551
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Liu X, Sadhukhan S, Sun S, Wagner GR, Hirschey MD, Qi L, Lin H, Locasale JW. High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet. Mol Cell Proteomics 2015; 14:1489-500. [PMID: 25795660 DOI: 10.1074/mcp.m114.044859] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 01/09/2023] Open
Abstract
The availability of acyl-Coenzyme A (acyl-CoA) thioester compounds affects numerous cellular functions including autophagy, lipid oxidation and synthesis, and post-translational modifications. Consequently, the acyl-CoA level changes tend to be associated with other metabolic alterations that regulate these critical cellular functions. Despite their biological importance, this class of metabolites remains difficult to detect and quantify using current analytical methods. Here we show a universal method for metabolomics that allows for the detection of an expansive set of acyl-CoA compounds and hundreds of other cellular metabolites. We apply this method to profile the dynamics of acyl-CoA compounds and corresponding alterations in metabolism across the metabolic network in response to high fat feeding in mice. We identified targeted metabolites (>50) and untargeted features (>1000) with significant changes (FDR < 0.05) in response to diet. A substantial extent of this metabolic remodeling exhibited correlated changes in acyl-CoA metabolism with acyl-carnitine metabolism and other features of the metabolic network that together can lead to the discovery of biomarkers of acyl-CoA metabolism. These findings show a robust acyl-CoA profiling method and identify coordinated changes of acyl-CoA metabolism in response to nutritional stress.
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Affiliation(s)
- Xiaojing Liu
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853
| | - Sushabhan Sadhukhan
- §Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Shengyi Sun
- ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Gregory R Wagner
- ‖Duke Molecular Physiology Institute, Duke University, Medical Center, Durham, North Carolina 27710; **Department of Medicine and Department of Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - Matthew D Hirschey
- ‖Duke Molecular Physiology Institute, Duke University, Medical Center, Durham, North Carolina 27710; **Department of Medicine and Department of Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - Ling Qi
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853; ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Hening Lin
- §Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Jason W Locasale
- From the ‡Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853; ¶Field of Biochemistry and Molecular Cell Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853;
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552
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Laemmle A, Hahn D, Hu L, Rüfenacht V, Gautschi M, Leibundgut K, Nuoffer JM, Häberle J. Fatal hyperammonemia and carbamoyl phosphate synthetase 1 (CPS1) deficiency following high-dose chemotherapy and autologous hematopoietic stem cell transplantation. Mol Genet Metab 2015; 114:438-44. [PMID: 25639153 DOI: 10.1016/j.ymgme.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/16/2022]
Abstract
Fatal hyperammonemia secondary to chemotherapy for hematological malignancies or following bone marrow transplantation has been described in few patients so far. In these, the pathogenesis of hyperammonemia remained unclear and was suggested to be multifactorial. We observed severe hyperammonemia (maximum 475 μmol/L) in a 2-year-old male patient, who underwent high-dose chemotherapy with carboplatin, etoposide and melphalan, and autologous hematopoietic stem cell transplantation for a neuroblastoma stage IV. Despite intensive care treatment, hyperammonemia persisted and the patient died due to cerebral edema. The biochemical profile with elevations of ammonia and glutamine (maximum 1757 μmol/L) suggested urea cycle dysfunction. In liver homogenates, enzymatic activity and protein expression of the urea cycle enzyme carbamoyl phosphate synthetase 1 (CPS1) were virtually absent. However, no mutation was found in CPS1 cDNA from liver and CPS1 mRNA expression was only slightly decreased. We therefore hypothesized that the acute onset of hyperammonemia was due to an acquired, chemotherapy-induced (posttranscriptional) CPS1 deficiency. This was further supported by in vitro experiments in HepG2 cells treated with carboplatin and etoposide showing a dose-dependent decrease in CPS1 protein expression. Due to severe hyperlactatemia, we analysed oxidative phosphorylation complexes in liver tissue and found reduced activities of complexes I and V, which suggested a more general mitochondrial dysfunction. This study adds to the understanding of chemotherapy-induced hyperammonemia as drug-induced CPS1 deficiency is suggested. Moreover, we highlight the need for urgent diagnostic and therapeutic strategies addressing a possible secondary urea cycle failure in future patients with hyperammonemia during chemotherapy and stem cell transplantation.
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Affiliation(s)
- Alexander Laemmle
- Division of Metabolism and Children's Research Center (CRC), University Children's Hospital, Zurich, Switzerland; Department of Pediatrics, University Children's Hospital, Bern, Switzerland.
| | - Dagmar Hahn
- University Institute of Clinical Chemistry, University of Bern, Switzerland.
| | - Liyan Hu
- Division of Metabolism and Children's Research Center (CRC), University Children's Hospital, Zurich, Switzerland.
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center (CRC), University Children's Hospital, Zurich, Switzerland.
| | - Matthias Gautschi
- Department of Pediatrics, University Children's Hospital, Bern, Switzerland; University Institute of Clinical Chemistry, University of Bern, Switzerland.
| | - Kurt Leibundgut
- Department of Pediatrics, University Children's Hospital, Bern, Switzerland.
| | - Jean-Marc Nuoffer
- Department of Pediatrics, University Children's Hospital, Bern, Switzerland; University Institute of Clinical Chemistry, University of Bern, Switzerland.
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center (CRC), University Children's Hospital, Zurich, Switzerland.
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553
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Hirschey MD, Zhao Y. Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation. Mol Cell Proteomics 2015; 14:2308-15. [PMID: 25717114 DOI: 10.1074/mcp.r114.046664] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 12/14/2022] Open
Abstract
Protein acetylation is a well-studied regulatory mechanism for several cellular processes, ranging from gene expression to metabolism. Recent discoveries of new post-translational modifications, including malonylation, succinylation, and glutarylation, have expanded our understanding of the types of modifications found on proteins. These three acidic lysine modifications are structurally similar but have the potential to regulate different proteins in different pathways. The deacylase sirtuin 5 (SIRT5) catalyzes the removal of these modifications from a wide range of proteins in different subcellular compartments. Here, we review these new modifications, their regulation by SIRT5, and their emerging role in cellular regulation and diseases.
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Affiliation(s)
- Matthew D Hirschey
- From the ‡Duke Molecular Physiology Institute, Sarah W. Stedman Metabolism and Nutrition Center, §Departments of Medicine & Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, NC 27710;
| | - Yingming Zhao
- ¶Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637
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554
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Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM. Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell 2015; 159:1615-25. [PMID: 25525879 DOI: 10.1016/j.cell.2014.11.046] [Citation(s) in RCA: 295] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/12/2014] [Accepted: 11/21/2014] [Indexed: 12/20/2022]
Abstract
Sirtuins (SIRTs) are critical enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, mitochondrial SIRT4 and SIRT5 have little to no deacetylase activity, and a robust catalytic activity for SIRT4 has been elusive. Here, we establish SIRT4 as a cellular lipoamidase that regulates the pyruvate dehydrogenase complex (PDH). Importantly, SIRT4 catalytic efficiency for lipoyl- and biotinyl-lysine modifications is superior to its deacetylation activity. PDH, which converts pyruvate to acetyl-CoA, has been known to be primarily regulated by phosphorylation of its E1 component. We determine that SIRT4 enzymatically hydrolyzes the lipoamide cofactors from the E2 component dihydrolipoyllysine acetyltransferase (DLAT), diminishing PDH activity. We demonstrate SIRT4-mediated regulation of DLAT lipoyl levels and PDH activity in cells and in vivo, in mouse liver. Furthermore, metabolic flux switching via glutamine stimulation induces SIRT4 lipoamidase activity to inhibit PDH, highlighting SIRT4 as a guardian of cellular metabolism.
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Affiliation(s)
- Rommel A Mathias
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA; Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Adam Oberstein
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Hanna G Budayeva
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Rumela Chakrabarti
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Elizabeth A Rowland
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas Shenk
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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555
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Shi L, Tu BP. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Curr Opin Cell Biol 2015; 33:125-31. [PMID: 25703630 PMCID: PMC4380630 DOI: 10.1016/j.ceb.2015.02.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/21/2015] [Accepted: 02/03/2015] [Indexed: 12/31/2022]
Abstract
Acetyl-CoA represents a key node in metabolism due to its intersection with many metabolic pathways and transformations. Emerging evidence reveals that cells monitor the levels of acetyl-CoA as a key indicator of their metabolic state, through distinctive protein acetylation modifications dependent on this metabolite. We offer the following conceptual model for understanding the role of this sentinel metabolite in metabolic regulation. High nucleocytosolic acetyl-CoA amounts are a signature of a “growth” or “fed” state and promote its utilization for lipid synthesis and histone acetylation. In contrast, under “survival” or “fasted” states, acetyl-CoA is preferentially directed into the mitochondria to promote mitochondrial-dependent activities such as the synthesis of ATP and ketone bodies. Fluctuations in acetyl-CoA within these subcellular compartments enable the substrate-level regulation of acetylation modifications, but also necessitates the function of sirtuin deacetylases to catalyze removal of spontaneous modifications that might be unintended. Thus, understanding the sources, fates, and consequences of acetyl-CoA as a carrier of two-carbon units has started to reveal its underappreciated but profound influence on the regulation of numerous life processes.
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Affiliation(s)
- Lei Shi
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, United States
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, United States.
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556
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Yates LM, Fiedler D. Establishing the Stability and Reversibility of Protein Pyrophosphorylation with Synthetic Peptides. Chembiochem 2015; 16:415-23. [DOI: 10.1002/cbic.201402589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 12/24/2022]
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557
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Pisithkul T, Patel NM, Amador-Noguez D. Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opin Microbiol 2015; 24:29-37. [PMID: 25597444 DOI: 10.1016/j.mib.2014.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 01/05/2023]
Abstract
In order to survive and compete in natural settings, bacteria must excel at quickly adapting their metabolism to fluctuations in nutrient availability and other environmental variables. This necessitates fast-acting post-translational regulatory mechanisms, that is, allostery or covalent modification, to control metabolic flux. While allosteric regulation has long been a well-established strategy for regulating metabolic enzyme activity in bacteria, covalent post-translational modes of regulation, such as phosphorylation or acetylation, have previously been regarded as regulatory mechanisms employed primarily by eukaryotic organisms. Recent findings, however, have shifted this perception and point to a widespread role for covalent posttranslational modification in the regulation of metabolic enzymes and fluxes in bacteria. This review provides an outline of the exciting recent advances in this area.
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Affiliation(s)
- Tippapha Pisithkul
- Cellular and Molecular Biology, University of Wisconsin-Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, United States
| | - Nishaben M Patel
- Department of Bacteriology, University of Wisconsin-Madison, United States
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558
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Abstract
![]()
Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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559
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Chen B, Zang W, Wang J, Huang Y, He Y, Yan L, Liu J, Zheng W. The chemical biology of sirtuins. Chem Soc Rev 2015; 44:5246-64. [DOI: 10.1039/c4cs00373j] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article reviews the tremendous accomplishments achieved during the past few years in the field of chemical biology for the physiologically and therapeutically important sirtuin family of Nε-acyl-lysine deacylase enzymes.
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Affiliation(s)
- Bing Chen
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Wenwen Zang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Juan Wang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yajun Huang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yanhua He
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Lingling Yan
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Jiajia Liu
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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560
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Seifert T, Malo M, Kokkola T, Engen K, Fridén-Saxin M, Wallén EAA, Lahtela-Kakkonen M, Jarho EM, Luthman K. Chroman-4-one- and Chromone-Based Sirtuin 2 Inhibitors with Antiproliferative Properties in Cancer Cells. J Med Chem 2014; 57:9870-88. [DOI: 10.1021/jm500930h] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tina Seifert
- Department
of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg, Kemivagen 10, SE-412
96 Göteborg, Sweden
| | - Marcus Malo
- Department
of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg, Kemivagen 10, SE-412
96 Göteborg, Sweden
| | - Tarja Kokkola
- School
of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Karin Engen
- Department
of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg, Kemivagen 10, SE-412
96 Göteborg, Sweden
| | - Maria Fridén-Saxin
- Department
of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg, Kemivagen 10, SE-412
96 Göteborg, Sweden
| | - Erik A. A. Wallén
- Division
of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FIN-00014 Helsinki, Finland
| | | | - Elina M. Jarho
- School
of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Kristina Luthman
- Department
of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg, Kemivagen 10, SE-412
96 Göteborg, Sweden
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561
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Ringel AE, Roman C, Wolberger C. Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2. Protein Sci 2014; 23:1686-97. [PMID: 25200501 PMCID: PMC4253809 DOI: 10.1002/pro.2546] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/03/2014] [Indexed: 01/07/2023]
Abstract
Sirtuins were originally shown to regulate a wide array of biological processes such as transcription, genomic stability, and metabolism by catalyzing the NAD(+) -dependent deacetylation of lysine residues. Recent proteomic studies have revealed a much wider array of lysine acyl modifications in vivo than was previously known, which has prompted a reevaluation of sirtuin substrate specificity. Several sirtuins have now been shown to preferentially remove propionyl, succinyl, and long-chain fatty acyl groups from lysines, which has changed our understanding of sirtuin biology. In light of these developments, we revisited the acyl specificity of several well-studied archaeal and bacterial sirtuins. We find that the Archaeoglobus fulgidus sirtuins, Sir2Af1 and Sir2Af2, preferentially remove succinyl and myristoyl groups, respectively. Crystal structures of Sir2Af1 bound to a succinylated peptide and Sir2Af2 bound to a myristoylated peptide show how the active site of each enzyme accommodates a noncanonical acyl chain. As compared to its structure in complex with an acetylated peptide, Sir2Af2 undergoes a conformational change that expands the active site to accommodate the myristoyl group. These findings point to both structural and biochemical plasticity in sirtuin active sites and provide further evidence that sirtuins from all three domains of life catalyze noncanonical deacylation.
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Affiliation(s)
- Alison E Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185
| | - Christina Roman
- The Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185,The Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185,
*Correspondence to: Cynthia Wolberger, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205. E-mail:
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562
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Du Y, Cai T, Li T, Xue P, Zhou B, He X, Wei P, Liu P, Yang F, Wei T. Lysine malonylation is elevated in type 2 diabetic mouse models and enriched in metabolic associated proteins. Mol Cell Proteomics 2014; 14:227-36. [PMID: 25418362 DOI: 10.1074/mcp.m114.041947] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein lysine malonylation, a newly identified protein post-translational modification (PTM), has been proved to be evolutionarily conserved and is present in both eukaryotic and prokaryotic cells. However, its potential roles associated with human diseases remain largely unknown. In the present study, we observed an elevated lysine malonylation in a screening of seven lysine acylations in liver tissues of db/db mice, which is a typical model of type 2 diabetes. We also detected an elevated lysine malonylation in ob/ob mice, which is another model of type 2 diabetes. We then performed affinity enrichment coupled with proteomic analysis on liver tissues of both wild-type (wt) and db/db mice and identified a total of 573 malonylated lysine sites from 268 proteins. There were more malonylated lysine sites and proteins in db/db than in wt mice. Five proteins with elevated malonylation were verified by immunoprecipitation coupled with Western blot analysis. Bioinformatic analysis of the proteomic results revealed the enrichment of malonylated proteins in metabolic pathways, especially those involved in glucose and fatty acid metabolism. In addition, the biological role of lysine malonylation was validated in an enzyme of the glycolysis pathway. Together, our findings support a potential role of protein lysine malonylation in type 2 diabetes with possible implications for its therapy in the future.
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Affiliation(s)
- Yipeng Du
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tanxi Cai
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Li
- ¶Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China
| | - Peng Xue
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Zhou
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong He
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wei
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingsheng Liu
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Taotao Wei
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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563
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Maolanon AR, Villadsen JS, Christensen NJ, Hoeck C, Friis T, Harris P, Gotfredsen CH, Fristrup P, Olsen CA. Methyl Effect in Azumamides Provides Insight Into Histone Deacetylase Inhibition by Macrocycles. J Med Chem 2014; 57:9644-57. [DOI: 10.1021/jm501399d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alex R. Maolanon
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jesper S. Villadsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Niels J. Christensen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Casper Hoeck
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Tina Friis
- Department
of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte H. Gotfredsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Christian A. Olsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
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564
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Kebede AF, Schneider R, Daujat S. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. FEBS J 2014; 282:1658-74. [DOI: 10.1111/febs.13047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Adam F. Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
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565
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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: 981] [Impact Index Per Article: 98.1] [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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566
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Cabezas-Cruz A, Lancelot J, Caby S, Oliveira G, Pierce RJ. Epigenetic control of gene function in schistosomes: a source of therapeutic targets? Front Genet 2014; 5:317. [PMID: 25309576 PMCID: PMC4159997 DOI: 10.3389/fgene.2014.00317] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/24/2014] [Indexed: 12/31/2022] Open
Abstract
The discovery of the epigenetic regulation of gene expression has revolutionized both our understanding of how genomes function and approaches to the therapy of numerous pathologies. Schistosomes are metazoan parasites and as such utilize most, if not all the epigenetic mechanisms in play in their vertebrate hosts: histone variants, histone tail modifications, non-coding RNA and, perhaps, DNA methylation. Moreover, we are acquiring an increasing understanding of the ways in which these mechanisms come into play during the complex schistosome developmental program. In turn, interest in the actors involved in epigenetic mechanisms, particularly the enzymes that carry out epigenetic modifications of histones or nucleic acid, as therapeutic targets has been stimulated by the finding that their inhibitors exert profound effects, not only on survival, but also on the reproductive function of Schistosoma mansoni. Here, we review our current knowledge, and what we can infer, about the role of epigenetic mechanisms in schistosome development, differentiation and survival. We will consider which epigenetic actors can be targeted for drug discovery and what strategies can be employed to develop potent, selective inhibitors as drugs to cure schistosomiasis.
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Affiliation(s)
- Alejandro Cabezas-Cruz
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Julien Lancelot
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Stéphanie Caby
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, Fundação Oswaldo Cruz, Center for Excellence in Bioinformatics, Centro de Pesquisas René Rachou, National Institute of Science and Technology in Tropical DiseasesBelo Horizonte, Brazil
| | - Raymond J. Pierce
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
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567
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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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568
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Barbi de Moura M, Uppala R, Zhang Y, Van Houten B, Goetzman ES. Overexpression of mitochondrial sirtuins alters glycolysis and mitochondrial function in HEK293 cells. PLoS One 2014; 9:e106028. [PMID: 25165814 PMCID: PMC4148395 DOI: 10.1371/journal.pone.0106028] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/30/2014] [Indexed: 01/15/2023] Open
Abstract
SIRT3, SIRT4, and SIRT5 are mitochondrial deacylases that impact multiple facets of energy metabolism and mitochondrial function. SIRT3 activates several mitochondrial enzymes, SIRT4 represses its targets, and SIRT5 has been shown to both activate and repress mitochondrial enzymes. To gain insight into the relative effects of the mitochondrial sirtuins in governing mitochondrial energy metabolism, SIRT3, SIRT4, and SIRT5 overexpressing HEK293 cells were directly compared. When grown under standard cell culture conditions (25 mM glucose) all three sirtuins induced increases in mitochondrial respiration, glycolysis, and glucose oxidation, but with no change in growth rate or in steady-state ATP concentration. Increased proton leak, as evidenced by oxygen consumption in the presence of oligomycin, appeared to explain much of the increase in basal oxygen utilization. Growth in 5 mM glucose normalized the elevations in basal oxygen consumption, proton leak, and glycolysis in all sirtuin over-expressing cells. While the above effects were common to all three mitochondrial sirtuins, some differences between the SIRT3, SIRT4, and SIRT5 expressing cells were noted. Only SIRT3 overexpression affected fatty acid metabolism, and only SIRT4 overexpression altered superoxide levels and mitochondrial membrane potential. We conclude that all three mitochondrial sirtuins can promote increased mitochondrial respiration and cellular metabolism. SIRT3, SIRT4, and SIRT5 appear to respond to excess glucose by inducing a coordinated increase of glycolysis and respiration, with the excess energy dissipated via proton leak.
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Affiliation(s)
- Michelle Barbi de Moura
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Radha Uppala
- Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Yuxun Zhang
- Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Eric S. Goetzman
- Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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569
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Zwaans BMM, Lombard DB. Interplay between sirtuins, MYC and hypoxia-inducible factor in cancer-associated metabolic reprogramming. Dis Model Mech 2014; 7:1023-32. [PMID: 25085992 PMCID: PMC4142723 DOI: 10.1242/dmm.016287] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In the early twentieth century, Otto Heinrich Warburg described an elevated rate of glycolysis occurring in cancer cells, even in the presence of atmospheric oxygen (the Warburg effect). Despite the inefficiency of ATP generation through glycolysis, the breakdown of glucose into lactate provides cancer cells with a number of advantages, including the ability to withstand fluctuations in oxygen levels, and the production of intermediates that serve as building blocks to support rapid proliferation. Recent evidence from many cancer types supports the notion that pervasive metabolic reprogramming in cancer and stromal cells is a crucial feature of neoplastic transformation. Two key transcription factors that play major roles in this metabolic reprogramming are hypoxia inducible factor-1 (HIF1) and MYC. Sirtuin-family deacetylases regulate diverse biological processes, including many aspects of tumor biology. Recently, the sirtuin SIRT6 has been shown to inhibit the transcriptional output of both HIF1 and MYC, and to function as a tumor suppressor. In this Review, we highlight the importance of HIF1 and MYC in regulating tumor metabolism and their regulation by sirtuins, with a main focus on SIRT6.
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Affiliation(s)
- Bernadette M M Zwaans
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
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570
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Giblin W, Skinner ME, Lombard DB. Sirtuins: guardians of mammalian healthspan. Trends Genet 2014; 30:271-86. [PMID: 24877878 PMCID: PMC4077918 DOI: 10.1016/j.tig.2014.04.007] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 12/12/2022]
Abstract
The first link between sirtuins and longevity was made 15 years ago in yeast. These initial studies sparked efforts by many laboratories working in diverse model organisms to elucidate the relations between sirtuins, lifespan, and age-associated dysfunction. Here, we discuss the current understanding of how sirtuins relate to aging. We focus primarily on mammalian sirtuins SIRT1, SIRT3, and SIRT6, the three sirtuins for which the most relevant data are available. Strikingly, a large body of evidence now indicates that these and other mammalian sirtuins suppress a variety of age-related pathologies and promote healthspan. Moreover, increased expression of SIRT1 or SIRT6 extends mouse lifespan. Overall, these data point to important roles for sirtuins in promoting mammalian health, and perhaps in modulating the aging process.
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Affiliation(s)
- William Giblin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mary E Skinner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA.
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571
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Abstract
Cellular proteins are decorated with a wide range of acetyl and other acyl modifications. Many studies have demonstrated regulation of site-specific acetylation by acetyltransferases and deacetylases. Acylation is emerging as a new type of lysine modification, but less is known about its overall regulatory role. Furthermore, the mechanisms of lysine acylation, its overlap with protein acetylation, and how it influences cellular function are major unanswered questions in the field. In this review, we discuss the known roles of acetyltransferases and deacetylases and the sirtuins as a conserved family of a nicotinamide adenine dinucleotide (NAD⁺)-dependent protein deacylases that are important for response to cellular stress and homeostasis. We also consider the evidence for an emerging idea of nonenzymatic protein acylation. Finally, we put forward the hypothesis that protein acylation is a form of protein "carbon stress" that the deacylases evolved to remove as a part of a global protein quality-control network.
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