501
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Gibson GE, Xu H, Chen HL, Chen W, Denton TT, Zhang S. Alpha-ketoglutarate dehydrogenase complex-dependent succinylation of proteins in neurons and neuronal cell lines. J Neurochem 2015; 134:86-96. [PMID: 25772995 DOI: 10.1111/jnc.13096] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/13/2015] [Accepted: 03/04/2015] [Indexed: 01/13/2023]
Abstract
Reversible post-translation modifications of proteins are common in all cells and appear to regulate many processes. Nevertheless, the enzyme(s) responsible for the alterations and the significance of the modification are largely unknown. Succinylation of proteins occurs and causes large changes in the structure of proteins; however, the source of the succinyl groups, the targets, and the consequences of these modifications on other proteins remain unknown. These studies focused on succinylation of mitochondrial proteins. The results demonstrate that the α-ketoglutarate dehydrogenase complex (KGDHC) can serve as a trans-succinylase that mediates succinylation in an α-ketoglutarate-dependent manner. Inhibition of KGDHC reduced succinylation of both cytosolic and mitochondrial proteins in cultured neurons and in a neuronal cell line. Purified KGDHC can succinylate multiple proteins including other enzymes of the tricarboxylic acid cycle leading to modification of their activity. Inhibition of KGDHC also modifies acetylation by modifying the pyruvate dehydrogenase complex. The much greater effectiveness of KGDHC than succinyl-CoA suggests that the catalysis owing to the E2k succinyltransferase is important. Succinylation appears to be a major signaling system and it can be mediated by KGDHC. Reversible post-translation modifications of proteins are common and may regulate many processes. Succinylation of proteins occurs and causes large changes in the structure of proteins. However, the source of the succinyl groups, the targets, and the consequences of these modifications on other proteins remains unknown. The results demonstrate that the mitochondrial α-ketoglutarate dehydrogenase complex (KGDHC) can succinylate multiple mitochondrial proteins and alter their function. Succinylation appears to be a major signaling system and it can be mediated by KGDHC.
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Affiliation(s)
- Gary E Gibson
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Hui Xu
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Huan-Lian Chen
- Brain and Mind Research Institute, Weill Cornell Medical College, Burke Medical Research Institute, White Plains, New York, USA
| | - Wei Chen
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Travis T Denton
- College of Pharmacy, Washington State University, Spokane, Washington, USA
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
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502
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Zhao X, Ning Q, Chai H, Ma Z. Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique. J Theor Biol 2015; 374:60-5. [PMID: 25843215 DOI: 10.1016/j.jtbi.2015.03.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 03/21/2015] [Accepted: 03/24/2015] [Indexed: 01/23/2023]
Abstract
As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimental approaches, computational predictions of succinylation sites are much desirable due to their convenient and fast speed. Currently, numerous computational models have been developed to identify PTMs sites through various types of two-class machine learning algorithms. These methods require both positive and negative samples for training. However, designation of the negative samples of PTMs was difficult and if it is not properly done can affect the performance of computational models dramatically. So that in this work, we implemented the first application of positive samples only learning (PSoL) algorithm to succinylation sites prediction problem, which was a special class of semi-supervised machine learning that used positive samples and unlabeled samples to train the model. Meanwhile, we proposed a novel succinylation sites computational predictor called SucPred (succinylation site predictor) by using multiple feature encoding schemes. Promising results were obtained by the SucPred predictor with an accuracy of 88.65% using 5-fold cross validation on the training dataset and an accuracy of 84.40% on the independent testing dataset, which demonstrated that the positive samples only learning algorithm presented here was particularly useful for identification of protein succinylation sites. Besides, the positive samples only learning algorithm can be applied to build predictors for other types of PTMs sites with ease. A web server for predicting succinylation sites was developed and was freely accessible at http://59.73.198.144:8088/SucPred/.
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Affiliation(s)
- Xiaowei Zhao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China.
| | - Qiao Ning
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China
| | - Haiting Chai
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China
| | - Zhiqiang Ma
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China.
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503
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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504
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Abstract
NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is a ubiquitin-like protein that activates the largest ubiquitin E3 ligase family, the cullin-RING ligases. Many non-cullin neddylation targets have been proposed in recent years. However, overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery, which makes validating potential NEDD8 targets challenging. Here, we re-evaluate studies of non-cullin targets of NEDD8 in light of the current understanding of the neddylation pathway, and suggest criteria for identifying genuine neddylation substrates under homeostatic conditions. We describe the biological processes that might be regulated by non-cullin neddylation, and the utility of neddylation inhibitors for research and as potential therapies. Understanding the biological significance of non-cullin neddylation is an exciting research prospect primed to reveal fundamental insights.
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505
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Acetylation site specificities of lysine deacetylase inhibitors in human cells. Nat Biotechnol 2015; 33:415-23. [PMID: 25751058 DOI: 10.1038/nbt.3130] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022]
Abstract
Lysine deacetylases inhibitors (KDACIs) are used in basic research, and many are being investigated in clinical trials for treatment of cancer and other diseases. However, their specificities in cells are incompletely characterized. Here we used quantitative mass spectrometry (MS) to obtain acetylation signatures for 19 different KDACIs, covering all 18 human lysine deacetylases. Most KDACIs increased acetylation of a small, specific subset of the acetylome, including sites on histones and other chromatin-associated proteins. Inhibitor treatment combined with genetic deletion showed that the effects of the pan-sirtuin inhibitor nicotinamide are primarily mediated by SIRT1 inhibition. Furthermore, we confirmed that the effects of tubacin and bufexamac on cytoplasmic proteins result from inhibition of HDAC6. Bufexamac also triggered an HDAC6-independent, hypoxia-like response by stabilizing HIF1-α, providing a possible mechanistic explanation of its adverse, pro-inflammatory effects. Our results offer a systems view of KDACI specificities, providing a framework for studying function of acetylation and deacetylases.
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506
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Yanshina DD, Bulygin KN, Malygin AA, Karpova GG. Hydroxylated histidine of human ribosomal protein uL2 is involved in maintaining the local structure of 28S rRNA in the ribosomal peptidyl transferase center. FEBS J 2015; 282:1554-66. [PMID: 25702831 DOI: 10.1111/febs.13241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 12/13/2022]
Abstract
Protein uL2 is essential for the catalytic activity of the ribosome and has a conserved shape in ribosomes from all domains of life. However, the sequence of its unstructured C-terminal loop apex that contacts the conserved 23S/28S rRNA helix (H) 93 near the ribosomal peptidyl transferase center differs in bacteria, archaea and eukaryotes. Eukaryote-specific residue His216 located in this loop in mammalian uL2 is hydroxylated in ribosomes. We used a set of chemical probes to explore the structure of an RNA that mimicked a segment of 28S rRNA domain V containing part of the uL2 binding site including H93, complexed with either natural (hydroxylated) or recombinant (unmodified) human uL2. It was found that both protein forms engage H93 during binding, but only natural uL2 (uL2n) protects it from hydroxyl radicals. The association of uL2n with RNA leads to changes in its structure at U4532 adjacent to the universally conserved U4531 (U2585, Escherichia coli numbering) involved in peptidyl transferase center formation, and at the universally conserved C4447 (2501) located in the ribosome near A4397 (2451) and C3909 (2063) belonging to the peptidyl transferase center. As a result, both nucleotides become strongly exposed to hydroxyl radicals. Our data argue that the hydroxyl group at His216 in the C-terminal loop apex of mammalian uL2 contributes to stabilization of a protein conformation that is favorable for binding to H93 of 28S rRNA and that this binding induces structural rearrangement in the regions close to the peptidyl transferase center in the mature ribosome.
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Affiliation(s)
- Darya D Yanshina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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507
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Hirschey MD, Zhao Y. Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation. Mol Cell Proteomics 2015; 14:2308-15. [PMID: 25717114 DOI: 10.1074/mcp.r114.046664] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 12/14/2022] Open
Abstract
Protein acetylation is a well-studied regulatory mechanism for several cellular processes, ranging from gene expression to metabolism. Recent discoveries of new post-translational modifications, including malonylation, succinylation, and glutarylation, have expanded our understanding of the types of modifications found on proteins. These three acidic lysine modifications are structurally similar but have the potential to regulate different proteins in different pathways. The deacylase sirtuin 5 (SIRT5) catalyzes the removal of these modifications from a wide range of proteins in different subcellular compartments. Here, we review these new modifications, their regulation by SIRT5, and their emerging role in cellular regulation and diseases.
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Affiliation(s)
- Matthew D Hirschey
- From the ‡Duke Molecular Physiology Institute, Sarah W. Stedman Metabolism and Nutrition Center, §Departments of Medicine & Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, NC 27710;
| | - Yingming Zhao
- ¶Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637
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508
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Yang M, Wang Y, Chen Y, Cheng Z, Gu J, Deng J, Bi L, Chen C, Mo R, Wang X, Ge F. Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis. Mol Cell Proteomics 2015; 14:796-811. [PMID: 25605462 DOI: 10.1074/mcp.m114.045922] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, remains one of the most prevalent human pathogens and a major cause of mortality worldwide. Metabolic network is a central mediator and defining feature of the pathogenicity of Mtb. Increasing evidence suggests that lysine succinylation dynamically regulates enzymes in carbon metabolism in both bacteria and human cells; however, its extent and function in Mtb remain unexplored. Here, we performed a global succinylome analysis of the virulent Mtb strain H37Rv by using high accuracy nano-LC-MS/MS in combination with the enrichment of succinylated peptides from digested cell lysates and subsequent peptide identification. In total, 1545 lysine succinylation sites on 626 proteins were identified in this pathogen. The identified succinylated proteins are involved in various biological processes and a large proportion of the succinylation sites are present on proteins in the central metabolism pathway. Site-specific mutations showed that succinylation is a negative regulatory modification on the enzymatic activity of acetyl-CoA synthetase. Molecular dynamics simulations demonstrated that succinylation affects the conformational stability of acetyl-CoA synthetase, which is critical for its enzymatic activity. Further functional studies showed that CobB, a sirtuin-like deacetylase in Mtb, functions as a desuccinylase of acetyl-CoA synthetase in in vitro assays. Together, our findings reveal widespread roles for lysine succinylation in regulating metabolism and diverse processes in Mtb. Our data provide a rich resource for functional analyses of lysine succinylation and facilitate the dissection of metabolic networks in this life-threatening pathogen.
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Affiliation(s)
- Mingkun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yan Wang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ying Chen
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhongyi Cheng
- §Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
| | - Jing Gu
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaoyu Deng
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lijun Bi
- ‖Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuangbin Chen
- **Jingjie PTM Biolabs (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Ran Mo
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xude Wang
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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509
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Pisithkul T, Patel NM, Amador-Noguez D. Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opin Microbiol 2015; 24:29-37. [PMID: 25597444 DOI: 10.1016/j.mib.2014.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 01/05/2023]
Abstract
In order to survive and compete in natural settings, bacteria must excel at quickly adapting their metabolism to fluctuations in nutrient availability and other environmental variables. This necessitates fast-acting post-translational regulatory mechanisms, that is, allostery or covalent modification, to control metabolic flux. While allosteric regulation has long been a well-established strategy for regulating metabolic enzyme activity in bacteria, covalent post-translational modes of regulation, such as phosphorylation or acetylation, have previously been regarded as regulatory mechanisms employed primarily by eukaryotic organisms. Recent findings, however, have shifted this perception and point to a widespread role for covalent posttranslational modification in the regulation of metabolic enzymes and fluxes in bacteria. This review provides an outline of the exciting recent advances in this area.
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Affiliation(s)
- Tippapha Pisithkul
- Cellular and Molecular Biology, University of Wisconsin-Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, United States
| | - Nishaben M Patel
- Department of Bacteriology, University of Wisconsin-Madison, United States
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510
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Abstract
![]()
Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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511
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Her YF, Maher LJ. Succinate Dehydrogenase Loss in Familial Paraganglioma: Biochemistry, Genetics, and Epigenetics. Int J Endocrinol 2015; 2015:296167. [PMID: 26294907 PMCID: PMC4532907 DOI: 10.1155/2015/296167] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/05/2015] [Indexed: 01/14/2023] Open
Abstract
It is counterintuitive that metabolic defects reducing ATP production can cause, rather than protect from, cancer. Yet this is precisely the case for familial paraganglioma, a form of neuroendocrine malignancy caused by loss of succinate dehydrogenase in the tricarboxylic acid cycle. Here we review biochemical, genetic, and epigenetic considerations in succinate dehydrogenase loss and present leading models and mysteries associated with this fascinating and important tumor.
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Affiliation(s)
- Yeng F. Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
- *L. James Maher III:
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512
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Effect of lysine to alanine mutations on the phosphate activation and BPTES inhibition of glutaminase. Neurochem Int 2014; 88:10-4. [PMID: 25510640 DOI: 10.1016/j.neuint.2014.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/24/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022]
Abstract
The GLS1 gene encodes a mitochondrial glutaminase that is highly expressed in brain, kidney, small intestine and many transformed cells. Recent studies have identified multiple lysine residues in glutaminase that are sites of N-acetylation. Interestingly, these sites are located within either a loop segment that regulates access of glutamine to the active site or the dimer:dimer interface that participates in the phosphate-dependent oligomerization and activation of the enzyme. These two segments also contain the binding sites for bis-2[5-phenylacetamido-1,2,4-thiadiazol-2-yl]ethylsulfide (BPTES), a highly specific and potent uncompetitive inhibitor of this glutaminase. BPTES is also the lead compound for development of novel cancer chemotherapeutic agents. To provide a preliminary assessment of the potential effects of N-acetylation, the corresponding lysine to alanine mutations were constructed in the hGACΔ1 plasmid. The wild type and mutated proteins were purified by Ni(+)-affinity chromatography and their phosphate activation and BPTES inhibition profiles were analyzed. Two of the alanine substitutions in the loop segment (K311A and K328A) and the one in the dimer:dimer interface (K396A) form enzymes that require greater concentrations of phosphate to produce half-maximal activation and exhibit greater sensitivity to BPTES inhibition. By contrast, the K320A mutation results in a glutaminase that exhibits near maximal activity in the absence of phosphate and is not inhibited by BPTES. Thus, lysine N-acetylation may contribute to the acute regulation of glutaminase activity in various tissues and alter the efficacy of BPTES-type inhibitors.
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513
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Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. Sci Rep 2014; 4:7331. [PMID: 25476580 PMCID: PMC4256647 DOI: 10.1038/srep07331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/11/2014] [Indexed: 12/16/2022] Open
Abstract
Recent studies have indicated that different post-translational modifications (PTMs) synergistically orchestrate specific biological processes by crosstalks. However, the preference of the crosstalk among different PTMs and the evolutionary constraint on the PTM crosstalk need further dissections. In this study, the in situ crosstalk at the same positions among three tyrosine PTMs including sulfation, nitration and phosphorylation were systematically analyzed. The experimentally identified sulfation, nitration and phosphorylation sites were collected and integrated with reliable predictions to perform large-scale analyses of in situ crosstalks. From the results, we observed that the in situ crosstalk between sulfation and nitration is significantly under-represented, whereas both sulfation and nitration prefer to co-occupy with phosphorylation at same tyrosines. Further analyses suggested that sulfation and nitration preferentially co-occur with phosphorylation at specific positions in proteins, and participate in distinct biological processes and functions. More interestingly, the long-term evolutionary analysis indicated that multi-PTM targeting tyrosines didn't show any higher conservation than singly modified ones. Also, the analysis of human genetic variations demonstrated that there is no additional functional constraint on inherited disease, cancer or rare mutations of multiply modified tyrosines. Taken together, our systematic analyses provided a better understanding of the in situ crosstalk among PTMs.
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514
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Ringel AE, Roman C, Wolberger C. Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2. Protein Sci 2014; 23:1686-97. [PMID: 25200501 PMCID: PMC4253809 DOI: 10.1002/pro.2546] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/03/2014] [Indexed: 01/07/2023]
Abstract
Sirtuins were originally shown to regulate a wide array of biological processes such as transcription, genomic stability, and metabolism by catalyzing the NAD(+) -dependent deacetylation of lysine residues. Recent proteomic studies have revealed a much wider array of lysine acyl modifications in vivo than was previously known, which has prompted a reevaluation of sirtuin substrate specificity. Several sirtuins have now been shown to preferentially remove propionyl, succinyl, and long-chain fatty acyl groups from lysines, which has changed our understanding of sirtuin biology. In light of these developments, we revisited the acyl specificity of several well-studied archaeal and bacterial sirtuins. We find that the Archaeoglobus fulgidus sirtuins, Sir2Af1 and Sir2Af2, preferentially remove succinyl and myristoyl groups, respectively. Crystal structures of Sir2Af1 bound to a succinylated peptide and Sir2Af2 bound to a myristoylated peptide show how the active site of each enzyme accommodates a noncanonical acyl chain. As compared to its structure in complex with an acetylated peptide, Sir2Af2 undergoes a conformational change that expands the active site to accommodate the myristoyl group. These findings point to both structural and biochemical plasticity in sirtuin active sites and provide further evidence that sirtuins from all three domains of life catalyze noncanonical deacylation.
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Affiliation(s)
- Alison E Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185
| | - Christina Roman
- The Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185,The Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimore, Maryland, 21205-2185,
*Correspondence to: Cynthia Wolberger, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205. E-mail:
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515
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Bernal V, Castaño-Cerezo S, Gallego-Jara J, Écija-Conesa A, de Diego T, Iborra JL, Cánovas M. Regulation of bacterial physiology by lysine acetylation of proteins. N Biotechnol 2014; 31:586-95. [DOI: 10.1016/j.nbt.2014.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/28/2014] [Accepted: 03/02/2014] [Indexed: 01/10/2023]
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516
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Castaño-Cerezo S, Bernal V, Post H, Fuhrer T, Cappadona S, Sánchez-Díaz NC, Sauer U, Heck AJR, Altelaar AFM, Cánovas M. Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. Mol Syst Biol 2014; 10:762. [PMID: 25518064 PMCID: PMC4299603 DOI: 10.15252/msb.20145227] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although protein acetylation is widely observed, it has been associated with few specific
regulatory functions making it poorly understood. To interrogate its functionality, we analyzed the
acetylome in Escherichia coli knockout mutants of cobB, the only
known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase.
For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins,
were identified and differentially quantified. Nearly 65% of these proteins are related to
metabolism. The global activity of CobB contributes to the deacetylation of a large number of
substrates and has a major impact on physiology. Apart from the regulation of acetyl-CoA synthetase,
we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the
glyoxylate shunt. Acetylation of the transcription factor RcsB prevents DNA binding, activating
flagella biosynthesis and motility, and increases acid stress susceptibility. Surprisingly, deletion
of patZ increased acetylation in acetate cultures, which suggests that it regulates
the levels of acetylating agents. The results presented offer new insights into functional roles of
protein acetylation in metabolic fitness and global cell regulation.
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Affiliation(s)
- Sara Castaño-Cerezo
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Vicente Bernal
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Nerea C Sánchez-Díaz
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Manuel Cánovas
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
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517
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Systematic identification of the lysine succinylation in the protozoan parasite Toxoplasma gondii. J Proteome Res 2014; 13:6087-95. [PMID: 25377623 DOI: 10.1021/pr500992r] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lysine succinylation is a new posttranslational modification identified in histone proteins of Toxoplasma gondii, an obligate intracellular parasite of the phylum Apicomplexa. However, very little is known about their scope and cellular distribution. Here, using LC-MS/MS to identify parasite peptides enriched by immunopurification with succinyl lysine antibody, we produced the first lysine succinylome in this parasite. Overall, a total of 425 lysine succinylation sites that occurred on 147 succinylated proteins were identified in extracellular Toxoplasma tachyzoites, which is a proliferative stage that results in acute toxoplasmosis. With the bioinformatics analysis, it is shown that these succinylated proteins are evolutionarily conserved and involved in a wide variety of cellular functions such as metabolism and epigenetic gene regulation and exhibit diverse subcellular localizations. Moreover, we defined five types of definitively conserved succinylation site motifs, and the results imply that lysine residue of a polypeptide with lysine on the +3 position and without lysine at the -1 to +2 position is a preferred substrate of lysine succinyltransferase. In conclusion, our findings suggest that lysine succinylation in Toxoplasma involves a diverse array of cellular functions, although the succinylation occurs at a low level.
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518
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Xie L, Liu W, Li Q, Chen S, Xu M, Huang Q, Zeng J, Zhou M, Xie J. First succinyl-proteome profiling of extensively drug-resistant Mycobacterium tuberculosis revealed involvement of succinylation in cellular physiology. J Proteome Res 2014; 14:107-19. [PMID: 25363132 DOI: 10.1021/pr500859a] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein lysine succinylation, an emerging protein post-translational modification widespread among eukaryotic and prokaryotic cells, represents an important regulator of cellular processes. However, the extent and function of lysine succinylation in Mycobacterium tuberculosis, especially extensively drug-resistant strain, remain elusive. Combining protein/peptide prefractionation, immunoaffinity enrichment, and LC-MS/MS analysis, a total of 686 succinylated proteins and 1739 succinylation sites of M. tuberculosis were identified, representing the first global profiling of M. tuberculosis lysine succinylation. The identified succinylated proteins are involved in a variety of cellular functions such as metabolic processes, transcription, translation, and stress responses and exhibit different subcellular localization via GO, protein interaction network, and other bioinformatic analysis. Notably, proteins involved in protein biosynthesis and carbon metabolism are preferred targets of lysine succinylation. Moreover, two prevalent sequence patterns: EK(suc) and K*****K(suc), can be found around the succinylation sites. There are 109 lysine-succinylated homologues in E. coli, suggesting highly conserved succinylated proteins. Succinylation was found to occur at the active sites predicted by Prosite signature including Rv0946c, indicating that lysine succinylation may affect their activities. There is extensive overlapping between acetylation sites and succinylation sites in M. tuberculosis. Many M. tuberculosis metabolic enzymes and antibiotic resistance proteins were succinylated. This study provides a basis for further characterization of the pathophysiological role of lysine succinylation in M. tuberculosis.
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Affiliation(s)
- Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715, China
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519
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Synthesis and succinylation of subtilin-like lantibiotics are strongly influenced by glucose and transition state regulator AbrB. Appl Environ Microbiol 2014; 81:614-22. [PMID: 25381239 DOI: 10.1128/aem.02579-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subtilin and the closely related entianin are class I lantibiotics produced by different subspecies of Bacillus subtilis. Both molecules are ribosomally synthesized peptide antibiotics with unusual ring structures. Subtilin-like lantibiotics develop strong antibiotic activities against various Gram-positive organisms with an efficiency similar to that of nisin from Lactococcus lactis. In contrast to nisin, subtilin-like lantibiotics partially undergo an additional posttranslational modification, where the N-terminal tryptophan residue becomes succinylated, resulting in drastically reduced antibiotic activities. A highly sensitive high-performance liquid chromatography (HPLC)-based quantification method enabled us to determine entianin and succinylated entianin (S-entianin) concentrations in the supernatant during growth. We show that entianin synthesis and the degree of succinylation drastically change with culture conditions. In particular, increasing glucose concentrations resulted in higher entianin amounts and lower proportions of S-entianin in Landy-based media. In contrast, no succinylation was observed in medium A with 10% glucose. Interestingly, glucose retarded the expression of entianin biosynthesis genes. Furthermore, deletion of the transition state regulator AbrB resulted in a 6-fold increased entianin production in medium A with 10% glucose. This shows that entianin biosynthesis in B. subtilis is strongly influenced by glucose, in addition to its regulation by the transition state regulator AbrB. Our results suggest that the mechanism underlying the succinylation of subtilin-like lantibiotics is enzymatically catalyzed and occurs in the extracellular space or at the cellular membrane.
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520
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Abstract
The ketone body β-hydroxybutyrate (βOHB) is a convenient carrier of energy from adipocytes to peripheral tissues during fasting or exercise. However, βOHB is more than just a metabolite, having important cellular signaling roles as well. βOHB is an endogenous inhibitor of histone deacetylases (HDACs) and a ligand for at least two cell surface receptors. In addition, the downstream products of βOHB metabolism including acetyl-CoA, succinyl-CoA, and NAD+ (nicotinamide adenine dinucleotide) themselves have signaling activities. These regulatory functions of βOHB serve to link the outside environment to cellular function and gene expression, and have important implications for the pathogenesis and treatment of metabolic diseases including type 2 diabetes.
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Affiliation(s)
- John C Newman
- Division of Geriatrics, University of California San Francisco, San Francisco, CA, USA; Gladstone Institutes, University of California San Francisco, 1650 Owens St., San Francisco, CA 94158, USA
| | - Eric Verdin
- Gladstone Institutes, University of California San Francisco, 1650 Owens St., San Francisco, CA 94158, USA.
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521
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Top-down analytical platforms for the characterization of the human salivary proteome. Bioanalysis 2014; 6:563-81. [PMID: 24568357 DOI: 10.4155/bio.13.349] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive analysis and characterization of the human salivary proteome is an important step towards the possible use of saliva for diagnostic and prognostic purposes. The contribution of the different sources to whole saliva, and the evaluation of individual variability and physiological modifications have been investigated by top-down proteomic approaches, disclosing the faceted and complex profile of the human salivary proteome. All this information is essential to develop saliva protein biomarkers. In this Review the major results obtained in the field by top-down platforms, and the improvements required to allow a more complete picture, will be discussed.
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522
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Kebede AF, Schneider R, Daujat S. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. FEBS J 2014; 282:1658-74. [DOI: 10.1111/febs.13047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Adam F. Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
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523
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The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 2014; 15:536-50. [PMID: 25053359 DOI: 10.1038/nrm3841] [Citation(s) in RCA: 966] [Impact Index Per Article: 96.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling. Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many biological processes through the regulation of protein interactions, activity and localization. In addition, proteins are frequently modified by other types of acylations, such as formylation, butyrylation, propionylation, succinylation, malonylation, myristoylation, glutarylation and crotonylation. The intricate link between lysine acylation and cellular metabolism has been clarified by the occurrence of several such metabolite-sensitive acylations and their selective removal by sirtuin deacylases. These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes.
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524
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Papanicolaou KN, O'Rourke B, Foster DB. Metabolism leaves its mark on the powerhouse: recent progress in post-translational modifications of lysine in mitochondria. Front Physiol 2014; 5:301. [PMID: 25228883 PMCID: PMC4151196 DOI: 10.3389/fphys.2014.00301] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/23/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine modifications have been studied extensively in the nucleus, where they play pivotal roles in gene regulation and constitute one of the pillars of epigenetics. In the cytoplasm, they are critical to proteostasis. However, in the last decade we have also witnessed the emergence of mitochondria as a prime locus for post-translational modification (PTM) of lysine thanks, in large measure, to evolving proteomic techniques. Here, we review recent work on evolving set of PTM that arise from the direct reaction of lysine residues with energized metabolic thioester-coenzyme A intermediates, including acetylation, succinylation, malonylation, and glutarylation. We highlight the evolutionary conservation, kinetics, stoichiometry, and cross-talk between members of this emerging family of PTMs. We examine the impact on target protein function and regulation by mitochondrial sirtuins. Finally, we spotlight work in the heart and cardiac mitochondria, and consider the roles acetylation and other newly-found modifications may play in heart disease.
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Affiliation(s)
- Kyriakos N Papanicolaou
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - D Brian Foster
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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525
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Sun G, Jiang M, Zhou T, Guo Y, Cui Y, Guo X, Sha J. Insights into the lysine acetylproteome of human sperm. J Proteomics 2014; 109:199-211. [DOI: 10.1016/j.jprot.2014.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/17/2014] [Accepted: 07/02/2014] [Indexed: 11/24/2022]
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526
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Pougovkina O, Te Brinke H, Wanders RJA, Houten SM, de Boer VCJ. Aberrant protein acylation is a common observation in inborn errors of acyl-CoA metabolism. J Inherit Metab Dis 2014; 37:709-14. [PMID: 24531926 DOI: 10.1007/s10545-014-9684-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
Inherited disorders of acyl-CoA metabolism, such as defects in amino acid metabolism and fatty acid oxidation can present with severe clinical symptoms either neonatally or later in life, but the pathophysiological mechanisms are often incompletely understood. We now report the discovery of a novel biochemical mechanism that could contribute to the pathophysiology of these disorders. We identified increased protein lysine butyrylation in short-chain acyl-CoA dehydrogenase (SCAD) deficient mice as a result of the accumulation of butyryl-CoA. Similarly, in SCAD deficient fibroblasts, lysine butyrylation was increased. Furthermore, malonyl-CoA decarboxylase (MCD) deficient patient cells had increased levels of malonylated lysines and propionyl-CoA carboxylase (PCC) deficient patient cells had increased propionylation of lysines. Since lysine acylation can greatly impact protein function, aberrant lysine acylation in inherited disorders associated with acyl-CoA accumulation may well play a role in their disease pathophysiology.
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Affiliation(s)
- Olga Pougovkina
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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527
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Kankotia S, Stacpoole PW. Dichloroacetate and cancer: new home for an orphan drug? Biochim Biophys Acta Rev Cancer 2014; 1846:617-29. [PMID: 25157892 DOI: 10.1016/j.bbcan.2014.08.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 02/06/2023]
Abstract
We reviewed the anti-cancer effects of DCA, an orphan drug long used as an investigational treatment for various acquired and congenital disorders of mitochondrial intermediary metabolism. Inhibition by DCA of mitochondrial pyruvate dehydrogenase kinases and subsequent reactivation of the pyruvate dehydrogenase complex and oxidative phosphorylation is the common mechanism accounting for the drug's anti-neoplastic effects. At least two fundamental changes in tumor metabolism are induced by DCA that antagonize tumor growth, metastases and survival: the first is the redirection of glucose metabolism from glycolysis to oxidation (reversal of the Warburg effect), leading to inhibition of proliferation and induction of caspase-mediated apoptosis. These effects have been replicated in both human cancer cell lines and in tumor implants of diverse germ line origin. The second fundamental change is the oxidative removal of lactate, via pyruvate, and the co-incident buffering of hydrogen ions by dehydrogenases located in the mitochondrial matrix. Preclinical studies demonstrate that DCA has additive or synergistic effects when used in combination with standard agents designed to modify tumor oxidative stress, vascular remodeling, DNA integrity or immunity. These findings and limited clinical results suggest that potentially fruitful areas for additional clinical trials include 1) adult and pediatric high grade astrocytomas; 2) BRAF-mutant cancers, such as melanoma, perhaps combined with other pro-oxidants; 3) tumors in which resistance to standard platinum-class drugs alone may be overcome with combination therapy; and 4) tumors of endodermal origin, in which extensive experimental research has demonstrated significant anti-proliferative, pro-apoptotic effects of DCA, leading to improved host survival.
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Affiliation(s)
- Shyam Kankotia
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Florida College of Medicine, Gainesville, FL, United States
| | - Peter W Stacpoole
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Florida College of Medicine, Gainesville, FL, United States; Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, United States.
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528
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Schugar RC, Moll AR, André d'Avignon D, Weinheimer CJ, Kovacs A, Crawford PA. Cardiomyocyte-specific deficiency of ketone body metabolism promotes accelerated pathological remodeling. Mol Metab 2014; 3:754-69. [PMID: 25353003 PMCID: PMC4209361 DOI: 10.1016/j.molmet.2014.07.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Exploitation of protective metabolic pathways within injured myocardium still remains an unclarified therapeutic target in heart disease. Moreover, while the roles of altered fatty acid and glucose metabolism in the failing heart have been explored, the influence of highly dynamic and nutritionally modifiable ketone body metabolism in the regulation of myocardial substrate utilization, mitochondrial bioenergetics, reactive oxygen species (ROS) generation, and hemodynamic response to injury remains undefined. METHODS Here we use mice that lack the enzyme required for terminal oxidation of ketone bodies, succinyl-CoA:3-oxoacid CoA transferase (SCOT) to determine the role of ketone body oxidation in the myocardial injury response. Tracer delivery in ex vivo perfused hearts coupled to NMR spectroscopy, in vivo high-resolution echocardiographic quantification of cardiac hemodynamics in nutritionally and surgically modified mice, and cellular and molecular measurements of energetic and oxidative stress responses are performed. RESULTS While germline SCOT-knockout (KO) mice die in the early postnatal period, adult mice with cardiomyocyte-specific loss of SCOT (SCOT-Heart-KO) remarkably exhibit no overt metabolic abnormalities, and no differences in left ventricular mass or impairments of systolic function during periods of ketosis, including fasting and adherence to a ketogenic diet. Myocardial fatty acid oxidation is increased when ketones are delivered but cannot be oxidized. To determine the role of ketone body oxidation in the remodeling ventricle, we induced pressure overload injury by performing transverse aortic constriction (TAC) surgery in SCOT-Heart-KO and αMHC-Cre control mice. While TAC increased left ventricular mass equally in both groups, at four weeks post-TAC, myocardial ROS abundance was increased in myocardium of SCOT-Heart-KO mice, and mitochondria and myofilaments were ultrastructurally disordered. Eight weeks post-TAC, left ventricular volume was markedly increased and ejection fraction was decreased in SCOT-Heart-KO mice, while these parameters remained normal in hearts of control animals. CONCLUSIONS These studies demonstrate the ability of myocardial ketone metabolism to coordinate the myocardial response to pressure overload, and suggest that the oxidation of ketone bodies may be an important contributor to free radical homeostasis and hemodynamic preservation in the injured heart.
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Affiliation(s)
- Rebecca C Schugar
- Department of Medicine, Center for Cardiovascular Research, Washington University, St. Louis, MO, USA
| | - Ashley R Moll
- Department of Medicine, Center for Cardiovascular Research, Washington University, St. Louis, MO, USA
| | | | - Carla J Weinheimer
- Department of Medicine, Center for Cardiovascular Research, Washington University, St. Louis, MO, USA
| | - Attila Kovacs
- Department of Medicine, Center for Cardiovascular Research, Washington University, St. Louis, MO, USA
| | - Peter A Crawford
- Department of Medicine, Center for Cardiovascular Research, Washington University, St. Louis, MO, USA ; Department of Genetics, Washington University, St. Louis, MO, USA
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529
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Roessler C, Nowak T, Pannek M, Gertz M, Nguyen GTT, Scharfe M, Born I, Sippl W, Steegborn C, Schutkowski M. Chemical probing of the human sirtuin 5 active site reveals its substrate acyl specificity and peptide-based inhibitors. Angew Chem Int Ed Engl 2014; 53:10728-32. [PMID: 25111069 DOI: 10.1002/anie.201402679] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/12/2022]
Abstract
Sirtuins are NAD(+)-dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide-based inhibitors that interact with the NAD(+) binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X-ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5.
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Affiliation(s)
- Claudia Roessler
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale (Germany)
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530
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Roessler C, Nowak T, Pannek M, Gertz M, Nguyen GTT, Scharfe M, Born I, Sippl W, Steegborn C, Schutkowski M. Chemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide-Based Inhibitors. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402679] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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531
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Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast. eLife 2014; 3:e03023. [PMID: 25073701 PMCID: PMC4129440 DOI: 10.7554/elife.03023] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms. DOI:http://dx.doi.org/10.7554/eLife.03023.001 Nearly all tumor cells contain abnormal number of chromosomes. This state is called aneuploidy, and can also cause embryos to be miscarried, or to be born with severe developmental disorders. Proteins are produced from the genes contained within chromosomes, and so cells with too many chromosomes produce too many of some proteins. How do these cells cope with this excess? Previous work identified one strategy where a gene called UBP6 is mutated to prevent it from working correctly. The UBP6 gene normally encodes a protein that removes a small tag (called ubiquitin) from other proteins. This tag normally marks other proteins that should be degraded; thus, if UBP6 is not working, more proteins are broken down. Dephoure et al. investigated the effect of aneuploidy on the proteins produced by 12 different types of yeast cell, which each had an extra chromosome. In general, the amount of each protein produced by these yeast increased depending on the number of extra copies of the matching genes found on the extra chromosome. However, this was not the case for around 20% of the proteins, which were found in lower amounts than expected. Dephoure et al. revealed that this was not because fewer proteins were made, but because more were broken down. These proteins may be targeted for degradation because they are unstable, as many of these proteins need to bind to other proteins to keep them stable—but these stabilizing proteins are not also over-produced. Aneuploidy in cells also has other effects, including changing the cells' metabolism so that the cells grow more slowly and do not respond as well to stress. However, Dephoure et al. found that, as well as reducing the number of proteins produced, deleting the UBP6 gene also increased the fitness of the cells. Targeting the protein encoded by the UBP6 gene, or others that also stop proteins being broken down, could therefore help to reduce the negative effects of aneuploidy for a cell. Whether targeting these genes or proteins could also help to treat the diseases and disorders that result from aneuploidy, such as Alzheimer's and Huntington's disease, remains to be investigated. DOI:http://dx.doi.org/10.7554/eLife.03023.002
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Affiliation(s)
- Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Sunyoung Hwang
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
| | - Ciara O'Sullivan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
| | - Stacie E Dodgson
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Eduardo M Torres
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
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532
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Buler M, Aatsinki SM, Izzi V, Uusimaa J, Hakkola J. SIRT5 is under the control of PGC-1α and AMPK and is involved in regulation of mitochondrial energy metabolism. FASEB J 2014; 28:3225-37. [PMID: 24687991 DOI: 10.1096/fj.13-245241] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The sirtuins (SIRTs; SIRT1-7) are a family of NAD(+)-dependent enzymes that dynamically regulate cellular physiology. Apart from SIRT1, the functions and regulatory mechanisms of the SIRTs are poorly defined. We explored regulation of the SIRT family by 2 energy metabolism-controlling factors: peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) and AMP-activated protein kinase (AMPK). Overexpression of PGC-1α in mouse primary hepatocytes increased SIRT5 mRNA expression 4-fold and also the protein in a peroxisome proliferator-activated receptor α (PPARα)- and estrogen-related receptor α (ERRα)-dependent manner. Furthermore, food withdrawal increased SIRT5 mRNA 1.3-fold in rat liver. Overexpression of AMPK in mouse hepatocytes increased expression of SIRT1, SIRT2, SIRT3, and SIRT6 <2-fold. In contrast, SIRT5 mRNA was down-regulated by 58%. The antidiabetes drug metformin (1 mM), an established AMPK activator, reduced the mouse SIRT5 protein level by 44% in cultured hepatocytes and by 31% in liver in vivo (300 mg/kg, 7 d). Metformin also induced hypersuccinylation of mitochondrial proteins. Moreover, SIRT5 overexpression increased ATP synthesis and oxygen consumption in HepG2 cells, but did not affect mitochondrial biogenesis. In summary, our results identified SIRT5 as a novel factor that controls mitochondrial function. Moreover, SIRT5 levels are regulated by PGC-1α and AMPK, which have opposite effects on its expression.-Buler, M., Aatsinki, S.-M., Izzi, V., Uusimaa, J., Hakkola, J. SIRT5 is under the control of PGC-1α and AMPK and is involved in regulation of mitochondrial energy metabolism.
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Affiliation(s)
- Marcin Buler
- Department of Pharmacology and Toxicology, Institute of Biomedicine, Medical Research Center Oulu and
| | - Sanna-Mari Aatsinki
- Department of Pharmacology and Toxicology, Institute of Biomedicine, Medical Research Center Oulu and
| | - Valerio Izzi
- Center for Cell-Matrix Research and Biocenter Oulu, Department of Medical Biochemistry and Molecular Biology, and
| | - Johanna Uusimaa
- Medical Research Center Oulu and Institute of Clinical Medicine and Pediatrics, Clinical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jukka Hakkola
- Department of Pharmacology and Toxicology, Institute of Biomedicine, Medical Research Center Oulu and
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533
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Xu Y, Li F, Lv L, Li T, Zhou X, Deng CX, Guan KL, Lei QY, Xiong Y. Oxidative stress activates SIRT2 to deacetylate and stimulate phosphoglycerate mutase. Cancer Res 2014; 74:3630-42. [PMID: 24786789 PMCID: PMC4303242 DOI: 10.1158/0008-5472.can-13-3615] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycolytic enzyme phosphoglycerate mutase (PGAM) plays an important role in coordinating energy production with generation of reducing power and the biosynthesis of nucleotide precursors and amino acids. Inhibition of PGAM by small RNAi or small molecule attenuates cell proliferation and tumor growth. PGAM activity is commonly upregulated in tumor cells, but how PGAM activity is regulated in vivo remains poorly understood. Here we report that PGAM is acetylated at lysine 100 (K100), an active site residue that is invariably conserved from bacteria, to yeast, plant, and mammals. K100 acetylation is detected in fly, mouse, and human cells and in multiple tissues and decreases PGAM2 activity. The cytosolic protein deacetylase sirtuin 2 (SIRT2) deacetylates and activates PGAM2. Increased levels of reactive oxygen species stimulate PGAM2 deacetylation and activity by promoting its interaction with SIRT2. Substitution of endogenous PGAM2 with an acetylation mimetic mutant K100Q reduces cellular NADPH production and inhibits cell proliferation and tumor growth. These results reveal a mechanism of PGAM2 regulation and NADPH homeostasis in response to oxidative stress that impacts cell proliferation and tumor growth.
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Affiliation(s)
- Yanping Xu
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Fulong Li
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Lei Lv
- Authors' Affiliations: Ministry of Education Key Laboratory of Molecular Medicine, and Department of Biochemistry and Molecular Biology, Shanghai Medical College, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences
| | - Tingting Li
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Xin Zhou
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Chu-Xia Deng
- Genetics of Development and Disease Branch, National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Kun-Liang Guan
- Authors' Affiliations: Ministry of Education Key Laboratory of Molecular Medicine, and Department of Biochemistry and Molecular Biology, Shanghai Medical College, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, California; and
| | - Qun-Ying Lei
- Authors' Affiliations: Ministry of Education Key Laboratory of Molecular Medicine, and Department of Biochemistry and Molecular Biology, Shanghai Medical College, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences,
| | - Yue Xiong
- Authors' Affiliations: Ministry of Education Key Laboratory of Molecular Medicine, and Department of Biochemistry and Molecular Biology, Shanghai Medical College, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina
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534
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Iesmantavicius V, Weinert BT, Choudhary C. Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol Cell Proteomics 2014; 13:1979-92. [PMID: 24961812 PMCID: PMC4125731 DOI: 10.1074/mcp.o113.035683] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The target of rapamycin (TOR) kinase senses the availability of nutrients and coordinates cellular growth and proliferation with nutrient abundance. Inhibition of TOR mimics nutrient starvation and leads to the reorganization of many cellular processes, including autophagy, protein translation, and vesicle trafficking. TOR regulates cellular physiology by modulating phosphorylation and ubiquitylation signaling networks; however, the global scope of such regulation is not fully known. Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified. The phosphoproteome was extensively modulated by rapamycin treatment, with more than 900 up-regulated sites one hour after rapamycin treatment. Dynamically regulated phosphoproteins were involved in diverse cellular processes, prominently including transcription, membrane organization, vesicle-mediated transport, and autophagy. Several hundred ubiquitylation sites were increased after rapamycin treatment, and about half as many decreased in abundance. We found that proteome, phosphorylation, and ubiquitylation changes converged on the Rsp5-ubiquitin ligase, Rsp5 adaptor proteins, and Rsp5 targets. Putative Rsp5 targets were biased for increased ubiquitylation, suggesting activation of Rsp5 by rapamycin. Rsp5 adaptor proteins, which recruit target proteins for Rsp5-dependent ubiquitylation, were biased for increased phosphorylation. Furthermore, we found that permeases and transporters, which are often ubiquitylated by Rsp5, were biased for reduced ubiquitylation and reduced protein abundance. The convergence of multiple proteome-level changes on the Rsp5 system indicates a key role of this pathway in the response to rapamycin treatment. Collectively, these data reveal new insights into the global proteome dynamics in response to rapamycin treatment and provide a first detailed view of the co-regulation of phosphorylation- and ubiquitylation-dependent signaling networks by this compound.
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Affiliation(s)
- Vytautas Iesmantavicius
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Brian T Weinert
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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535
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Raijmakers R, Olsen JV, Aebersold R, Heck AJR. PRIME-XS, a European infrastructure for proteomics. Mol Cell Proteomics 2014; 13:1901-4. [PMID: 24958170 DOI: 10.1074/mcp.e114.040162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PRIME-XS consortium is a pan-European infrastructure for proteomics. As a prologue to this special issue of Molecular & Cellular Proteomics on the research activities of the PRIME-XS consortium, we, as the guest editors of this issue, provide an overview of the structure and activities of this consortium, which is funded by the European Union's 7th Framework Programme for Research and Technological Development.
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Affiliation(s)
- Reinout Raijmakers
- From the *Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Jesper V Olsen
- ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; ‖Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
| | - Albert J R Heck
- From the *Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands;
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536
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Okanishi H, Kim K, Masui R, Kuramitsu S. Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus. Mol Cell Proteomics 2014; 13:2382-98. [PMID: 24938286 DOI: 10.1074/mcp.m113.035659] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent studies of protein post-translational modifications revealed that various types of lysine acylation occur in eukaryotic and bacterial proteins. Lysine propionylation, a newly discovered type of acylation, occurs in several proteins, including some histones. In this study, we identified 361 propionylation sites in 183 mid-exponential phase and late stationary phase proteins from Thermus thermophilus HB8, an extremely thermophilic eubacterium. Functional classification of the propionylproteins revealed that the number of propionylation sites in metabolic enzymes increased in late stationary phase, irrespective of protein abundance. The propionylation sites on proteins expressed in mid-exponential and late stationary phases partially overlapped. Furthermore, amino acid frequencies in the vicinity of propionylation sites differed, not only between the two growth phases but also relative to acetylation sites. In addition, 33.8% of mid-exponential phase-specific and 80.0% of late stationary phase-specific propionylations (n ≥ 2) implied that specific mechanisms regulate propionylation in the cell. Moreover, the limited degree of overlap between lysine propionylation (36.8%) and acetylation (49.2%) sites in 67 proteins that were both acetylated and propionylated strongly suggested that the two acylation reactions are regulated separately by specific enzymes and may serve different functions. Finally, we also found that eight propionylation sites overlapped with acetylation sites critical for protein functions such as Schiff-base formation and ligand binding.
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Affiliation(s)
- Hiroki Okanishi
- From the *Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Kwang Kim
- From the *Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- From the *Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- From the *Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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537
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Abstract
Cellular proteins are decorated with a wide range of acetyl and other acyl modifications. Many studies have demonstrated regulation of site-specific acetylation by acetyltransferases and deacetylases. Acylation is emerging as a new type of lysine modification, but less is known about its overall regulatory role. Furthermore, the mechanisms of lysine acylation, its overlap with protein acetylation, and how it influences cellular function are major unanswered questions in the field. In this review, we discuss the known roles of acetyltransferases and deacetylases and the sirtuins as a conserved family of a nicotinamide adenine dinucleotide (NAD⁺)-dependent protein deacylases that are important for response to cellular stress and homeostasis. We also consider the evidence for an emerging idea of nonenzymatic protein acylation. Finally, we put forward the hypothesis that protein acylation is a form of protein "carbon stress" that the deacylases evolved to remove as a part of a global protein quality-control network.
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538
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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539
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Tan M, Peng C, Anderson KA, Chhoy P, Xie Z, Dai L, Park J, Chen Y, Huang H, Zhang Y, Ro J, Wagner GR, Green MF, Madsen AS, Schmiesing J, Peterson BS, Xu G, Ilkayeva OR, Muehlbauer MJ, Braulke T, Mühlhausen C, Backos DS, Olsen CA, McGuire PJ, Pletcher SD, Lombard DB, Hirschey MD, Zhao Y. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab 2014; 19:605-17. [PMID: 24703693 PMCID: PMC4108075 DOI: 10.1016/j.cmet.2014.03.014] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 11/17/2013] [Accepted: 01/27/2014] [Indexed: 01/20/2023]
Abstract
We report the identification and characterization of a five-carbon protein posttranslational modification (PTM) called lysine glutarylation (Kglu). This protein modification was detected by immunoblot and mass spectrometry (MS), and then comprehensively validated by chemical and biochemical methods. We demonstrated that the previously annotated deacetylase, sirtuin 5 (SIRT5), is a lysine deglutarylase. Proteome-wide analysis identified 683 Kglu sites in 191 proteins and showed that Kglu is highly enriched on metabolic enzymes and mitochondrial proteins. We validated carbamoyl phosphate synthase 1 (CPS1), the rate-limiting enzyme in urea cycle, as a glutarylated protein and demonstrated that CPS1 is targeted by SIRT5 for deglutarylation. We further showed that glutarylation suppresses CPS1 enzymatic activity in cell lines, mice, and a model of glutaric acidemia type I disease, the last of which has elevated glutaric acid and glutaryl-CoA. This study expands the landscape of lysine acyl modifications and increases our understanding of the deacylase SIRT5.
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Affiliation(s)
- Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kristin A Anderson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Peter Chhoy
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Zhongyu Xie
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Lunzhi Dai
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jeongsoon Park
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yue Chen
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yi Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jennifer Ro
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory R Wagner
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michelle F Green
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Andreas S Madsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Brett S Peterson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Guofeng Xu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Olga R Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - 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
| | - Christian A Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter J McGuire
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA.
| | - Yingming Zhao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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540
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Unsuspected task for an old team: succinate, fumarate and other Krebs cycle acids in metabolic remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1330-7. [PMID: 24699309 DOI: 10.1016/j.bbabio.2014.03.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/17/2014] [Accepted: 03/25/2014] [Indexed: 12/15/2022]
Abstract
Seventy years from the formalization of the Krebs cycle as the central metabolic turntable sustaining the cell respiratory process, key functions of several of its intermediates, especially succinate and fumarate, have been recently uncovered. The presumably immutable organization of the cycle has been challenged by a number of observations, and the variable subcellular location of a number of its constitutive protein components is now well recognized, although yet unexplained. Nonetheless, the most striking observations have been made in the recent period while investigating human diseases, especially a set of specific cancers, revealing the crucial role of Krebs cycle intermediates as factors affecting genes methylation and thus cell remodeling. We review here the recent advances and persisting incognita about the role of Krebs cycle acids in diverse aspects of cellular life and human pathology.
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541
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Weinert BT, Iesmantavicius V, Moustafa T, Schölz C, Wagner SA, Magnes C, Zechner R, Choudhary C. Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. Mol Syst Biol 2014; 10:716. [PMID: 24489116 PMCID: PMC4023402 DOI: 10.1002/msb.134766] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lysine acetylation is a frequently occurring posttranslational modification; however, little is known about the origin and regulation of most sites. Here we used quantitative mass spectrometry to analyze acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. We found that acetylation accumulated in growth‐arrested cells in a manner that depended on acetyl‐CoA generation in distinct subcellular compartments. Mitochondrial acetylation levels correlated with acetyl‐CoA concentration in vivo and acetyl‐CoA acetylated lysine residues nonenzymatically in vitro. We developed a method to estimate acetylation stoichiometry and found that the vast majority of mitochondrial and cytoplasmic acetylation had a very low stoichiometry. However, mitochondrial acetylation occurred at a significantly higher basal level than cytoplasmic acetylation, consistent with the distinct acetylation dynamics and higher acetyl‐CoA concentration in mitochondria. High stoichiometry acetylation occurred mostly on histones, proteins present in histone acetyltransferase and deacetylase complexes, and on transcription factors. These data show that a majority of acetylation occurs at very low levels in exponentially growing yeast and is uniformly affected by exposure to acetyl‐CoA.
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Affiliation(s)
- Brian T Weinert
- The NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Copenhagen, Denmark
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542
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Kalesh KA, Tate EW. A succinyl lysine-based photo-cross-linking peptide probe for Sirtuin 5. Org Biomol Chem 2014; 12:4310-3. [DOI: 10.1039/c4ob00773e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A succinylation-specific photo-cross-linking peptide probe has been developed for the NAD+-dependent hydrolase Sirtuin 5.
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Affiliation(s)
| | - Edward W. Tate
- Department of Chemistry
- Imperial College London
- London SW7 2AZ, UK
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543
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Olsen CA. An update on lysine deacylases targeting the expanding "acylome". ChemMedChem 2013; 9:434-7. [PMID: 24375937 DOI: 10.1002/cmdc.201300421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 11/12/2022]
Abstract
Lysine ε-amino acetylation has long been recognized as an epigenetically relevant post-translational modification of multiple residues in histone proteins. However, it has become clear that lysine acetylation is not restricted to histones, and therefore, it may be involved in the regulation of a wide variety of proteins, some of which have been identified and studied in detail. More recently, post-translational modifications of lysine side chains by additional acyl groups have also been identified, and some of these appear to be regulated by histone deacetylases (HDACs) and/or sirtuins. In this Concept, new developments are discussed with emphasis on the enzymes that have been shown to catalyze the cleavage of these novel marks, including new assays and inhibitors. Ultimately, a deeper understand of these mechanisms should facilitate the development of ligands with therapeutic potential.
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Affiliation(s)
- Christian A Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, 2800 (Denmark).
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544
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Liu Z, Wang Y, Gao T, Pan Z, Cheng H, Yang Q, Cheng Z, Guo A, Ren J, Xue Y. CPLM: a database of protein lysine modifications. Nucleic Acids Res 2013; 42:D531-6. [PMID: 24214993 PMCID: PMC3964993 DOI: 10.1093/nar/gkt1093] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We reported an integrated database of Compendium of Protein Lysine Modifications (CPLM; http://cplm.biocuckoo.org) for protein lysine modifications (PLMs), which occur at active ε-amino groups of specific lysine residues in proteins and are critical for orchestrating various biological processes. The CPLM database was updated from our previously developed database of Compendium of Protein Lysine Acetylation (CPLA), which contained 7151 lysine acetylation sites in 3311 proteins. Here, we manually collected experimentally identified substrates and sites for 12 types of PLMs, including acetylation, ubiquitination, sumoylation, methylation, butyrylation, crotonylation, glycation, malonylation, phosphoglycerylation, propionylation, succinylation and pupylation. In total, the CPLM database contained 203,972 modification events on 189,919 modified lysines in 45,748 proteins for 122 species. With the dataset, we totally identified 76 types of co-occurrences of various PLMs on the same lysine residues, and the most abundant PLM crosstalk is between acetylation and ubiquitination. Up to 53.5% of acetylation and 33.1% of ubiquitination events co-occur at 10 746 lysine sites. Thus, the various PLM crosstalks suggested that a considerable proportion of lysines were competitively and dynamically regulated in a complicated manner. Taken together, the CPLM database can serve as a useful resource for further research of PLMs.
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Affiliation(s)
- Zexian Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
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545
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Colak G, Xie Z, Zhu AY, Dai L, Lu Z, Zhang Y, Wan X, Chen Y, Cha YH, Lin H, Zhao Y, Tan M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics 2013; 12:3509-20. [PMID: 24176774 DOI: 10.1074/mcp.m113.031567] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine succinylation is a newly identified protein post-translational modification pathway present in both prokaryotic and eukaryotic cells. However, succinylation substrates and regulatory enzyme(s) remain largely unknown, hindering the biological study of this modification. Here we report the identification of 2,580 bacterial lysine succinylation sites in 670 proteins and 2,803 lysine acetylation (Kac) sites in 782 proteins, representing the first lysine succinylation dataset and the largest Kac dataset in wild-type E. coli. We quantified dynamic changes of the lysine succinylation and Kac substrates in response to high glucose. Our data showed that high-glucose conditions led to more lysine-succinylated proteins and enhanced the abundance of succinyllysine peptides more significantly than Kac peptides, suggesting that glucose has a more profound effect on succinylation than on acetylation. We further identified CobB, a known Sir2-like bacterial lysine deacetylase, as the first prokaryotic desuccinylation enzyme. The identification of bacterial CobB as a bifunctional enzyme with lysine desuccinylation and deacetylation activities suggests that the eukaryotic Kac-regulatory enzymes may have enzymatic activities on various lysine acylations with very different structures. In addition, it is highly likely that lysine succinylation could have unique and more profound regulatory roles in cellular metabolism relative to lysine acetylation under some physiological conditions.
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Affiliation(s)
- Gozde Colak
- Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois 60637
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