151
|
Bontemps-Gallo S, Gaviard C, Richards CL, Kentache T, Raffel SJ, Lawrence KA, Schindler JC, Lovelace J, Dulebohn DP, Cluss RG, Hardouin J, Gherardini FC. Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. Front Microbiol 2018; 9:2036. [PMID: 30233522 PMCID: PMC6127242 DOI: 10.3389/fmicb.2018.02036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
The post-translational modification of proteins has been shown to be extremely important in prokaryotes. Using a highly sensitive mass spectrometry-based proteomics approach, we have characterized the acetylome of B. burgdorferi. As previously reported for other bacteria, a relatively low number (5%) of the potential genome-encoded proteins of B. burgdorferi were acetylated. Of these, the vast majority were involved in central metabolism and cellular information processing (transcription, translation, etc.). Interestingly, these critical cell functions were targeted during both ML (mid-log) and S (stationary) phases of growth. However, acetylation of target proteins in ML phase was limited to single lysine residues while these same proteins were acetylated at multiple sites during S phase. To determine the acetyl donor in B. burgdorferi, we used mutants that targeted the sole acetate metabolic/anabolic pathway in B. burgdorferi (lipid I synthesis). B. burgdorferi strains B31-A3, B31-A3 ΔackA (acetyl-P- and acetyl-CoA-) and B31-A3 Δpta (acetyl-P+ and acetyl-CoA-) were grown to S phase and the acetylation profiles were analyzed. While only two proteins were acetylated in the ΔackA mutant, 140 proteins were acetylated in the Δpta mutant suggesting that acetyl-P was the primary acetyl donor in B. burgdorferi. Using specific enzymatic assays, we were able to demonstrate that hyperacetylation of proteins in S phase appeared to play a role in decreasing the enzymatic activity of at least two glycolytic proteins. Currently, we hypothesize that acetylation is used to modulate enzyme activities during different stages of growth. This strategy would allow the bacteria to post-translationally stimulate the activity of key glycolytic enzymes by deacetylation rather than expending excessive energy synthesizing new proteins. This would be an appealing, low-energy strategy for a bacterium with limited metabolic capabilities. Future work focuses on identifying potential protein deacetylase(s) to complete our understanding of this important biological process.
Collapse
Affiliation(s)
- Sébastien Bontemps-Gallo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Charlotte Gaviard
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Crystal L Richards
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Takfarinas Kentache
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Sandra J Raffel
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kevin A Lawrence
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Joseph C Schindler
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Joseph Lovelace
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Daniel P Dulebohn
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Robert G Cluss
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Julie Hardouin
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Frank C Gherardini
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| |
Collapse
|
152
|
James AM, Smith CL, Smith AC, Robinson AJ, Hoogewijs K, Murphy MP. The Causes and Consequences of Nonenzymatic Protein Acylation. Trends Biochem Sci 2018; 43:921-932. [PMID: 30131192 DOI: 10.1016/j.tibs.2018.07.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/26/2022]
Abstract
Thousands of protein acyl modification sites have now been identified in vivo. However, at most sites the acylation stoichiometry is low, making functional enzyme-driven regulation in the majority of cases unlikely. As unmediated acylation can occur on the surface of proteins when acyl-CoA thioesters react with nucleophilic cysteine and lysine residues, slower nonenzymatic processes likely underlie most protein acylation. Here, we review how nonenzymatic acylation of nucleophilic lysine and cysteine residues occurs; the factors that enhance acylation at particular sites; and the strategies that have evolved to limit protein acylation. We conclude that protein acylation is an unavoidable consequence of the central role of reactive thioesters in metabolism. Finally, we propose a hypothesis for why low-stoichiometry protein acylation is selected against by evolution and how it might contribute to degenerative processes such as aging.
Collapse
Affiliation(s)
- Andrew M James
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Cassandra L Smith
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Anthony C Smith
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Alan J Robinson
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Kurt Hoogewijs
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK; Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Michael P Murphy
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| |
Collapse
|
153
|
James AM, Smith AC, Smith CL, Robinson AJ, Murphy MP. Proximal Cysteines that Enhance Lysine N-Acetylation of Cytosolic Proteins in Mice Are Less Conserved in Longer-Living Species. Cell Rep 2018; 24:1445-1455. [PMID: 30089256 PMCID: PMC6092265 DOI: 10.1016/j.celrep.2018.07.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/19/2018] [Accepted: 07/01/2018] [Indexed: 12/29/2022] Open
Abstract
Acetyl-coenzyme A (CoA) is an abundant metabolite that can also alter protein function through non-enzymatic N-acetylation of protein lysines. This N-acetylation is greatly enhanced in vitro if an adjacent cysteine undergoes initial S-acetylation, as this can lead to S→N transfer of the acetyl moiety. Here, using modeled mouse structures of 619 proteins N-acetylated in mouse liver, we show lysine N-acetylation is greater in vivo if a cysteine is within ∼10 Å. Extension to the genomes of 52 other mammalian and bird species shows pairs of proximal cysteine and N-acetylated lysines are less conserved, implying most N-acetylation is detrimental. Supporting this, there is less conservation of cytosolic pairs of proximal cysteine and N-acetylated lysines in species with longer lifespans. As acetyl-CoA levels are linked to nutrient supply, these findings suggest how dietary restriction could extend lifespan and how pathologies resulting from dietary excess may occur.
Collapse
Affiliation(s)
- Andrew M James
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Anthony C Smith
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Cassandra L Smith
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Alan J Robinson
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michael P Murphy
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| |
Collapse
|
154
|
Gano LB, Liang LP, Ryan K, Michel CR, Gomez J, Vassilopoulos A, Reisdorph N, Fritz KS, Patel M. Altered mitochondrial acetylation profiles in a kainic acid model of temporal lobe epilepsy. Free Radic Biol Med 2018; 123:116-124. [PMID: 29778462 PMCID: PMC6082368 DOI: 10.1016/j.freeradbiomed.2018.05.063] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022]
Abstract
Impaired bioenergetics and oxidative damage in the mitochondria are implicated in the etiology of temporal lobe epilepsy, and hyperacetylation of mitochondrial proteins has recently emerged as a critical negative regulator of mitochondrial functions. However, the roles of mitochondrial acetylation and activity of the primary mitochondrial deacetylase, SIRT3, have not been explored in acquired epilepsy. We investigated changes in mitochondrial acetylation and SIRT3 activity in the development of chronic epilepsy in the kainic acid rat model of TLE. Hippocampal measurements were made at 48 h, 1 week and 12 weeks corresponding to the acute, latent and chronic stages of epileptogenesis. Assessment of hippocampal bioenergetics demonstrated a ≥ 27% decrease in the ATP/ADP ratio at all phases of epileptogenesis (p < 0.05), whereas cellular NAD+ levels were decreased by ≥ 41% in the acute and latent time points (p < 0.05), but not in chronically epileptic rats. In spontaneously epileptic rats, we found decreased protein expression of SIRT3 and a 60% increase in global mitochondrial acetylation, as well as enhanced acetylation of the known SIRT3 substrates MnSOD, Ndufa9 of Complex I and IDH2 (all p < 0.05), suggesting SIRT3 dysfunction in chronic epilepsy. Mass spectrometry-based acetylomics investigation of hippocampal mitochondria demonstrated a 79% increase in unique acetylated proteins from rats in the chronic phase vs. controls. Pathway analysis identified numerous mitochondrial bioenergetic pathways affected by mitochondrial acetylation. These results suggest SIRT3 dysfunction and aberrant protein acetylation may contribute to mitochondrial dysfunction in chronic epilepsy.
Collapse
Affiliation(s)
- Lindsey B Gano
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Li-Ping Liang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristen Ryan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Cole R Michel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joe Gomez
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Athanassios Vassilopoulos
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nichole Reisdorph
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristofer S Fritz
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Manisha Patel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
155
|
Zaballa ME, van der Goot FG. The molecular era of protein S-acylation: spotlight on structure, mechanisms, and dynamics. Crit Rev Biochem Mol Biol 2018; 53:420-451. [DOI: 10.1080/10409238.2018.1488804] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- María-Eugenia Zaballa
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
156
|
Hershberger KA, Abraham DM, Liu J, Locasale JW, Grimsrud PA, Hirschey MD. Ablation of Sirtuin5 in the postnatal mouse heart results in protein succinylation and normal survival in response to chronic pressure overload. J Biol Chem 2018; 293:10630-10645. [PMID: 29769314 PMCID: PMC6036188 DOI: 10.1074/jbc.ra118.002187] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/04/2018] [Indexed: 01/16/2023] Open
Abstract
Mitochondrial Sirtuin 5 (SIRT5) is an NAD+-dependent demalonylase, desuccinylase, and deglutarylase that controls several metabolic pathways. A number of recent studies point to SIRT5 desuccinylase activity being important in maintaining cardiac function and metabolism under stress. Previously, we described a phenotype of increased mortality in whole-body SIRT5KO mice exposed to chronic pressure overload compared with their littermate WT controls. To determine whether the survival phenotype we reported was due to a cardiac-intrinsic or cardiac-extrinsic effect of SIRT5, we developed a tamoxifen-inducible, heart-specific SIRT5 knockout (SIRT5KO) mouse model. Using our new animal model, we discovered that postnatal cardiac ablation of Sirt5 resulted in persistent accumulation of protein succinylation up to 30 weeks after SIRT5 depletion. Succinyl proteomics revealed that succinylation increased on proteins of oxidative metabolism between 15 and 31 weeks after ablation. Heart-specific SIRT5KO mice were exposed to chronic pressure overload to induce cardiac hypertrophy. We found that, in contrast to whole-body SIRT5KO mice, there was no difference in survival between heart-specific SIRT5KO mice and their littermate controls. Overall, the data presented here suggest that survival of SIRT5KO mice may be dictated by a multitissue or prenatal effect of SIRT5.
Collapse
Affiliation(s)
- Kathleen A Hershberger
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701 and
- the Department of Pharmacology and Cancer Biology
| | - Dennis M Abraham
- Department of Medicine, Division of Cardiology and Duke Cardiovascular Physiology Core, and
| | - Juan Liu
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701 and
- the Department of Pharmacology and Cancer Biology
| | - Jason W Locasale
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701 and
- the Department of Pharmacology and Cancer Biology
| | - Paul A Grimsrud
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701 and
| | - Matthew D Hirschey
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701 and
- the Department of Pharmacology and Cancer Biology
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, North Carolina 27710
| |
Collapse
|
157
|
Yao S, Udenigwe CC. Peptidomics of potato protein hydrolysates: implications of post-translational modifications in food peptide structure and behaviour. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172425. [PMID: 30109062 PMCID: PMC6083715 DOI: 10.1098/rsos.172425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Post-translational modifications (PTMs) often occur in proteins and play a regulatory role in protein function. There is an increasing interest in the bioactivity of food protein-derived peptides, but the occurrence of PTMs and their influence on food peptide structure and behaviour remain largely unknown. In this study, the shotgun-based peptidomics strategy was used to identify the occurrence of PTMs in peptides generated from potato protein hydrolysis using digestive proteases. Diverse PTMs were found in the potato peptides, including acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, de-amidation of asparagine/glutamine, methylation and trimethylation, methionine oxidation and N-terminal pyro-glutamyl residue formation. The modifications may have been formed naturally or as a result of chemical reactions during isolation and enzymatic processing of the potato proteins. Most of the PTMs were calculated to decrease the isoelectric point and increase molecular hydrophobicity of the peptides, which will influence their bioactivity while also potentially altering their solubility in an aqueous environment. This is the first study to unravel that food-derived peptides can be widely modified by PTMs associated with notable changes in peptide chemical properties. The findings have broader implications on the bioavailability, biomolecular interactions and biological activities of food peptides.
Collapse
Affiliation(s)
- Shixiang Yao
- College of Food Science, Southwest University, Chongqing 400715, People's Republic of China
- School of Nutrition Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1H 8L1
| | - Chibuike C. Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1H 8L1
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1N 6N5
| |
Collapse
|
158
|
Bonds AC, Sampson NS. More than cholesterol catabolism: regulatory vulnerabilities in Mycobacterium tuberculosis. Curr Opin Chem Biol 2018; 44:39-46. [PMID: 29906645 DOI: 10.1016/j.cbpa.2018.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/09/2018] [Indexed: 11/17/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the epitome of persistent. Mtb is the pathogen that causes tuberculosis, the leading cause of death by infection worldwide. The success of this pathogen is due in part to its clever ability to adapt to its host environment and its effective manipulation of the host immune system. A major contributing factor to the survival and virulence of Mtb is its acquisition and metabolism of host derived lipids including cholesterol. Accumulating evidence suggests that the catabolism of cholesterol during infection is highly regulated by cholesterol catabolites. We review what is known about how regulation interconnects with cholesterol catabolism. This framework provides support for an indirect approach to drug development that targets Mtb cholesterol metabolism through dysregulation of nutrient utilization pathways.
Collapse
Affiliation(s)
- Amber C Bonds
- Molecular and Cellular Pharmacology Program, Stony Brook University, Stony Brook, NY 11794-8651, United States
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States.
| |
Collapse
|
159
|
Xu JY, Xu Y, Xu Z, Zhai LH, Ye Y, Zhao Y, Chu X, Tan M, Ye BC. Protein Acylation is a General Regulatory Mechanism in Biosynthetic Pathway of Acyl-CoA-Derived Natural Products. Cell Chem Biol 2018; 25:984-995.e6. [PMID: 29887264 DOI: 10.1016/j.chembiol.2018.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/25/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022]
Abstract
Coenzyme A (CoA) esters of short fatty acids (acyl-CoAs) function as key precursors for the biosynthesis of various natural products and the dominant donors for lysine acylation. Herein, we investigated the functional interplay between beneficial and adverse effects of acyl-CoA supplements on the production of acyl-CoA-derived natural products in microorganisms by using erythromycin-biosynthesized Saccharopolyspora erythraea as a model: accumulation of propionyl-CoA benefited erythromycin biosynthesis, but lysine propionylation inhibited the activities of important enzymes involved in biosynthetic pathways of erythromycin. The results showed that the overexpression of NAD+-dependent deacylase could circumvent the inhibitory effects of high acyl-CoA concentrations. In addition, we demonstrated the similar lysine acylation mechanism in other acyl-CoA-derived natural product biosynthesis, such as malonyl-CoA-derived alkaloid and butyryl-CoA-derived bioalcohol. These observations systematically uncovered the important role of protein acylation on interaction between the accumulation of high concentrations of acyl-CoAs and the efficiency of their use in metabolic pathways.
Collapse
Affiliation(s)
- Jun-Yu Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yingming Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
| | - Bang-Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
160
|
Weinert BT, Narita T, Satpathy S, Srinivasan B, Hansen BK, Schölz C, Hamilton WB, Zucconi BE, Wang WW, Liu WR, Brickman JM, Kesicki EA, Lai A, Bromberg KD, Cole PA, Choudhary C. Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome. Cell 2018; 174:231-244.e12. [PMID: 29804834 DOI: 10.1016/j.cell.2018.04.033] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/21/2018] [Accepted: 04/24/2018] [Indexed: 12/29/2022]
Abstract
The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators. Here, we combined quantitative proteomics with CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to reveal a comprehensive map of regulated acetylation sites and their dynamic turnover rates. CBP/p300 acetylates thousands of sites, including signature histone sites and a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Time-resolved acetylome analyses identified a subset of CBP/p300-regulated sites with very rapid (<30 min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP/p300 targets, and the resource dataset provides a framework for investigating CBP/p300 functions and for understanding the impact of small-molecule inhibitors targeting its catalytic and bromodomain activities.
Collapse
Affiliation(s)
- Brian T Weinert
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Takeo Narita
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Balaji Srinivasan
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Bogi K Hansen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christian Schölz
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Biology-DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Beth E Zucconi
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Wesley W Wang
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Biology-DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Edward A Kesicki
- Acylin Therapeutics, Inc., 1616 Eastlake Ave E, #200, Seattle, WA 98102, USA; Petra Pharma Corp., 430 E. 29th St. Suite 835, New York, NY 10016, USA
| | - Albert Lai
- Discovery, Global Pharmaceutical Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Kenneth D Bromberg
- Discovery, Global Pharmaceutical Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| |
Collapse
|
161
|
Scott I, Wang L, Wu K, Thapa D, Sack MN. GCN5L1/BLOS1 Links Acetylation, Organelle Remodeling, and Metabolism. Trends Cell Biol 2018; 28:346-355. [PMID: 29477615 PMCID: PMC5912981 DOI: 10.1016/j.tcb.2018.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/17/2018] [Accepted: 01/30/2018] [Indexed: 12/17/2022]
Abstract
General control of amino acid synthesis 5 (GCN5) like-1 (GCN5L1) was identified as a novel gene with sequence homology to the histone acetyltransferase Gcn5. Subsequent protein-interaction studies identified GCN5L1 as a subunit of the multiprotein lysosome biogenesis complex, resulting in an alternative designation as biogenesis of lysosome-related organelle complex 1 subunit 1 (BLOS1 or BLOC1S1). Despite the distinct nomenclatures, GCN5L1/BLOS1 has been shown to play crucial roles in mitochondria, endosomes, lysosomes, and synaptic vesicle precursors (SVPs). GCN5L1/BLOS1 controls mitochondrial protein acetylation, modulates metabolic pathways, and orchestrates retrograde mitochondria-to-nucleus signaling. It also contributes to endosome-lysosome and vesicle trafficking and to endolysosomal function. Here we discuss the intracellular roles of GCN5L1/BLOS1 in the hope of linking mitochondria-centric effects to cytosolic vesicle biology.
Collapse
Affiliation(s)
- Iain Scott
- Cardiology Division, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Lingdi Wang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kaiyuan Wu
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Dharendra Thapa
- Cardiology Division, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Michael N Sack
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
162
|
Rocha B, Rodrigues AR, Tomada I, Martins MJ, Guimarães JT, Gouveia AM, Almeida H, Neves D. Energy restriction, exercise and atorvastatin treatment improve endothelial dysfunction and inhibit miRNA-155 in the erectile tissue of the aged rat. Nutr Metab (Lond) 2018; 15:28. [PMID: 29686722 PMCID: PMC5902942 DOI: 10.1186/s12986-018-0265-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/03/2018] [Indexed: 02/06/2023] Open
Abstract
Background Endothelial dysfunction underlies cardiovascular disease that frequently affects aged individuals. Characterized by local decrease in nitric oxide, it results from down-regulation of endothelial nitric oxide synthase (eNOS) expression/activity. Aiming to elucidate the molecular mechanisms involved in age-related endothelial dysfunction and to unveil potential therapeutic targets, we tested how diet pattern, exercise and atorvastatin modulate the expression of eNOS, inducible NOS (iNOS), endothelin-1, sirtuins (SIRT) and microRNA-155 in the erectile tissue of high-fat fed aged rats. Methods Sprague-Dawley male rats fed with high-fat diet until they completed 12 months were grouped and subjected to energy restriction (ER), ER and atorvastatin, or, ER, atorvastatin and physical exercise. Controls were fed with standard rodent chow. The blood pressure was measured using the tail-cuff method before sacrifice at 18 months. Glucose, total cholesterol, HDL, triglyceride and CRP were assessed in blood and eNOS, endothelin-1, iNOS and sirtuins were detected by immunofluorescence in the penis sections; eNOS, endothelin-1, iNOS, SIRT2-4 and SIRT6-7 were semi-quantified by western blotting in tissue homogenates. MicroRNA-155 was quantified using RT-PCR in formalin-fixed paraffin embedded sections. To compare the studied variables, two-tail student t test was used. Results Atorvastatin promotes eNOS expression and is more efficient than ER or exercise in the control of hyperlipidemia and inflammation. Among the studied sirtuins, detected for the first time in the erectile tissue of the aged rat, SIRT2 aligns with eNOS expression. Both proteins exhibit over-expression in animals with combined exercise, atorvastatin and ER. Analysis of microRNA-155 expression also suggests its intervention in the regulation of eNOS expression. ER, particularly when combined with atorvastatin, was able to reverse the increase of iNOS and endothelin-1 in high-fat fed rats. Conclusions The present results indicate that the association of ER, atorvastatin and exercise is more efficient than isolated interventions in the prevention of endothelial dysfunction.
Collapse
Affiliation(s)
- B Rocha
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - A R Rodrigues
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - I Tomada
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,3Faculty of Biotechnology, Portuguese Catholic University, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal.,Hospital CUF Porto, Estrada da Circunvalação, 14341, 4100-180 Porto, Portugal
| | - M J Martins
- Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,5Department of Biomedicine - Biochemistry Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - J T Guimarães
- 5Department of Biomedicine - Biochemistry Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,6Institute of Public Health, University of Porto, Rua das Taipas, 135, 4050-600 Porto, Portugal.,Clinical Pathology Department of São João Hospital Centre, Porto, Portugal
| | - A M Gouveia
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.,8Faculty of Nutrition and Food Sciences, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - H Almeida
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - D Neves
- 1Department of Biomedicine - Experimental Biology Unit, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S) Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| |
Collapse
|
163
|
Kumar S, Lombard DB. Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology. Crit Rev Biochem Mol Biol 2018; 53:311-334. [PMID: 29637793 DOI: 10.1080/10409238.2018.1458071] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sirtuins are NAD+-dependent protein deacylases/ADP-ribosyltransferases that have emerged as candidate targets for new therapeutics to treat metabolic disorders and other diseases, including cancer. The sirtuin SIRT5 resides primarily in the mitochondrial matrix and catalyzes the removal of negatively charged lysine acyl modifications; succinyl, malonyl, and glutaryl groups. Evidence has now accumulated to document the roles of SIRT5 as a significant regulator of cellular homeostasis, in a context- and cell-type specific manner, as has been observed previously for other sirtuin family members. SIRT5 regulates protein substrates involved in glycolysis, the TCA cycle, fatty acid oxidation, electron transport chain, ketone body formation, nitrogenous waste management, and ROS detoxification, among other processes. SIRT5 plays pivotal roles in cardiac physiology and stress responses and is involved in the regulation of numerous aspects of myocardial energy metabolism. SIRT5 is implicated in neoplasia, as both a tumor promoter and suppressor in a context-specific manner, and may serve a protective function in the setting of neurodegenerative disorders. Here, we review the current understanding of functional impacts of SIRT5 on its metabolic targets, and its molecular functions in both normal and pathological conditions. Finally, we will discuss the potential utility of SIRT5 as a drug target and also summarize the current status, progress, and challenges in developing small molecule compounds to modulate SIRT5 activity with high potency and specificity.
Collapse
Affiliation(s)
- Surinder Kumar
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA
| | - David B Lombard
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA.,b Institute of Gerontology , University of Michigan , Ann Arbor , MI , USA
| |
Collapse
|
164
|
Kutil Z, Novakova Z, Meleshin M, Mikesova J, Schutkowski M, Barinka C. Histone Deacetylase 11 Is a Fatty-Acid Deacylase. ACS Chem Biol 2018; 13:685-693. [PMID: 29336543 DOI: 10.1021/acschembio.7b00942] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Histone deacetylase 11 (HDAC11) is a sole member of the class IV HDAC subfamily with negligible intrinsic deacetylation activity. Here, we report in vitro profiling of HDAC11 deacylase activities, and our data unequivocally show that the enzyme efficiently removes acyl moieties spanning 8-18 carbons from the side chain nitrogen of the lysine residue of a peptidic substrate. Additionally, N-linked lipoic acid and biotin are removed by the enzyme, although with lower efficacy. Catalytic efficiencies toward dodecanoylated and myristoylated peptides were 77 700 and 149 000 M-1 s-1, respectively, making HDAC11 the most proficient fatty-acid deacylase of the HDAC family. Interestingly, HDAC11 is strongly inhibited by free myristic, palmitic, and stearic acids with inhibition constants of 6.5, 0.9, and 1.6 μM, respectively. At the same time, its deacylase activity is stimulated more than 2.5-fold by both palmitoyl-coenzyme A and myristoyl-coenzyme A, pointing toward metabolic control of the enzymatic activity by fatty-acid metabolites. Our data reveal novel enzymatic activity of HDAC11 that can, in turn, facilitate the uncovering of additional biological functions of the enzyme as well as the design of isoform-specific HDAC inhibitors.
Collapse
Affiliation(s)
- Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Marat Meleshin
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Jana Mikesova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Mike Schutkowski
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| |
Collapse
|
165
|
Lee SY, Choi YS, Kim EH, Cheong HK, Lee YJ, Lee JG, Ye Y, Ryu KS. Nonenzymatic acetylation of ubiquitin Lys side chains is modulated by their neighboring residues. FEBS J 2018; 285:1277-1289. [PMID: 29430834 DOI: 10.1111/febs.14404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/14/2018] [Accepted: 02/06/2018] [Indexed: 01/21/2023]
Abstract
Nonenzymatic acetylation of Lys side chains (Lys-SCs) by various in vivo reactive molecules has been suggested to play novel regulatory roles. Ubiquitin (UB) has seven Lys residues that are utilized for synthesis of specific poly-UB chains. To understand the nature of these Lys-SC modifications, the chemical acetylation rate and pKa and Hill coefficient of each UB-Lys-SC were measured. Mutagenesis studies combined with the determination of activation energy indicated that specific neighboring residues of the Lys-SCs have a potential catalytic activity during nonenzymatic acetylation. Based on the shared chemistry between nonenzymatic Lys acetylation and ubiquitylation, the characterized chemical properties of the UB-Lys-SCs could be a reference for deciphering both mechanisms. Our NMR approaches could be useful for studying general nonenzymatic Lys acylations of various proteins.
Collapse
Affiliation(s)
- Seo-Yeon Lee
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea
| | - Yun-Seok Choi
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejon, South Korea.,Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Eun-Hee Kim
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea
| | - Hae-Kap Cheong
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea
| | - Yun-Ju Lee
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea
| | - Jin-Gu Lee
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD, USA.,Center for Genetic Medicine Research, Children's National Health Systems, Washington, DC, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD, USA
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, Cheongju-Si, South Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejon, South Korea
| |
Collapse
|
166
|
Yan L. Redox imbalance stress in diabetes mellitus: Role of the polyol pathway. Animal Model Exp Med 2018; 1:7-13. [PMID: 29863179 PMCID: PMC5975374 DOI: 10.1002/ame2.12001] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022] Open
Abstract
In diabetes mellitus, the polyol pathway is highly active and consumes approximately 30% glucose in the body. This pathway contains 2 reactions catalyzed by aldose reductase (AR) and sorbitol dehydrogenase, respectively. AR reduces glucose to sorbitol at the expense of NADPH, while sorbitol dehydrogenase converts sorbitol to fructose at the expense of NAD+, leading to NADH production. Consumption of NADPH, accumulation of sorbitol, and generation of fructose and NADH have all been implicated in the pathogenesis of diabetes and its complications. In this review, the roles of this pathway in NADH/NAD+ redox imbalance stress and oxidative stress in diabetes are highlighted. A potential intervention using nicotinamide riboside to restore redox balance as an approach to fighting diabetes is also discussed.
Collapse
Affiliation(s)
- Liang‐jun Yan
- Department of Pharmaceutical SciencesUNT System College of PharmacyUniversity of North Texas Health Science CenterFort WorthTXUSA
| |
Collapse
|
167
|
Xie C, Shen H, Zhang H, Yan J, Liu Y, Yao F, Wang X, Cheng Z, Tang TS, Guo C. Quantitative proteomics analysis reveals alterations of lysine acetylation in mouse testis in response to heat shock and X-ray exposure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:464-472. [DOI: 10.1016/j.bbapap.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
|
168
|
Liu YT, Pan Y, Lai F, Yin XF, Ge R, He QY, Sun X. Comprehensive analysis of the lysine acetylome and its potential regulatory roles in the virulence of Streptococcus pneumoniae. J Proteomics 2018; 176:46-55. [DOI: 10.1016/j.jprot.2018.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/18/2018] [Accepted: 01/25/2018] [Indexed: 12/28/2022]
|
169
|
Walsh CT, Tu BP, Tang Y. Eight Kinetically Stable but Thermodynamically Activated Molecules that Power Cell Metabolism. Chem Rev 2018; 118:1460-1494. [PMID: 29272116 PMCID: PMC5831524 DOI: 10.1021/acs.chemrev.7b00510] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1 ) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites.
Collapse
Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA
| | - Benjamin P. Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
| |
Collapse
|
170
|
Features and regulation of non-enzymatic post-translational modifications. Nat Chem Biol 2018; 14:244-252. [DOI: 10.1038/nchembio.2575] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/12/2018] [Indexed: 02/02/2023]
|
171
|
A posttranslational modification of the mitotic kinesin Eg5 that enhances its mechanochemical coupling and alters its mitotic function. Proc Natl Acad Sci U S A 2018; 115:E1779-E1788. [PMID: 29432173 DOI: 10.1073/pnas.1718290115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Numerous posttranslational modifications have been described in kinesins, but their consequences on motor mechanics are largely unknown. We investigated one of these-acetylation of lysine 146 in Eg5-by creating an acetylation mimetic lysine to glutamine substitution (K146Q). Lysine 146 is located in the α2 helix of the motor domain, where it makes an ionic bond with aspartate 91 on the neighboring α1 helix. Molecular dynamics simulations predict that disrupting this bond enhances catalytic site-neck linker coupling. We tested this using structural kinetics and single-molecule mechanics and found that the K146Q mutation increases motor performance under load and coupling of the neck linker to catalytic site. These changes convert Eg5 from a motor that dissociates from the microtubule at low load into one that is more tightly coupled and dissociation resistant-features shared by kinesin 1. These features combined with the increased propensity to stall predict that the K146Q Eg5 acetylation mimetic should act in the cell as a "brake" that slows spindle pole separation, and we have confirmed this by expressing this modified motor in mitotically active cells. Thus, our results illustrate how a posttranslational modification of a kinesin can be used to fine tune motor behavior to meet specific physiological needs.
Collapse
|
172
|
Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
173
|
Abstract
SIGNIFICANCE Pyridine dinucleotides, nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP), were discovered more than 100 years ago as necessary cofactors for fermentation in yeast extracts. Since that time, these molecules have been recognized as fundamental players in a variety of cellular processes, including energy metabolism, redox homeostasis, cellular signaling, and gene transcription, among many others. Given their critical role as mediators of cellular responses to metabolic perturbations, it is unsurprising that dysregulation of NAD and NADP metabolism has been associated with the pathobiology of many chronic human diseases. Recent Advances: A biochemistry renaissance in biomedical research, with its increasing focus on the metabolic pathobiology of human disease, has reignited interest in pyridine dinucleotides, which has led to new insights into the cell biology of NAD(P) metabolism, including its cellular pharmacokinetics, biosynthesis, subcellular localization, and regulation. This review highlights these advances to illustrate the importance of NAD(P) metabolism in the molecular pathogenesis of disease. CRITICAL ISSUES Perturbations of NAD(H) and NADP(H) are a prominent feature of human disease; however, fundamental questions regarding the regulation of the absolute levels of these cofactors and the key determinants of their redox ratios remain. Moreover, an integrated topological model of NAD(P) biology that combines the metabolic and other roles remains elusive. FUTURE DIRECTIONS As the complex regulatory network of NAD(P) metabolism becomes illuminated, sophisticated new approaches to manipulating these pathways in specific organs, cells, or organelles will be developed to target the underlying pathogenic mechanisms of disease, opening doors for the next generation of redox-based, metabolism-targeted therapies. Antioxid. Redox Signal. 28, 180-212.
Collapse
Affiliation(s)
- Joshua P Fessel
- 1 Department of Medicine, Vanderbilt University , Nashville, Tennessee
| | - William M Oldham
- 2 Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts.,3 Department of Medicine, Harvard Medical School , Boston, Massachusetts
| |
Collapse
|
174
|
Exogenous H 2S switches cardiac energy substrate metabolism by regulating SIRT3 expression in db/db mice. J Mol Med (Berl) 2018; 96:281-299. [PMID: 29349500 DOI: 10.1007/s00109-017-1616-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/26/2017] [Accepted: 12/18/2017] [Indexed: 01/24/2023]
Abstract
Hydrogen sulfide (H2S) is involved in diverse physiological functions, such as anti-hypertension, anti-proliferation, regulating ATP synthesis, and reactive oxygen species production. Sirtuin 3 (SIRT3) is a NAD + -dependent deacetylase that regulates mitochondrial energy metabolism. The role of H2S in energy metabolism in diabetic cardiomyopathy (DCM) may be related to regulate SIRT3 expression; however, this role remains to be elucidated. We hypothesized that exogenous H2S could switch cardiac energy metabolic substrate preference by lysine acetylation through promoting the expression of SIRT3 in cardiac tissue of db/db mice. Db/db mice, neonatal rat cardiomyocytes, and H9c2 cell line with the treatment of high glucose, oleate, and palmitate were used as animal and cellular models of type 2 diabetes. Using LC-MS/MS, we identified 76 proteins that increased acetylation, including 8 enzymes related to fatty acid β-oxidation and 7 enzymes of the tricarboxylic acid (TCA) cycle in the db/db mice hearts compared to those with the treatment of NaHS. Exogenous H2S restored the expression of NAMPT and the ratio of NAD+/NADH enhanced the expression and activity of SIRT3. As a result of activation of SIRT3, the acetylation level and activity of fatty acid β-oxidation enzyme LCAD and the acetylation of glucose oxidation enzymes PDH, IDH2, and CS were reduced which resulted in activation of PDH, IDH2, and CS. Our finding suggested that H2S induced a switch in cardiac energy substrate utilization from fatty acid β-oxidation to glucose oxidation in DCM through regulating SIRT3 pathway. KEY MESSAGES H2S regulated the acetylation level and activities of enzymes in fatty acid oxidation and glucose oxidation in cardiac tissues of db/db mice. Exogenous H2S decreased mitochondrial acetylation level through upregulating the expression and activity of SIRT3 in vivo and in vitro. H2S induced a switch in cardiac energy substrate utilization from fatty acid oxidation to glucose.
Collapse
|
175
|
Yang Y, Tong M, Bai X, Liu X, Cai X, Luo X, Zhang P, Cai W, Vallée I, Zhou Y, Liu M. Comprehensive Proteomic Analysis of Lysine Acetylation in the Foodborne Pathogen Trichinella spiralis. Front Microbiol 2018; 8:2674. [PMID: 29375535 PMCID: PMC5768625 DOI: 10.3389/fmicb.2017.02674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/21/2017] [Indexed: 01/08/2023] Open
Abstract
Lysine acetylation is a dynamic and highly conserved post-translational modification that plays a critical role in regulating diverse cellular processes. Trichinella spiralis is a foodborne parasite with a considerable socio-economic impact. However, to date, little is known regarding the role of lysine acetylation in this parasitic nematode. In this study, we utilized a proteomic approach involving anti-acetyl lysine-based enrichment and highly sensitive mass spectrometry to identify the global acetylated proteome and investigate lysine acetylation in T. spiralis. In total, 3872 lysine modification sites were identified in 1592 proteins that are involved in a wide variety of biological processes. Consistent with the results of previous studies, a large number of the acetylated proteins appear to be involved in metabolic and biosynthetic processes. Interestingly, according to the functional enrichment analysis, 29 acetylated proteins were associated with phagocytosis, suggesting an important role of lysine acetylation in this process. Among the identified proteins, 15 putative acetylation motifs were detected. The presence of serine downstream of the lysine acetylation site was commonly observed in the regions surrounding the sites. Moreover, protein interaction network analysis revealed that various interactions are regulated by protein acetylation. These data represent the first report of the acetylome of T. spiralis and provide an important resource for further explorations of the role of lysine acetylation in this foodborne pathogen.
Collapse
Affiliation(s)
- Yong Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China.,Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Mingwei Tong
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xue Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaolei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuepeng Cai
- China Institute of Veterinary Drug Control, Beijing, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peihao Zhang
- Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Wei Cai
- Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Isabelle Vallée
- JRU BIPAR, ANSES, École Nationale Vétérinaire d'Alfort, INRA, Université Paris-Est, Animal Health Laboratory, Maisons-Alfort, France
| | - Yonghua Zhou
- Jiangsu Institute of Parasitic Disease, Wuxi, China
| | - Mingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
176
|
Dhillon RS, Richards JG. Hypoxia induces selective modifications to the acetylome in the brain of zebrafish (Danio rerio). Comp Biochem Physiol B Biochem Mol Biol 2018; 224:79-87. [PMID: 29309913 DOI: 10.1016/j.cbpb.2017.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 10/18/2022]
Abstract
Reversible protein acetylation is an important regulatory mechanism for modulating protein function. The cellular protein acetylome is in large part dictated by the cellular redox balance, and in particular [NAD+]. While the relationship between hypoxia, redox balance, energy charge and resulting mitochondrial dysfunction has been examined in the context of hypoxia-linked pathologies, little is known about the direct effects of decreases in environmental oxygen on reversible lysine acetylation, and the resulting modifications to mitochondrial metabolism. To address this knowledge gap, we exposed zebrafish (Danio rerio) to 16 h of hypoxia (2.21 kPa) and quantified acetylation levels of 1220 proteins using whole-cell proteomics in samples of brain taken from normoxic and hypoxic zebrafish. In addition, we examined the effects of hypoxia on cytoplasmic and mitochondrial redox status, whole-cell energetics, the activity of the mitochondrial NAD+-dependent deacetylase SIRT3, and electron transport chain complex activities to determine if there is an association between hypoxia-induced metabolic disturbances, protein acetylation, and mitochondrial function. Our results (1) reveal several key changes in the acetylation status of proteins in the brain, primarily within the mitochondria; (2) show significant fluctuations in cytoplasmic and mitochondrial redox status within the brain during hypoxia exposure; and (3) provide evidence that lysine acetylation may be related to large changes in electron transport and ATP-synthase complex activities and adenylate status in zebrafish exposed to hypoxic stress. Together, these data provide new insights into the role of protein modifications in mitochondrial metabolism during hypoxia.
Collapse
Affiliation(s)
- Rashpal S Dhillon
- Wisconsin Institute for Discovery, Department of Biomolecular Chemistry, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI 53715, USA; Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
177
|
Goetzman ES, Gong Z, Schiff M, Wang Y, Muzumdar RH. Metabolic pathways at the crossroads of diabetes and inborn errors. J Inherit Metab Dis 2018; 41:5-17. [PMID: 28952033 PMCID: PMC6757345 DOI: 10.1007/s10545-017-0091-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/30/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
Research over the past two decades has led to advances in our understanding of the genetic and metabolic factors that underlie the pathogenesis of type 2 diabetes mellitus (T2DM). While T2DM is defined by its hallmark metabolic symptoms, the genetic risk factors for T2DM are more immune-related than metabolism-related, and the observed metabolic disease may be secondary to chronic inflammation. Regardless, these metabolic changes are not benign, as the accumulation of some metabolic intermediates serves to further drive the inflammation and cell stress, eventually leading to insulin resistance and ultimately to T2DM. Because many of the biochemical changes observed in the pre-diabetic state (i.e., ectopic lipid storage, increased acylcarnitines, increased branched-chain amino acids) are also observed in patients with rare inborn errors of fatty acid and amino acid metabolism, an interesting question is raised regarding whether isolated metabolic gene defects can confer an increased risk for T2DM. In this review, we attempt to address this question by summarizing the literature regarding the metabolic pathways at the crossroads of diabetes and inborn errors of metabolism. Studies using cell culture and animal models have revealed that, within a given pathway, disrupting some genes can lead to insulin resistance while for others there may be no effect or even improved insulin sensitivity. This differential response to ablating a single metabolic gene appears to be dependent upon the specific metabolic intermediates that accumulate and whether these intermediates subsequently activate inflammatory pathways. This highlights the need for future studies to determine whether certain inborn errors may confer increased risk for diabetes as the patients age.
Collapse
Affiliation(s)
- Eric S Goetzman
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
- Children's Hospital of Pittsburgh, Rangos 5117, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA.
| | - Zhenwei Gong
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Manuel Schiff
- UMR1141, PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Reference Center for Inborn Errors of Metabolism, Robert Debré University Hospital, APHP, Paris, France
| | - Yan Wang
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Radhika H Muzumdar
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| |
Collapse
|
178
|
Chen J, Li F, Liu Y, Shen W, Du X, He L, Meng Z, Ma X, Wang Y. Systematic identification of mitochondrial lysine succinylome in silkworm (Bombyx mori) midgut during the larval gluttonous stage. J Proteomics 2017; 174:61-70. [PMID: 29288090 DOI: 10.1016/j.jprot.2017.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/12/2017] [Accepted: 12/25/2017] [Indexed: 12/12/2022]
Abstract
Lysine succinylation is a newly identified protein post-translational modification (PTM) of lysine residues. Increasing evidences demonstrate that this modification is prevalent in mitochondria and regulates many vital cellular processes, especially metabolism. Here, we determined the succinylome of the silkworm (Bombyx mori) midgut mitochondria during the larval gluttonous stage (the fifth instar) using succinylated peptides enrichment coupled with nano HPLC/MS/MS. A total of 1884 lysine succinylation sites on 373 mitochondrial proteins were identified. The bioinformatic analysis reveal that succinylated proteins are significantly enriched in central metabolic processes and mitochondrial protein synthesis. Several apoptosis and detoxification related enzymes or proteins are succinylated. The findings suggest the crucial role of lysine succinylation in silkworm midgut metabolism and resistance. Our data provide a rich resource for further analysis of lysine succinylation in silkworm. SIGNIFICANCE Insect midgut is the vital tissue for nutrient metabolism and also for xenobiotic metabolism. There is a growing body of knowledge on regulation of midgut function at the gene or protein levels in silkworm, however, the regulation at post-translation modification level remains largely unknown. We provide a first global analysis of the mitochondrial lysine succinylome in silkworm midgut. A total of 1884 lysine succinylation sites on 373 mitochondrial proteins were identified. Bioinformatics results suggest an important role of this modification in regulating metabolism and mitochondrial protein synthesis. Our data greatly expand the catalog of lysine succinylation substrates and sites in insects, and represents an important resource for understanding the physiological function of lysine succinylation in insect midgut.
Collapse
Affiliation(s)
- Jine Chen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fengbo Li
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan Liu
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weifeng Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Du
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lihua He
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhiqi Meng
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | | | - Yongqiang Wang
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
179
|
He M, Han Z, Liu L, Zheng YG. Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| |
Collapse
|
180
|
He M, Han Z, Liu L, Zheng YG. Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases. Angew Chem Int Ed Engl 2017; 57:1162-1184. [PMID: 28786225 DOI: 10.1002/anie.201704745] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/20/2022]
Abstract
The side-chain acetylation of lysine residues in histones and non-histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT-mediated histone acetylation has an effect on all DNA-templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.
Collapse
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| |
Collapse
|
181
|
Abstract
Glycolysis, the breakdown of glucose, is one of the most conserved and extensively studied biochemical pathways. Designing principles from chemistry and thermodynamics allow for energy production, biosynthesis and cellular communication. However, the kinetics or metabolic flux through the pathway also determines its function. Recently, there have been numerous developments that establish new allosteric interactions of glycolytic enzymes with small molecule metabolites and other mechanisms that may cooperate to allow for addition complex regulation of glycolysis. This review surveys these newfound sources of glycolysis regulation and discusses their possible roles in establishing kinetic design principles of glycolysis.
Collapse
Affiliation(s)
- Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
182
|
Non-enzymatic N-acetylation of Lysine Residues by AcetylCoA Often Occurs via a Proximal S-acetylated Thiol Intermediate Sensitive to Glyoxalase II. Cell Rep 2017; 18:2105-2112. [PMID: 28249157 PMCID: PMC6381604 DOI: 10.1016/j.celrep.2017.02.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 12/03/2016] [Accepted: 02/03/2017] [Indexed: 12/31/2022] Open
Abstract
Acetyl coenzyme A (AcCoA), a key intermediate in mitochondrial metabolism, N-acetylates lysine residues, disrupting and, in some cases, regulating protein function. The mitochondrial lysine deacetylase Sirtuin 3 (Sirt3) reverses this modification with benefits reported in diabetes, obesity, and aging. We show that non-enzymatic lysine N-acetylation by AcCoA is greatly enhanced by initial acetylation of a cysteine residue, followed by SN-transfer of the acetyl moiety to a nearby lysine on mitochondrial proteins and synthetic peptides. The frequent occurrence of an S-acetyl intermediate before lysine N-acetylation suggests that proximity to a thioester is a key determinant of lysine susceptibility to acetylation. The thioesterase glyoxalase II (Glo2) can limit protein S-acetylation, thereby preventing subsequent lysine N-acetylation. This suggests that the hitherto obscure role of Glo2 in mitochondria is to act upstream of Sirt3 in minimizing protein N-acetylation, thus limiting protein dysfunction when AcCoA accumulates. AcCoA and acetylglutathione reversibly acetylate protein cysteine residues Non-enzymatic lysine acetylation proceeds via a proximal S-acetylated thiol intermediate Glyoxalase II and glutathione limit lysine N-acetylation and N-succinylation These findings have implications for N-acetylation of lysines in regulation and pathology
Collapse
|
183
|
Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification. J Mol Biol 2017; 430:102-118. [PMID: 29183786 DOI: 10.1016/j.jmb.2017.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 01/24/2023]
Abstract
Protein methylation is one of the major post-translational modifications (PTMs) in the cell. In Saccharomyces cerevisiae, over 20 protein methyltransferases (MTases) and their respective substrates have been identified. However, the way in which these MTases are modified and potentially subject to regulation remains poorly understood. Here, we investigated six overexpressed S. cerevisiae protein MTases (Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1) to identify PTMs of potential functional relevance. We identified 48 PTM sites across the six MTases, including phosphorylation, acetylation and methylation. Forty-two sites are novel. We contextualized the PTM sites in structural models of the MTases and revealed that many fell in catalytic pockets or enzyme-substrate interfaces. These may regulate MTase activity. Finally, we compared PTMs on Hmt1 with those on its human homologs PRMT1, PRMT3, CARM1, PRMT6 and PRMT8. This revealed that several PTMs are conserved from yeast to human, whereas others are only found in Hmt1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD006767.
Collapse
|
184
|
Pannek M, Simic Z, Fuszard M, Meleshin M, Rotili D, Mai A, Schutkowski M, Steegborn C. Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features. Nat Commun 2017; 8:1513. [PMID: 29138502 PMCID: PMC5686155 DOI: 10.1038/s41467-017-01701-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/07/2017] [Indexed: 12/22/2022] Open
Abstract
Sirtuins are evolutionary conserved NAD+-dependent protein lysine deacylases. The seven human isoforms, Sirt1-7, regulate metabolism and stress responses and are considered therapeutic targets for aging-related diseases. Sirt4 locates to mitochondria and regulates fatty acid metabolism and apoptosis. In contrast to the mitochondrial deacetylase Sirt3 and desuccinylase Sirt5, no prominent deacylase activity and structural information are available for Sirt4. Here we describe acyl substrates and crystal structures for Sirt4. The enzyme shows isoform-specific acyl selectivity, with significant activity against hydroxymethylglutarylation. Crystal structures of Sirt4 from Xenopus tropicalis reveal a particular acyl binding site with an additional access channel, rationalizing its activities. The structures further identify a conserved, isoform-specific Sirt4 loop that folds into the active site to potentially regulate catalysis. Using these results, we further establish efficient Sirt4 activity assays, an unusual Sirt4 regulation by NADH, and Sirt4 effects of pharmacological modulators.
Collapse
Affiliation(s)
- Martin Pannek
- Department of Biochemistry, University of Bayreuth, 95440, Bayreuth, Germany
| | - Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06108, Halle, Germany
| | - Matthew Fuszard
- Department of Biochemistry, University of Bayreuth, 95440, Bayreuth, Germany
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06108, Halle, Germany
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs, Pasteur Institute Italy, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185, Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Pasteur Institute Italy, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185, Rome, Italy
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06108, Halle, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, 95440, Bayreuth, Germany.
| |
Collapse
|
185
|
Dhillon RS, Denu JM. Using comparative biology to understand how aging affects mitochondrial metabolism. Mol Cell Endocrinol 2017; 455:54-61. [PMID: 28025033 DOI: 10.1016/j.mce.2016.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/24/2016] [Accepted: 12/16/2016] [Indexed: 02/06/2023]
Abstract
Lifespan varies considerably among even closely related species, as exemplified by rodents and primates. Despite these disparities in lifespan, most studies have focused on intra-specific aging pathologies, primarily within a select few systems. While mice have provided much insight into aging biology, it is unclear if such a short-lived species lack defences against senescence that may have evolved in related longevous species. Many age-related diseases have been linked to mitochondrial dysfunction that are measured by decreased energy generation, structural damage to cellular components, and even cell death. Post translational modifications (PTMs) orchestrate many of the pathways associated with cellular metabolism, and are thought to be a key regulator in biological senescence. We propose hyperacylation as one such modification that may be implicated in numerous mitochondrial impairments affecting energy metabolism.
Collapse
Affiliation(s)
- Rashpal S Dhillon
- Department of Biomolecular Chemistry, University of Wisconsin- Madison, Madison, WI 53715, USA.
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin- Madison, Madison, WI 53715, USA
| |
Collapse
|
186
|
Biochemical Analysis of Histone Succinylation. Biochem Res Int 2017; 2017:8529404. [PMID: 29225971 PMCID: PMC5684591 DOI: 10.1155/2017/8529404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 11/18/2022] Open
Abstract
Posttranslational modification (PTM) of proteins is used to regulate protein activity and stability. Histone PTMs are regarded as some of the most important, as they can directly regulate gene expression through chromatin reorganization. Recently, histone proteins were found to undergo succinylation, adding to other well-known PTMs such as acetylation, methylation, and phosphorylation. However, there is little information regarding the enzyme which catalyzes histone lysine succinylation. In fact, it is unclear whether this reaction is enzymatic. In this study, we tested histone succinylation activity in vitro using cell nuclear extracts of HepG2 cells. Although whole nuclear extracts did not show histone succinylation activity, we found that an SP 1.0 M KCl fraction of nuclear extracts indeed had such activity. These data offer the first direct evidence that histone succinylation is an enzymatic PTM as are other histone codes in the nucleus.
Collapse
|
187
|
Reid MA, Dai Z, Locasale JW. The impact of cellular metabolism on chromatin dynamics and epigenetics. Nat Cell Biol 2017; 19:1298-1306. [PMID: 29058720 PMCID: PMC5886854 DOI: 10.1038/ncb3629] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/15/2017] [Indexed: 12/12/2022]
Abstract
The substrates used to modify nucleic acids and chromatin are affected by nutrient availability and the activity of metabolic pathways. Thus, cellular metabolism constitutes a fundamental component of chromatin status and thereby of genome regulation. Here we describe the biochemical and genetic principles of how metabolism can influence chromatin biology and epigenetics, discuss the functional roles of this interplay in developmental and cancer biology, and present future directions in this rapidly emerging area.
Collapse
Affiliation(s)
- Michael A. Reid
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
| | - Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
| |
Collapse
|
188
|
Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA. Characterization of histone acylations links chromatin modifications with metabolism. Nat Commun 2017; 8:1141. [PMID: 29070843 PMCID: PMC5656686 DOI: 10.1038/s41467-017-01384-9] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 09/14/2017] [Indexed: 12/30/2022] Open
Abstract
Over the last decade, numerous histone acyl post-translational modifications (acyl-PTMs) have been discovered, of which the functional significance is still under intense study. Here, we use high-resolution mass spectrometry to accurately quantify eight acyl-PTMs in vivo and after in vitro enzymatic assays. We assess the ability of seven histone acetyltransferases (HATs) to catalyze acylations on histones in vitro using short-chain acyl-CoA donors, proving that they are less efficient towards larger acyl-CoAs. We also observe that acyl-CoAs can acylate histones through non-enzymatic mechanisms. Using integrated metabolomic and proteomic approaches, we achieve high correlation (R 2 > 0.99) between the abundance of acyl-CoAs and their corresponding acyl-PTMs. Moreover, we observe a dose-dependent increase in histone acyl-PTM abundances in response to acyl-CoA supplementation in in nucleo reactions. This study represents a comprehensive profiling of scarcely investigated low-abundance histone marks, revealing that concentrations of acyl-CoAs affect histone acyl-PTM abundances by both enzymatic and non-enzymatic mechanisms.
Collapse
Affiliation(s)
- Johayra Simithy
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dylan M Marchione
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Gleb A Bazilevsky
- Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cheryl E McCullough
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert S Magin
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market Street Suite 560, Philadelphia, PA, 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, and the Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
189
|
Effect of lysine succinylation on the regulation of 2-oxoglutarate dehydrogenase inhibitor, OdhI, involved in glutamate production in Corynebacterium glutamicum. Biosci Biotechnol Biochem 2017; 81:2130-2138. [PMID: 28899215 DOI: 10.1080/09168451.2017.1372182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In Corynebacterium glutamicum, the activity of the 2-oxoglutarate dehydrogenase (ODH) complex is negatively regulated by the unphosphorylated form of OdhI protein, which is critical for L-glutamate overproduction. We examined the potential impact of protein acylation at lysine (K)-132 of OdhI in C. glutamicum ATCC13032. The K132E succinylation-mimic mutation reduced the ability of OdhI to bind OdhA, the catalytic subunit of the ODH complex, which reduced the inhibition of ODH activity. In vitro succinylation of OdhI protein also reduced the ability to inhibit ODH, and the K132R mutation blocked the effect. These results suggest that succinylation at K132 may attenuate the OdhI function. Consistent with these results, the C. glutamicum mutant strain with OdhI-K132E showed decreased L-glutamate production. Our results indicated that not only phosphorylation but also succinylation of OdhI protein may regulate L-glutamate production in C. glutamicum.
Collapse
|
190
|
Liu S, Yu H, Liu Y, Liu X, Zhang Y, Bu C, Yuan S, Chen Z, Xie G, Li W, Xu B, Yang J, He L, Jin T, Xiong Y, Sun L, Liu X, Han C, Cheng Z, Liang J, Shang Y. Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis. Mol Cell 2017; 67:853-866.e5. [PMID: 28803779 DOI: 10.1016/j.molcel.2017.07.011] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/02/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
Lysine crotonylation (Kcr) is a newly identified histone modification that is associated with active transcription in mammalian cells. Here we report that the chromodomain Y-like transcription corepressor CDYL negatively regulates histone Kcr by acting as a crotonyl-CoA hydratase to convert crotonyl-CoA to β-hydroxybutyryl-CoA. We showed that the negative regulation of histone Kcr by CDYL is intrinsically linked to its transcription repression activity and functionally implemented in the reactivation of sex chromosome-linked genes in round spermatids and genome-wide histone replacement in elongating spermatids. Significantly, Cdyl transgenic mice manifest dysregulation of histone Kcr and reduction of male fertility with a decreased epididymal sperm count and sperm cell motility. Our study uncovers a biochemical pathway in the regulation of histone Kcr and implicates CDYL-regulated histone Kcr in spermatogenesis, adding to the understanding of the physiology of male reproduction and the mechanism of the spermatogenic failure in AZFc (Azoospermia Factor c)-deleted infertile men.
Collapse
Affiliation(s)
- Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Huajing Yu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongqing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yu Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou), Co. Ltd., Hangzhou 310018, China
| | - Shuai Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhe Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guojia Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bosen Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tong Jin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yundong Xiong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohui Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chunsheng Han
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou), Co. Ltd., Hangzhou 310018, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
191
|
Affiliation(s)
- Matthew G Vander Heiden
- From the Koch Institute for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA; and the Dana-Farber Cancer Institute, Boston
| |
Collapse
|
192
|
Abstract
In this issue of Cell Chemical Biology, Bowman and colleagues show that the mitochondrial enzyme ACSF3 generates malonyl-CoA from malonate, in turn regulating metabolic flux and mitochondrial protein malonylation (Bowman et al., 2017). The study reveals a mechanism to generate mitochondrial malonyl-CoA and how this molecule impacts mitochondrial biology.
Collapse
Affiliation(s)
- David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
193
|
Abstract
Recent studies have revealed the existence of a plethora of previously unknown protein acyl-lysine modifications, affecting the functions of targets involved in diverse cellular processes. A recent study from the Hirschey laboratory has provided new chemical insights into the mechanisms of protein acylation.
Collapse
|
194
|
Taylor EB. Functional Properties of the Mitochondrial Carrier System. Trends Cell Biol 2017; 27:633-644. [PMID: 28522206 DOI: 10.1016/j.tcb.2017.04.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/16/2017] [Accepted: 04/18/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial carrier system (MCS) transports small molecules between mitochondria and the cytoplasm. It is integral to the core mitochondrial function to regulate cellular chemistry by metabolism. The mammalian MCS comprises the transporters of the 53-member canonical SLC25A family and a lesser number of identified noncanonical transporters. The recent discovery and investigations of the mitochondrial pyruvate carrier (MPC) illustrate the diverse effects a single mitochondrial carrier may exert on cellular function. However, the transport selectivities of many carriers remain unknown, and most have not been functionally investigated in mammalian cells. The mechanisms coordinating their function as a unified system remain undefined. Increased accessibility to molecular genetic and metabolomic technologies now greatly enables investigation of the MCS. Continued investigation of the MCS may reveal how mitochondria encode complex regulatory information within chemical thermodynamic gradients. This understanding may enable precision modulation of cellular chemistry to counteract the dysmetabolism inherent in disease.
Collapse
Affiliation(s)
- Eric B Taylor
- Department of Biochemistry, Fraternal Order of the Eagles Diabetes Center, Holden Comprehensive Cancer Center, Abboud Cardiovascular Research Center, Pappajohn Biomedical Discovery Institute, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
195
|
Ye Q, Ji QQ, Yan W, Yang F, Wang ED. Acetylation of lysine ϵ-amino groups regulates aminoacyl-tRNA synthetase activity in Escherichia coli. J Biol Chem 2017; 292:10709-10722. [PMID: 28455447 DOI: 10.1074/jbc.m116.770826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/16/2017] [Indexed: 11/06/2022] Open
Abstract
Previous proteomic analyses have shown that aminoacyl-tRNA synthetases in many organisms can be modified by acetylation of Lys. In this present study, leucyl-tRNA synthetase and arginyl-tRNA synthetase from Escherichia coli (EcLeuRS and EcArgRS) were overexpressed and purified and found to be acetylated on Lys residues by MS. Gln scanning mutagenesis revealed that Lys619, Lys624, and Lys809 in EcLeuRS and Lys126 and Lys408 in EcArgRS might play important roles in enzyme activity. Furthermore, we utilized a novel protein expression system to obtain enzymes harboring acetylated Lys at specific sites and investigated their catalytic activity. Acetylation of these Lys residues could affect their aminoacylation activity by influencing amino acid activation and/or the affinity for tRNA. In vitro assays showed that acetyl-phosphate nonenzymatically acetylates EcLeuRS and EcArgRS and suggested that the sirtuin class deacetylase CobB might regulate acetylation of these two enzymes. These findings imply a potential regulatory role for Lys acetylation in controlling the activity of aminoacyl-tRNA synthetases and thus protein synthesis.
Collapse
Affiliation(s)
- Qing Ye
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Quan-Quan Ji
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Wei Yan
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Fang Yang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and .,the School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| |
Collapse
|
196
|
Golubev A, Hanson AD, Gladyshev VN. Non-enzymatic molecular damage as a prototypic driver of aging. J Biol Chem 2017; 292:6029-6038. [PMID: 28264930 PMCID: PMC5391736 DOI: 10.1074/jbc.r116.751164] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The chemical potentialities of metabolites far exceed metabolic requirements. The required potentialities are realized mostly through enzymatic catalysis. The rest are realized spontaneously through organic reactions that (i) occur wherever appropriate reactants come together, (ii) are so typical that many have proper names (e.g. Michael addition, Amadori rearrangement, and Pictet-Spengler reaction), and (iii) often have damaging consequences. There are many more causes of non-enzymatic damage to metabolites than reactive oxygen species and free radical processes (the "usual suspects"). Endogenous damage accumulation in non-renewable macromolecules and spontaneously polymerized material is sufficient to account for aging and differentiates aging from wear-and-tear of inanimate objects by deriving it from metabolism, the essential attribute of life.
Collapse
Affiliation(s)
- Alexey Golubev
- From the Department of Biochemistry, Saint-Petersburg State University, Saint Petersburg 199034, Russia,
| | - Andrew D Hanson
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, and
| | - Vadim N Gladyshev
- the Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
197
|
Ma Y, Yang M, Lin X, Liu X, Huang H, Ge F. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria. J Proteome Res 2017; 16:2030-2043. [DOI: 10.1021/acs.jproteome.7b00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yanyan Ma
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Huang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
198
|
A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation. Cell Metab 2017; 25:823-837.e8. [PMID: 28380375 PMCID: PMC5399522 DOI: 10.1016/j.cmet.2017.03.006] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 09/26/2016] [Accepted: 03/10/2017] [Indexed: 11/23/2022]
Abstract
The mechanisms underlying the formation of acyl protein modifications remain poorly understood. By investigating the reactivity of endogenous acyl-CoA metabolites, we found a class of acyl-CoAs that undergo intramolecular catalysis to form reactive intermediates that non-enzymatically modify proteins. Based on this mechanism, we predicted, validated, and characterized a protein modification: 3-hydroxy-3-methylglutaryl(HMG)-lysine. In a model of altered HMG-CoA metabolism, we found evidence of two additional protein modifications: 3-methylglutaconyl(MGc)-lysine and 3-methylglutaryl(MG)-lysine. Using quantitative proteomics, we compared the "acylomes" of two reactive acyl-CoA species, namely HMG-CoA and glutaryl-CoA, which are generated in different pathways. We found proteins that are uniquely modified by each reactive metabolite, as well as common proteins and pathways. We identified the tricarboxylic acid cycle as a pathway commonly regulated by acylation and validated malate dehydrogenase as a key target. These data uncover a fundamental relationship between reactive acyl-CoA species and proteins and define a new regulatory paradigm in metabolism.
Collapse
|
199
|
Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metab 2017; 25:838-855.e15. [PMID: 28380376 PMCID: PMC5444661 DOI: 10.1016/j.cmet.2017.03.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 09/26/2016] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
Abstract
Sirtuins are NAD+-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine. The metabolites leading to these post-translational modifications are intermediates in leucine oxidation, and we show a primary role for SIRT4 in controlling this pathway in mice. Furthermore, we find that dysregulated leucine metabolism in SIRT4KO mice leads to elevated basal and stimulated insulin secretion, which progressively develops into glucose intolerance and insulin resistance. These findings identify a robust enzymatic activity for SIRT4, uncover a mechanism controlling branched-chain amino acid flux, and position SIRT4 as a crucial player maintaining insulin secretion and glucose homeostasis during aging.
Collapse
Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Kelsey Fisher-Wellman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Darren Stuart
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Brett S Peterson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Jonathan D Douros
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Gregory R Wagner
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Michelle F Green
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - R Michael Sivley
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Robert D Stevens
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John A Capra
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jonathan E Campbell
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Deborah M Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA.
| |
Collapse
|
200
|
Nagano-Shoji M, Hamamoto Y, Mizuno Y, Yamada A, Kikuchi M, Shirouzu M, Umehara T, Yoshida M, Nishiyama M, Kosono S. Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum. Mol Microbiol 2017; 104:677-689. [PMID: 28256782 DOI: 10.1111/mmi.13658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2017] [Indexed: 12/29/2022]
Abstract
Protein Nε-acylation is emerging as a ubiquitous post-translational modification. In Corynebacterium glutamicum, which is utilized for industrial production of l-glutamate, the levels of protein acetylation and succinylation change drastically under the conditions that induce glutamate overproduction. Here, the acylation of phosphoenolpyruvate carboxylase (PEPC), an anaplerotic enzyme that supplies oxaloacetate for glutamate overproduction was characterized. It was shown that acetylation of PEPC at lysine 653 decreased enzymatic activity, leading to reduced glutamate production. An acetylation-mimic (KQ) mutant of K653 showed severely reduced glutamate production, while the corresponding KR mutant showed normal production levels. Using an acetyllysine-incorporated PEPC protein, we verified that K653-acetylation negatively regulates PEPC activity. In addition, NCgl0616, a sirtuin-type deacetylase, deacetylated K653-acetylated PEPC in vitro. Interestingly, the specific activity of PEPC was increased during glutamate overproduction, which was blocked by the K653R mutation or deletion of sirtuin-type deacetylase homologues. These findings suggested that deacetylation of K653 by NCgl0616 likely plays a role in the activation of PEPC, which maintains carbon flux under glutamate-producing conditions. PEPC deletion increased protein acetylation levels in cells under glutamate-producing conditions, supporting the hypothesis that PEPC is responsible for a large carbon flux change under glutamate-producing conditions.
Collapse
Affiliation(s)
- Megumi Nagano-Shoji
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Kyowa Hakko Bio Co, Ltd., Chiyoda-ku, Tokyo, Japan
| | - Yuma Hamamoto
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Kyowa Hakko Bio Co, Ltd., Chiyoda-ku, Tokyo, Japan
| | - Yuta Mizuno
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Kyowa Hakko Bio Co, Ltd., Chiyoda-ku, Tokyo, Japan
| | - Ayuka Yamada
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaki Kikuchi
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Takashi Umehara
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| |
Collapse
|