunction early in life. Herein, we utilize a SWATH mass spectrometry approach to quantify proteomic alterations of rat brain mitochondria between embryonic and postnatal stages. We found this method to be highly reproducible, enabling the identification of alterations in many biochemical pathways and mitochondrial properties. This insight into the distinct changes in these biological pathways to maintain homeostasis under divergent conditions will help elucidate the pathological changes occurring in disease states.
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Affiliation(s)
- Lance M Villeneuve
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States.
| | - Kelly L Stauch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States.
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States.
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88
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König AC, Hartl M, Boersema PJ, Mann M, Finkemeier I. The mitochondrial lysine acetylome of Arabidopsis. Mitochondrion 2014; 19 Pt B:252-60. [PMID: 24727099 DOI: 10.1016/j.mito.2014.03.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 01/01/2023]
Abstract
Posttranslational modifications are essential regulators of protein functions as they can modify enzyme activities or protein-molecule interactions by changing the charge state or chemical properties of their target amino acid. The acetyl moiety of the central energy metabolite acetyl-CoA can be transferred to the ε-amino group of lysine, a process known as lysine acetylation which is implicated in the regulation of key metabolic enzymes in various organisms. Since plant mitochondria are of great importance for plant growth and development and as they house key enzymes of oxidative phosphorylation and photorespiration, it is essential to investigate the occurrence of lysine acetylation in this organelle. Here we characterised the plant mitochondrial acetylome of Arabidopsis mitochondria by LC-MS/MS analysis. In total 120 lysine-acetylated mitochondrial proteins containing 243 acetylated sites were identified. These proteins were mapped into functional categories showing that many proteins with essential functions from the tricaboxylic cycle and the respiratory chain are lysine-acetylated, as well as proteins involved in photorespiration, amino acid and protein metabolism, and redox regulation. Immuno-detection of mitochondrial proteins revealed that many lysine-acetylated proteins reside in native protein complexes. Furthermore, in vitro experiments demonstrated that lysine acetylation can occur non-enzymatically in Arabidopsis mitochondria at physiological matrix pH.
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Affiliation(s)
- Ann-Christine König
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Köln, Germany
| | - Markus Hartl
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Köln, Germany
| | - Paul J Boersema
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Köln, Germany.
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89
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Amado FM, Barros A, Azevedo AL, Vitorino R, Ferreira R. An integrated perspective and functional impact of the mitochondrial acetylome. Expert Rev Proteomics 2014; 11:383-94. [PMID: 24661243 DOI: 10.1586/14789450.2014.899470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Growing evidence suggests that a range of reversible protein post-translational modifications such as acetylation regulates mitochondria signalling, impacting cellular homeostasis. However, the extent of this type of regulation in the control of mitochondria functionality is just beginning to be discovered, aided by the availability of high-resolution mass spectrometers and bioinformatic tools. Data mining from literature on protein acetylation profiling focused on mitochondria isolated from tissues retrieved more than 1395 distinct proteins, corresponding to more than 4858 acetylation sites. ClueGo analysis of identified proteins highlighted oxidative phosphorylation, tricarboxylic acid cycle, fatty acid oxidation and amino acid metabolism as the biological processes more prone to regulation through acetylation. This review also examines the physiological relevance of protein acetylation on the molecular pathways harbored in mitochondria under distinct pathophysiological conditions as caloric restriction and alcohol-induced liver damage. This integrative perspective will certainly help to envisage future studies targeting the regulation of mitochondrial functionality.
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Affiliation(s)
- Francisco M Amado
- School of Health Sciences, QOPNA, University of Aveiro, Aveiro, Portugal
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90
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Abstract
Stemming from the pioneering studies of bioenergetics in the 1950s, 1960s, and 1970s, mitochondria have become ingrained in the collective psyche of scientists as the "powerhouses" of the cell. While this remains a worthy moniker, more recent efforts have revealed that these organelles are home to a vast array of metabolic and signaling processes and possess a proteomic landscape that is both highly varied and largely uncharted. As mitochondrial dysfunction is increasingly being implicated in a spectrum of human diseases, it is imperative that we construct a more complete framework of these organelles by systematically defining the functions of their component parts. Powerful new approaches in biochemistry and systems biology are helping to fill in the gaps.
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Affiliation(s)
- David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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91
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Bharathi SS, Zhang Y, Mohsen AW, Uppala R, Balasubramani M, Schreiber E, Uechi G, Beck ME, Rardin MJ, Vockley J, Verdin E, Gibson BW, Hirschey MD, Goetzman ES. Sirtuin 3 (SIRT3) protein regulates long-chain acyl-CoA dehydrogenase by deacetylating conserved lysines near the active site. J Biol Chem 2013; 288:33837-33847. [PMID: 24121500 DOI: 10.1074/jbc.m113.510354] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Long-chain acyl-CoA dehydrogenase (LCAD) is a key mitochondrial fatty acid oxidation enzyme. We previously demonstrated increased LCAD lysine acetylation in SIRT3 knockout mice concomitant with reduced LCAD activity and reduced fatty acid oxidation. To study the effects of acetylation on LCAD and determine sirtuin 3 (SIRT3) target sites, we chemically acetylated recombinant LCAD. Acetylation impeded substrate binding and reduced catalytic efficiency. Deacetylation with recombinant SIRT3 partially restored activity. Residues Lys-318 and Lys-322 were identified as SIRT3-targeted lysines. Arginine substitutions at Lys-318 and Lys-322 prevented the acetylation-induced activity loss. Lys-318 and Lys-322 flank residues Arg-317 and Phe-320, which are conserved among all acyl-CoA dehydrogenases and coordinate the enzyme-bound FAD cofactor in the active site. We propose that acetylation at Lys-318/Lys-322 causes a conformational change which reduces hydride transfer from substrate to FAD. Medium-chain acyl-CoA dehydrogenase and acyl-CoA dehydrogenase 9, two related enzymes with lysines at positions equivalent to Lys-318/Lys-322, were also efficiently deacetylated by SIRT3 following chemical acetylation. These results suggest that acetylation/deacetylation at Lys-318/Lys-322 is a mode of regulating fatty acid oxidation. The same mechanism may regulate other acyl-CoA dehydrogenases.
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Affiliation(s)
- Sivakama S Bharathi
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Yuxun Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Al-Walid Mohsen
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Radha Uppala
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Manimalha Balasubramani
- Genomics and Proteomics Core Facility, University of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Emanuel Schreiber
- Genomics and Proteomics Core Facility, University of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Guy Uechi
- Genomics and Proteomics Core Facility, University of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Megan E Beck
- Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania 15224
| | | | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224; Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania 15224
| | - Eric Verdin
- Gladstone Institutes and University of California, San Francisco, California 94158
| | | | - Matthew D Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center Duke University, Medical Center, Durham, North Carolina 27704
| | - Eric S Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224; Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania 15224.
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92
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Guha M, Avadhani NG. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion 2013; 13:577-91. [PMID: 24004957 DOI: 10.1016/j.mito.2013.08.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/20/2013] [Accepted: 08/27/2013] [Indexed: 12/25/2022]
Abstract
Mitochondria play a central role not only in energy production but also in the integration of metabolic pathways as well as signals for apoptosis and autophagy. It is becoming increasingly apparent that mitochondria in mammalian cells play critical roles in the initiation and propagation of various signaling cascades. In particular, mitochondrial metabolic and respiratory states and status on mitochondrial genetic instability are communicated to the nucleus as an adaptive response through retrograde signaling. Each mammalian cell contains multiple copies of the mitochondrial genome (mtDNA). A reduction in mtDNA copy number has been reported in various human pathological conditions such as diabetes, obesity, neurodegenerative disorders, aging and cancer. Reduction in mtDNA copy number disrupts mitochondrial membrane potential (Δψm) resulting in dysfunctional mitochondria. Dysfunctional mitochondria trigger retrograde signaling and communicate their changing metabolic and functional state to the nucleus as an adaptive response resulting in an altered nuclear gene expression profile and altered cell physiology and morphology. In this review, we provide an overview of the various modes of mitochondrial retrograde signaling focusing particularly on the Ca(2+)/Calcineurin mediated retrograde signaling. We discuss the contribution of the key factors of the pathway such as Calcineurin, IGF1 receptor, Akt kinase and HnRNPA2 in the propagation of signaling and their role in modulating genetic and epigenetic changes favoring cellular reprogramming towards tumorigenesis.
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Affiliation(s)
- Manti Guha
- Department of Animal Biology and the Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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