401
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Madsen AS, Andersen C, Daoud M, Anderson KA, Laursen JS, Chakladar S, Huynh FK, Colaço AR, Backos DS, Fristrup P, Hirschey MD, Olsen CA. Investigating the Sensitivity of NAD+-dependent Sirtuin Deacylation Activities to NADH. J Biol Chem 2016; 291:7128-41. [PMID: 26861872 DOI: 10.1074/jbc.m115.668699] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Indexed: 11/06/2022] Open
Abstract
Protein lysine posttranslational modification by an increasing number of different acyl groups is becoming appreciated as a regulatory mechanism in cellular biology. Sirtuins are class III histone deacylases that use NAD(+)as a co-substrate during amide bond hydrolysis. Several studies have described the sirtuins as sensors of the NAD(+)/NADH ratio, but it has not been formally tested for all the mammalian sirtuinsin vitro To address this problem, we first synthesized a wide variety of peptide-based probes, which were used to identify the range of hydrolytic activities of human sirtuins. These probes included aliphatic ϵ-N-acyllysine modifications with hydrocarbon lengths ranging from formyl (C1) to palmitoyl (C16) as well as negatively charged dicarboxyl-derived modifications. In addition to the well established activities of the sirtuins, "long chain" acyllysine modifications were also shown to be prone to hydrolytic cleavage by SIRT1-3 and SIRT6, supporting recent findings. We then tested the ability of NADH, ADP-ribose, and nicotinamide to inhibit these NAD(+)-dependent deacylase activities of the sirtuins. In the commonly used 7-amino-4-methylcoumarin-coupled fluorescence-based assay, the fluorophore has significant spectral overlap with NADH and therefore cannot be used to measure inhibition by NADH. Therefore, we turned to an HPLC-MS-based assay to directly monitor the conversion of acylated peptides to their deacylated forms. All tested sirtuin deacylase activities showed sensitivity to NADH in this assay. However, the inhibitory concentrations of NADH in these assays are far greater than the predicted concentrations of NADH in cells; therefore, our data indicate that NADH is unlikely to inhibit sirtuinsin vivo These data suggest a re-evaluation of the sirtuins as direct sensors of the NAD(+)/NADH ratio.
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Affiliation(s)
- Andreas S Madsen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark, the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark,
| | - Christian Andersen
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Mohammad Daoud
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kristin A Anderson
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Jonas S Laursen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Saswati Chakladar
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Frank K Huynh
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Ana R Colaço
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Donald S Backos
- the Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Peter Fristrup
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Matthew D Hirschey
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Christian A Olsen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark, the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark,
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402
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Seidel J, Klockenbusch C, Schwarzer D. Investigating Deformylase and Deacylase Activity of Mammalian and Bacterial Sirtuins. Chembiochem 2016; 17:398-402. [DOI: 10.1002/cbic.201500611] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Cordula Klockenbusch
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
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403
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Cheng Y, Hou T, Ping J, Chen G, Chen J. Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model. Proteome Sci 2016; 14:3. [PMID: 26843850 PMCID: PMC4739109 DOI: 10.1186/s12953-016-0092-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/26/2016] [Indexed: 02/07/2023] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is a clinical frequent disease. However, its pathogenesis still needs further study, especially the mechanism at the molecular level. The recent identified novel protein post-translational modification, lysine succinylation was reported involved in diverse metabolism and cellular processes. In this study, we performed the quantitative succinylome analysis in the liver of NAFLD model to elucidate the regulatory role of lysine succinylation in NAFLD progression. Methods Firstly, experimental model of NAFLD was induced by carbon tetrachloride injection and supplementary high-lipid and low-protein diet. Then series histochemical and biochemical variables were determined. For the quantitative succinylome analysis, tandem mass tags (TMT)-labeling, highly sensitive immune-affinity purification, liquid chromatography-tandem mass spectrometry techniques were applied. Bioinformatics analysis including gene ontology annotation based classification; Wolfpsort based subcellular prediction; function enrichment; protein-protein interaction network construction and conserved succinylation site motifs extraction were performed to decipher the differentially changed succinylated proteins and sites and p-value < 0.05 was selected as threshold. Results Totally, 815 succinylation sites on 407 proteins were identified, of which 243 succinylation acetylation sites on 178 proteins showed changed succinylation level with the threshold fold change > 1.5. Theses differentially changed succinylated proteins were involved in diverse metabolism pathways and cellular processes including carbon metabolism, amino acid metabolism, fat acid metabolism, binding and catalyzing, anti-oxidation and xenobiotics metabolism. Besides, these differentially changed succinylated proteins were prominently localized to cytoplasm and mitochondria. Moreover, 8 conserved succinylation site motifs were extracted around the succinylation sites. Conclusions Protein succinylation was an extensive post-translation modification in rat. The changed succinylation level in diverse proteins may disturb multiple metabolism pathways and promote non-alcoholic fatty liver disease development. This study provided a basis for further characterization of the pathophysiological role of lysine succinylation in NAFLD progression, which laid a foundation for the innovation of novel NAFLD drugs and therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0092-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Cheng
- Department of liver disease, Hospital for Infectious Diseases of Pudong New Area, Shanghai, 201299 P. R. China ; Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Tianlu Hou
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Jian Ping
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Gaofeng Chen
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
| | - Jianjie Chen
- Department of liver disease, Hospital for Infectious Diseases of Pudong New Area, Shanghai, 201299 P. R. China ; Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 P. R. China
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404
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Abstract
The purpose of this review is to provide an overview of the complexity of the epigenetic target space. Chemical modifications of histones and nucleic acids constitute a key epigenetic mechanism. Whereas modifications such as methylation and acetylation are well-known, there are many additional, less explored modifications described here. The writers, readers and erasers of such diverse modifications, which constitute a major portion of the potential epigenetic target space, are discussed, in addition to the various other protein families that do not fall under these three categories. Finally, disease relevance and druggability of epigenetic targets are discussed with concluding remarks about the richness and diversity they will provide for future targeted therapies.
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Affiliation(s)
- Vineet Pande
- Discovery Sciences, Janssen-Pharmaceutical Companies of Johnson & Johnson , Turnhoutseweg 30, Beerse 2340, Belgium
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405
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He D, Wang Q, Li M, Damaris RN, Yi X, Cheng Z, Yang P. Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed. J Proteome Res 2016; 15:879-90. [PMID: 26767346 DOI: 10.1021/acs.jproteome.5b00805] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.
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Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xingling Yi
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Zhongyi Cheng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
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406
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Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends Biochem Sci 2016; 41:231-244. [PMID: 26822488 DOI: 10.1016/j.tibs.2015.12.006] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022]
Abstract
Reversible protein acetylation is a major regulatory mechanism for controlling protein function. Through genetic manipulations, dietary perturbations, and new proteomic technologies, the diverse functions of protein acetylation are coming into focus. Protein acetylation in mitochondria has taken center stage, revealing that 63% of mitochondrially localized proteins contain lysine acetylation sites. We summarize the field and discuss salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylation, nonenzymatic acetylation, and molecular models for regulatory acetylations that display high and low stoichiometry.
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407
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Sidoli S, Yuan ZF, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton LM, Cao XJ, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, Garcia BA. Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics 2016; 15:1459-69. [PMID: 25641854 DOI: 10.1002/pmic.201400483] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
MS-based proteomics has become the most utilized tool to characterize histone PTMs. Since histones are highly enriched in lysine and arginine residues, lysine derivatization has been developed to prevent the generation of short peptides (<6 residues) during trypsin digestion. One of the most adopted protocols applies propionic anhydride for derivatization. However, the propionyl group is not sufficiently hydrophobic to fully retain the shortest histone peptides in RP LC, and such procedure also hampers the discovery of natural propionylation events. In this work we tested 12 commercially available anhydrides, selected based on their safety and hydrophobicity. Performance was evaluated in terms of yield of the reaction, MS/MS fragmentation efficiency, and drift in retention time using the following samples: (i) a synthetic unmodified histone H3 tail, (ii) synthetic modified histone peptides, and (iii) a histone extract from cell lysate. Results highlighted that seven of the selected anhydrides increased peptide retention time as compared to propionic, and several anhydrides such as benzoic and valeric led to high MS/MS spectra quality. However, propionic anhydride derivatization still resulted, in our opinion, as the best protocol to achieve high MS sensitivity and even ionization efficiency among the analyzed peptides.
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Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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408
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Abstract
Tumorigenesis is dependent on the reprogramming of cellular metabolism as both direct and indirect consequence of oncogenic mutations. A common feature of cancer cell metabolism is the ability to acquire necessary nutrients from a frequently nutrient-poor environment and utilize these nutrients to both maintain viability and build new biomass. The alterations in intracellular and extracellular metabolites that can accompany cancer-associated metabolic reprogramming have profound effects on gene expression, cellular differentiation, and the tumor microenvironment. In this Perspective, we have organized known cancer-associated metabolic changes into six hallmarks: (1) deregulated uptake of glucose and amino acids, (2) use of opportunistic modes of nutrient acquisition, (3) use of glycolysis/TCA cycle intermediates for biosynthesis and NADPH production, (4) increased demand for nitrogen, (5) alterations in metabolite-driven gene regulation, and (6) metabolic interactions with the microenvironment. While few tumors display all six hallmarks, most display several. The specific hallmarks exhibited by an individual tumor may ultimately contribute to better tumor classification and aid in directing treatment.
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Affiliation(s)
- Natalya N Pavlova
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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409
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Aftabi Y, Colagar AH, Mehrnejad F. An in silico approach to investigate the source of the controversial interpretations about the phenotypic results of the human AhR-gene G1661A polymorphism. J Theor Biol 2016; 393:1-15. [PMID: 26776670 DOI: 10.1016/j.jtbi.2016.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 12/11/2015] [Accepted: 01/01/2016] [Indexed: 12/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) acts as an enhancer binding ligand-activated intracellular receptor. Chromatin remodeling components and general transcription factors such as TATA-binding protein (TBP) are evoked on AhR-target genes by interaction with its flexible transactivation domain (TAD). AhR-G1661A single nucleotide polymorphism (SNP: rs2066853) causes an arginine to lysine substitution in the acidic sub-domain of TAD at position 554 (R554K). Although, numerous studies associate the SNP with some abnormalities such as cancer, other reliable investigations refuse the associations. Consequently, the interpretation of the phenotypic results of G1661A-transition has been controversial. In this study, an in silico analysis were performed to investigate the possible effects of the transition on AhR-mRNA, protein structure, interaction properties and modifications. The analysis revealed that the R554K substitution affects secondary structure and solvent accessibility of adjacent residues. Also, it causes to decreasing of the AhR stability; altering the hydropathy features of the local sequence and changing the pattern of the residues at the binding site of the TAD-acidic sub-domain. Generating of new sites for ubiquitination and acetylation for AhR-K554 variant respectively at positions 544 and 560 was predicted. Our findings intensify the idea that the AhR-G1661A transition may affects AhR-TAD interactions, especially with the TBP, which influence AhR-target genes expression. However, the previously reported flexibility of the modular TAD could act as an intervening factor, moderate the SNP effects and causes distinct outcomes in different individuals and tissues.
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Affiliation(s)
- Younes Aftabi
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Post Code: 47416-95447, Mazandaran, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Post Code: 47416-95447, Mazandaran, Iran.
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, P.O. Box: 14395-1561, Tehran, Iran
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410
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Quantitative Analysis of the Sirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells. Methods Mol Biol 2016; 1410:23-37. [PMID: 26867736 DOI: 10.1007/978-1-4939-3524-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lysine (Lys) succinylation is a recently discovered protein posttranslational modification pathway that is evolutionarily conserved from bacteria to mammals. It is regulated by Sirt5, a member of the class III histone deacetylases (HDACs) or the Sirtuins. Recent studies demonstrated that Lys succinylation and Sirt5 are involved in diverse cellular metabolic processes including urea cycle, ammonia transfer, and glucose metabolism. In this chapter, we describe the general protocol to identify Sirt5-regulated Lys succinylation substrates and a computational method to calculate the absolute modification stoichiometries of Lys succinylation sites. The strategy employs Stable Isotope Labeling of Amino acid in Cell culture (SILAC) and the immunoaffinity enrichment of Lys succinylated peptides to identify the Lys succinylation sites that are significantly upregulated in Sirt5 knockout mouse embryonic fibroblast cells.
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411
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Ourailidou ME, Zwinderman MRH, Dekker FJ. Bioorthogonal metabolic labelling with acyl-CoA reporters: targeting protein acylation. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00446b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioorthogonal labels in protein acylation: advantages and disadvantages of metaBO(W)lic tagging with acyl-CoA(RROWS).
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Affiliation(s)
- Maria. E. Ourailidou
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
| | - Martijn R. H. Zwinderman
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
| | - Frank J. Dekker
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
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412
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Horlacher O, Lisacek F, Müller M. Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries. J Proteome Res 2015; 15:721-31. [PMID: 26653734 DOI: 10.1021/acs.jproteome.5b00877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental improvements in post-translational modification (PTM) detection by tandem mass spectrometry (MS/MS) has allowed the identification of vast numbers of PTMs. Open modification searches (OMSs) of MS/MS data, which do not require prior knowledge of the modifications present in the sample, further increased the diversity of detected PTMs. Despite much effort, there is still a lack of functional annotation of PTMs. One possibility to narrow the annotation gap is to mine MS/MS data deposited in public repositories and to correlate the PTM presence with biological meta-information attached to the data. Since the data volume can be quite substantial and contain tens of millions of MS/MS spectra, the data mining tools must be able to cope with big data. Here, we present two tools, Liberator and MzMod, which are built using the MzJava class library and the Apache Spark large scale computing framework. Liberator builds large MS/MS spectrum libraries, and MzMod searches them in an OMS mode. We applied these tools to a recently published set of 25 million spectra from 30 human tissues and present tissue specific PTMs. We also compared the results to the ones obtained with the OMS tool MODa and the search engine X!Tandem.
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Affiliation(s)
- Oliver Horlacher
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva 1211, Switzerland.,Centre Universitaire de Bioinformatique, University of Geneva , Geneva 1211, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva 1211, Switzerland.,Centre Universitaire de Bioinformatique, University of Geneva , Geneva 1211, Switzerland
| | - Markus Müller
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva 1211, Switzerland.,Centre Universitaire de Bioinformatique, University of Geneva , Geneva 1211, Switzerland
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413
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George J, Nihal M, Singh CK, Zhong W, Liu X, Ahmad N. Pro-Proliferative Function of Mitochondrial Sirtuin Deacetylase SIRT3 in Human Melanoma. J Invest Dermatol 2015; 136:809-818. [PMID: 26743598 DOI: 10.1016/j.jid.2015.12.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 11/28/2022]
Abstract
Melanoma, the most aggressive form of skin cancer, is often fatal if not treated early. Therefore, novel target-based strategies are required to combat this neoplasm. The objective of this study was to determine the role and functional significance of the mitochondrial sirtuin 3 (SIRT3) in melanoma. We found that compared with normal primary and immortalized human melanocytes, SIRT3 is significantly overexpressed in multiple human melanoma cells at mRNA and protein levels. Further, employing human tissue microarray, we found that SIRT3 is significantly upregulated in clinical melanoma tissues, compared with melanocytic nevi tissues. Furthermore, a short hairpin RNA-mediated knockdown of SIRT3 in human melanoma cells resulted in (i) a decrease in cellular proliferation, colony formation, and cellular migration; (ii) induction of senescence as shown by an increase in senescence-associated beta-galactosidase activity and formation of senescence-associated heterochromatin foci as well as an increase in mRNA and protein levels of p16(INK4a) and p21(Waf1); (iii) G1-phase arrest of the cell cycle; and (iv) decreases in mRNA and protein levels of cyclins (D1, E1) and cyclin-dependent kinases (2, 4, and 6). Conversely, forced exogenous overexpression of SIRT3 promoted an increase in proliferative potential of Hs294T melanoma cells and normal immortalized Mel-ST melanocytes. Finally, we found that SIRT3 knockdown significantly inhibited tumorigenesis in a xenograft model in vivo. To our knowledge, this is the first study supporting the pro-proliferative function of SIRT3 in melanoma.
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Affiliation(s)
- Jasmine George
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA
| | - Minakshi Nihal
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA
| | - Chandra K Singh
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA
| | - Weixiong Zhong
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA; William S. Middleton VA Medical Center, Madison, Wisconsin, USA.
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414
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Lawrence M, Daujat S, Schneider R. Lateral Thinking: How Histone Modifications Regulate Gene Expression. Trends Genet 2015; 32:42-56. [PMID: 26704082 DOI: 10.1016/j.tig.2015.10.007] [Citation(s) in RCA: 571] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
The DNA of each cell is wrapped around histone octamers, forming so-called 'nucleosomal core particles'. These histone proteins have tails that project from the nucleosome and many residues in these tails can be post-translationally modified, influencing all DNA-based processes, including chromatin compaction, nucleosome dynamics, and transcription. In contrast to those present in histone tails, modifications in the core regions of the histones had remained largely uncharacterised until recently, when some of these modifications began to be analysed in detail. Overall, recent work has shown that histone core modifications can not only directly regulate transcription, but also influence processes such as DNA repair, replication, stemness, and changes in cell state. In this review, we focus on the most recent developments in our understanding of histone modifications, particularly those on the lateral surface of the nucleosome. This region is in direct contact with the DNA and is formed by the histone cores. We suggest that these lateral surface modifications represent a key insight into chromatin regulation in the cell. Therefore, lateral surface modifications form a key area of interest and a focal point of ongoing study in epigenetics.
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415
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Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S. Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction. Microbiologyopen 2015; 5:152-73. [PMID: 26663479 PMCID: PMC4767432 DOI: 10.1002/mbo3.320] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/23/2015] [Accepted: 11/03/2015] [Indexed: 11/06/2022] Open
Abstract
The bacterium Corynebacterium glutamicum is utilized during industrial fermentation to produce amino acids such as L-glutamate. During L-glutamate fermentation, C. glutamicum changes the flux of central carbon metabolism to favor L-glutamate production, but the molecular mechanisms that explain these flux changes remain largely unknown. Here, we found that the profiles of two major lysine acyl modifications were significantly altered upon glutamate overproduction in C. glutamicum; acetylation decreased, whereas succinylation increased. A label-free semi-quantitative proteomic analysis identified 604 acetylated proteins with 1328 unique acetylation sites and 288 succinylated proteins with 651 unique succinylation sites. Acetylation and succinylation targeted enzymes in central carbon metabolic pathways that are directly related to glutamate production, including the 2-oxoglutarate dehydrogenase complex (ODHC), a key enzyme regulating glutamate overproduction. Structural mapping revealed that several critical lysine residues in the ODHC components were susceptible to acetylation and succinylation. Furthermore, induction of glutamate production was associated with changes in the extent of acetylation and succinylation of lysine, suggesting that these modifications may affect the activity of enzymes involved in glutamate production. Deletion of phosphotransacetylase decreased the extent of protein acetylation in nonproducing condition, suggesting that acetyl phosphate-dependent acetylation is active in C. glutamicum. However, no effect was observed on the profiles of acetylation and succinylation in glutamate-producing condition upon disruption of acetyl phosphate metabolism or deacetylase homologs. It was considered likely that the reduced acetylation in glutamate-producing condition may reflect metabolic states where the flux through acid-producing pathways is very low, and substrates for acetylation do not accumulate in the cell. Succinylation would occur more easily than acetylation in such conditions where the substrates for both acetylation and succinylation are limited. This is the first study investigating the acetylome and succinylome of C. glutamicum, and it provides new insight into the roles of acyl modifications in C. glutamicum biology.
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Affiliation(s)
- Yuta Mizuno
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Kyowa Hakko Bio Co., Ltd., Tokyo, Japan
| | - Megumi Nagano-Shoji
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Kyowa Hakko Bio Co., Ltd., Tokyo, Japan
| | - Shosei Kubo
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Department of Environmental Materials Science, Tokyo Denki University, Tokyo, Japan
| | - Yumi Kawamura
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kawasaki
- Department of Environmental Materials Science, Tokyo Denki University, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,RIKEN Center for Sustainable Resource Science, Saitama, Japan
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416
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Wang Y, Stowe RL, Pinello CE, Tian G, Madoux F, Li D, Zhao LY, Li JL, Wang Y, Wang Y, Ma H, Hodder P, Roush WR, Liao D. Identification of histone deacetylase inhibitors with benzoylhydrazide scaffold that selectively inhibit class I histone deacetylases. ACTA ACUST UNITED AC 2015; 22:273-84. [PMID: 25699604 DOI: 10.1016/j.chembiol.2014.12.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 11/14/2014] [Accepted: 12/17/2014] [Indexed: 12/18/2022]
Abstract
Inhibitors of histone deacetylases (HDACi) hold considerable therapeutic promise as clinical anticancer therapies. However, currently known HDACi exhibit limited isoform specificity, off-target activity, and undesirable pharmaceutical properties. Thus, HDACi with new chemotypes are needed to overcome these limitations. Here, we identify a class of HDACi with a previously undescribed benzoylhydrazide scaffold that is selective for the class I HDACs. These compounds are competitive inhibitors with a fast-on/slow-off HDAC-binding mechanism. We show that the lead compound, UF010, inhibits cancer cell proliferation via class I HDAC inhibition. This causes global changes in protein acetylation and gene expression, resulting in activation of tumor suppressor pathways and concurrent inhibition of several oncogenic pathways. The isotype selectivity coupled with interesting biological activities in suppressing tumor cell proliferation support further preclinical development of the UF010 class of compounds for potential therapeutic applications.
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Affiliation(s)
- Yunfei Wang
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Ryan L Stowe
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Christie E Pinello
- The Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Guimei Tian
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Franck Madoux
- The Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Dawei Li
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA; Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China
| | - Lisa Y Zhao
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Jian-Liang Li
- Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, FL 32827, USA
| | - Yuren Wang
- Reaction Biology Corporation, 1 Great Valley Parkway Suite 2, Malvern, PA 19355, USA
| | - Yuan Wang
- Reaction Biology Corporation, 1 Great Valley Parkway Suite 2, Malvern, PA 19355, USA
| | - Haiching Ma
- Reaction Biology Corporation, 1 Great Valley Parkway Suite 2, Malvern, PA 19355, USA
| | - Peter Hodder
- Department of Molecular Therapeutics, Scripps Florida, Jupiter, FL 33458, USA; The Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - William R Roush
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA.
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417
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Li Y, Liu T, Liao S, Li Y, Lan Y, Wang A, Wang Y, He B. A mini-review on Sirtuin activity assays. Biochem Biophys Res Commun 2015; 467:459-66. [DOI: 10.1016/j.bbrc.2015.09.172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
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418
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Abstract
Acetylation is a dynamic post-translational modification that is attached to protein substrates by lysine acetyltransferases (KATs) and removed by lysine deacetylases (KDACs). While these enzymes are best characterized as histone modifiers and regulators of gene transcription, work in a number of systems highlights that acetylation is a pervasive modification and suggests a broad scope for KAT and KDAC functions in the cell. As we move beyond generating lists of acetylated proteins, the acetylation field is in dire need of robust tools to connect acetylation and deacetylation machineries to their respective substrates and to dissect the function of individual sites. The Saccharomyces cerevisiae model system provides such a toolkit in the context of both tried and true genetic techniques and cutting-edge proteomic and cell imaging methods. Here, we review these methods in the context of their contributions to acetylation research thus far and suggest strategies for addressing lingering questions in the field.
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419
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Azevedo C, Saiardi A. Why always lysine? The ongoing tale of one of the most modified amino acids. Adv Biol Regul 2015; 60:144-150. [PMID: 26482291 DOI: 10.1016/j.jbior.2015.09.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022]
Abstract
The complex physiology of living organisms must be finely-tuned to permit the flexibility required to respond to the changing environment. Evolution has provided an interconnected and intricate array of regulatory mechanisms to facilitate this fine-tuning. The number of genes cannot alone explain the complexity of these mechanisms. Rather, signalling is regulated at multiple levels, from genomic to transcriptional, translational and post-translational. Post-translational modification (PTM) of proteins offers an additional level of regulation after protein synthesis that allows a rapid, controlled and reversible response to environmental cues. Many amino acid side chains are post-translationally modified. These modifications can either be enzymatic, such as the phosphorylation of serine, threonine and tyrosine residues, or non-enzymatic, such as the nitrosylation of cysteine residues. Strikingly, lysine residues are targeted by a particularly high number of PTMs including acetylation, methylation, ubiquitination and sumoylation. Additionally, lysines have recently been identified as the target of the non-enzymatic PTM polyphosphorylation. This novel PTM sees linear chains of inorganic polyphosphates (polyP) covalently attached to lysine residues. Interestingly, polyphosphorylation is indirectly dependent on inositol pyrophosphates, a class of cellular messengers. The attachment of polyP to lysine occurs through the phosphoramidate bond, which, unlike the phosphester bond, is unstable under the conditions used in common mass spectroscopy. This characteristic, together with the diversity of lysine PTMs, suggests that many other lysine modifications may still remain unidentified, raising the intriguing possibility that lysine PTMs may be the major means by which signalling pathways modify protein behaviour.
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Affiliation(s)
- Cristina Azevedo
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
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420
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Lempradl A, Pospisilik JA, Penninger JM. Exploring the emerging complexity in transcriptional regulation of energy homeostasis. Nat Rev Genet 2015; 16:665-81. [PMID: 26460345 DOI: 10.1038/nrg3941] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Obesity and its associated diseases are expected to affect more than 1 billion people by the year 2030. These figures have sparked intensive research into the molecular control of food intake, nutrient distribution, storage and metabolism--processes that are collectively termed energy homeostasis. Recent decades have also seen dramatic developments in our understanding of gene regulation at the signalling, chromatin and post-transcriptional levels. The seemingly exponential growth in this complexity now poses a major challenge for translational researchers in need of simplified but accurate paradigms for clinical use. In this Review, we consider the current understanding of transcriptional control of energy homeostasis, including both transcriptional and epigenetic regulators, and crosstalk between pathways. We also provide insights into emerging developments and challenges in this field.
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Affiliation(s)
- Adelheid Lempradl
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - J Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohr-Gasse 3, 1030 Vienna, Austria
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421
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Zhdanov R, Schirmer E, Venkatasubramani AV, Kerr A, Mandrou E, Rodriguez Blanco G, Kagansky A. Lipids contribute to epigenetic control via chromatin structure and functions. SCIENCEOPEN RESEARCH 2015. [DOI: 10.14293/s2199-1006.1.sor-life.auxytr.v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Isolated cases of experimental evidence over the last few decades have shown that, where specifically tested, both prokaryotes and eukaryotes have specific lipid molecules bound to nucleoproteins of the genome. In vitro, some of these lipids exhibit stoichiometric association with DNA polynucleotides with differential affinities toward certain secondary and tertiary structures. Hydrophobic interactions with inner nuclear membrane could provide attractive anchor points for lipid-modified nucleoproteins in organizing the dynamic genome and accordingly there are precedents for covalent bonds between lipids and core histones and, under certain conditions, even DNA. Advances in biophysics, functional genomics, and proteomics in recent years brought about the first sparks of light that promises to uncover some coherent new level of the epigenetic code governed by certain types of lipid–lipid, DNA–lipid, and protein–lipid interactions among other biochemical lipid transactions in the nucleus. Here, we review some of the older and more recent findings and speculate on how critical nuclear lipid transactions are for individual cells, tissues, and organisms.
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422
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Cluntun AA, Huang H, Dai L, Liu X, Zhao Y, Locasale JW. The rate of glycolysis quantitatively mediates specific histone acetylation sites. Cancer Metab 2015; 3:10. [PMID: 26401273 PMCID: PMC4579576 DOI: 10.1186/s40170-015-0135-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 08/28/2015] [Indexed: 01/01/2023] Open
Abstract
Background Glucose metabolism links metabolic status to protein acetylation. However, it remains poorly understood to what extent do features of glucose metabolism contribute to protein acetylation and whether the process can be dynamically and quantitatively regulated by differing rates of glycolysis. Results Here, we show that titratable rates of glycolysis with corresponding changes in the levels of glycolytic intermediates result in a graded remodeling of a bulk of the metabolome and resulted in gradual changes in total histone acetylation levels. Dynamic histone acetylation levels were found and most strongly correlated with acetyl coenzyme A (ac-CoA) levels and inversely associated with the ratio of ac-CoA to free CoA. A multiplexed stable isotopic labeling by amino acids in cell culture (SILAC)-based proteomics approach revealed that the levels of half of identified histone acetylation sites as well as other lysine acylation modifications are tuned by the rate of glycolysis demonstrating that glycolytic rate affects specific acylation sites. Conclusions We demonstrate that histone acylation is directly sensed by glucose flux in a titratable, dose-dependent manner that is modulated by glycolytic flux and that a possible function of the Warburg Effect, a metabolic state observed in cancers with enhanced glucose metabolism, is to confer specific signaling effects on cells.
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Affiliation(s)
- Ahmad A Cluntun
- Graduate Field of Biochemistry, Molecular Cell Biology, Cornell University, Ithaca, NY USA ; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL USA
| | - Lunzhi Dai
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Xiaojing Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY USA
| | - Yingming Zhao
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Jason W Locasale
- Graduate Field of Biochemistry, Molecular Cell Biology, Cornell University, Ithaca, NY USA ; Division of Nutritional Sciences, Cornell University, Ithaca, NY USA ; Department of Pharmacology and Cancer Biology, Duke University Medical School, Durham, NC USA ; Duke Cancer Institute, Duke University Medical School, Durham, NC USA ; Duke Molecular Physiology Institute, Duke University Medical School, Durham, NC USA
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423
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Pan J, Chen R, Li C, Li W, Ye Z. Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus. J Proteome Res 2015; 14:4309-18. [DOI: 10.1021/acs.jproteome.5b00485] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianyi Pan
- Institute
of Proteomics and
Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ran Chen
- Institute
of Proteomics and
Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Chuchu Li
- Institute
of Proteomics and
Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weiyan Li
- Institute
of Proteomics and
Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhicang Ye
- Institute
of Proteomics and
Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
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424
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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425
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Roessler C, Tüting C, Meleshin M, Steegborn C, Schutkowski M. A Novel Continuous Assay for the Deacylase Sirtuin 5 and Other Deacetylases. J Med Chem 2015; 58:7217-23. [PMID: 26308971 DOI: 10.1021/acs.jmedchem.5b00293] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sirtuins are NAD(+) dependent lysine deacylases involved in many regulatory processes like control of metabolic pathways, DNA repair, and stress response. Modulators of sirtuin activity are needed as tools for uncovering the biological function of these enzymes and as potential therapeutics. Systematic discovery of such modulators is hampered by the lack of efficient and simple continuous activity assays running at low sirtuin concentrations in microtiter plates. Here we describe an improved continuous sirtuin 5 assay based on the coupling of the sirtuin reaction to a proteolytic cleavage using internally fluorescence-quenched substrates. Systematic optimization of a carbamoyl phosphate synthetase 1 derived, glutarylated peptide yielded a Sirt5 substrate with k(cat)/K(M) value of 337,000 M(-1) s(-1), which represents the best sirtuin substrate described so far. These extraordinary substrate properties allowed reliable determination of Ki values for different inhibitors in the presence of only 10 nM sirtuin in microtiter plate format. Assay conditions could be transferred effectively to other lysine deacetylases, like sirtuin 2 and sirtuin 3, which now enables more efficient development of sirtuin targeting drugs.
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Affiliation(s)
- Claudia Roessler
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Christian Tüting
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Marat Meleshin
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth , Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Mike Schutkowski
- Department of Enzymology, Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
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426
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Singhal A, Arora G, Virmani R, Kundu P, Khanna T, Sajid A, Misra R, Joshi J, Yadav V, Samanta S, Saini N, Pandey AK, Visweswariah SS, Hentschker C, Becher D, Gerth U, Singh Y. Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase. J Biol Chem 2015; 290:26218-34. [PMID: 26350458 DOI: 10.1074/jbc.m115.687269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 02/02/2023] Open
Abstract
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.
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Affiliation(s)
- Anshika Singhal
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Gunjan Arora
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India, the Translational Health Science and Technology Institute, Faridabad 121001, India
| | - Richa Virmani
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Parijat Kundu
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Tanya Khanna
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Andaleeb Sajid
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Jayadev Joshi
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vikas Yadav
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Sintu Samanta
- the Indian Institute of Science, Bangalore 560012, India, and
| | - Neeru Saini
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Amit K Pandey
- the Translational Health Science and Technology Institute, Faridabad 121001, India,
| | | | - Christian Hentschker
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Dörte Becher
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Ulf Gerth
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Yogendra Singh
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India,
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427
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Zhao Y, Garcia BA. Comprehensive Catalog of Currently Documented Histone Modifications. Cold Spring Harb Perspect Biol 2015; 7:a025064. [PMID: 26330523 DOI: 10.1101/cshperspect.a025064] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
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Affiliation(s)
- Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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428
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Hentchel KL, Escalante-Semerena JC. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Microbiol Mol Biol Rev 2015; 79:321-46. [PMID: 26179745 PMCID: PMC4503791 DOI: 10.1128/mmbr.00020-15] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. Although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic acids (e.g., short-, medium-, and long-chain mono- and dicarboxylic aliphatics and aromatics) to modify a large suite of targets. Acetylation of biomolecules has been studied for decades within the context of histone-dependent regulation of gene expression and antibiotic resistance. It was not until the early 2000s that the connection between metabolism, physiology, and protein acetylation was reported. This was the first instance of a metabolic enzyme (acetyl coenzyme A [acetyl-CoA] synthetase) whose activity was controlled by acetylation via a regulatory system responsive to physiological cues. The above-mentioned system was comprised of an acyltransferase and a partner deacylase. Given the reversibility of the acylation process, this system is also referred to as reversible lysine acylation (RLA). A wealth of information has been obtained since the discovery of RLA in prokaryotes, and we are just beginning to visualize the extent of the impact that this regulatory system has on cell function.
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Affiliation(s)
- Kristy L Hentchel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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429
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Wang Y, Han Y, Fan E, Zhang K. Analytical strategies used to identify the readers of histone modifications: A review. Anal Chim Acta 2015; 891:32-42. [PMID: 26388362 DOI: 10.1016/j.aca.2015.06.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
Abstract
The so-called "readers" of histone post-translational modifications (HPTMs) refer to proteins or complexes that are recruited to HPTMs thus eventually regulate gene transcription. To identify these "readers", mass spectrometry plays an essential role following various enriching strategies. These enriching methods include the use of modified histone peptides/proteins or chemically synthesized histones/nucleosomes containing desired HPTMs to enrich the readers of HPTMs. Despite the peptide- or protein-based assay is straightforward and easy to perform for most labs, this strategy has limited applications for those weak or combinational interactions among various HPTMs and false-positive results are a potential big problem. While the results derived from synthesized histone proteins/nucleosomes is more reliable as it mimics the real chromatic conditions thus is able to analyze the binders of those cross-talked HPTMs, usually the synthesis is so difficult that their applications are impeded for high throughput analysis. In this review, an overview of these analytical techniques is provided and their advantages and disadvantages are discussed.
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Affiliation(s)
- Ye Wang
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Yanpu Han
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Jungong Road No. 516, 200093 Shanghai, China.
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, 300070 Tianjin, China; Department of Chemistry, Nankai University, 300071 Tianjin, China.
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430
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Montgomery DC, Sorum AW, Guasch L, Nicklaus MC, Meier JL. Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors. ACTA ACUST UNITED AC 2015; 22:1030-1039. [PMID: 26190825 DOI: 10.1016/j.chembiol.2015.06.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
The finding that chromatin modifications are sensitive to changes in cellular cofactor levels potentially links altered tumor cell metabolism and gene expression. However, the specific enzymes and metabolites that connect these two processes remain obscure. Characterizing these metabolic-epigenetic axes is critical to understanding how metabolism supports signaling in cancer, and developing therapeutic strategies to disrupt this process. Here, we describe a chemical approach to define the metabolic regulation of lysine acetyltransferase (KAT) enzymes. Using a novel chemoproteomic probe, we identify a previously unreported interaction between palmitoyl coenzyme A (palmitoyl-CoA) and KAT enzymes. Further analysis reveals that palmitoyl-CoA is a potent inhibitor of KAT activity and that fatty acyl-CoA precursors reduce cellular histone acetylation levels. These studies implicate fatty acyl-CoAs as endogenous regulators of histone acetylation, and suggest novel strategies for the investigation and metabolic modulation of epigenetic signaling.
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Affiliation(s)
- David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Alexander W Sorum
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
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431
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Kosono S, Tamura M, Suzuki S, Kawamura Y, Yoshida A, Nishiyama M, Yoshida M. Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source. PLoS One 2015; 10:e0131169. [PMID: 26098117 PMCID: PMC4476798 DOI: 10.1371/journal.pone.0131169] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/29/2015] [Indexed: 11/19/2022] Open
Abstract
Lysine residues can be post-translationally modified by various acyl modifications in bacteria and eukarya. Here, we showed that two major acyl modifications, acetylation and succinylation, were changed in response to the carbon source in the Gram-positive model bacterium Bacillus subtilis. Acetylation was more common when the cells were grown on glucose, glycerol, or pyruvate, whereas succinylation was upregulated when the cells were grown on citrate, reflecting the metabolic states that preferentially produce acetyl-CoA and succinyl-CoA, respectively. To identify and quantify changes in acetylation and succinylation in response to the carbon source, we performed a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate. We identified 629 acetylated proteins with 1355 unique acetylation sites and 204 succinylated proteins with 327 unique succinylation sites. Acetylation targeted different metabolic pathways under the two growth conditions: branched-chain amino acid biosynthesis and purine metabolism in glucose and the citrate cycle in citrate. Succinylation preferentially targeted the citrate cycle in citrate. Acetylation and succinylation mostly targeted different lysine residues and showed a preference for different residues surrounding the modification sites, suggesting that the two modifications may depend on different factors such as characteristics of acyl-group donors, molecular environment of the lysine substrate, and/or the modifying enzymes. Changes in acetylation and succinylation were observed in proteins involved in central carbon metabolism and in components of the transcription and translation machineries, such as RNA polymerase and the ribosome. Mutations that modulate protein acylation affected B. subtilis growth. A mutation in acetate kinase (ackA) increased the global acetylation level, suggesting that acetyl phosphate-dependent acetylation is common in B. subtilis, just as it is in Escherichia coli. Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.
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Affiliation(s)
- Saori Kosono
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- * E-mail:
| | - Masaru Tamura
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shota Suzuki
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yumi Kawamura
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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432
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Nishida Y, Rardin MJ, Carrico C, He W, Sahu AK, Gut P, Najjar R, Fitch M, Hellerstein M, Gibson BW, Verdin E. SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target. Mol Cell 2015; 59:321-32. [PMID: 26073543 DOI: 10.1016/j.molcel.2015.05.022] [Citation(s) in RCA: 358] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 03/27/2015] [Accepted: 05/11/2015] [Indexed: 02/01/2023]
Abstract
Protein acylation links energetic substrate flux with cellular adaptive responses. SIRT5 is a NAD(+)-dependent lysine deacylase and removes both succinyl and malonyl groups. Using affinity enrichment and label free quantitative proteomics, we characterized the SIRT5-regulated lysine malonylome in wild-type (WT) and Sirt5(-/-) mice. 1,137 malonyllysine sites were identified across 430 proteins, with 183 sites (from 120 proteins) significantly increased in Sirt5(-/-) animals. Pathway analysis identified glycolysis as the top SIRT5-regulated pathway. Importantly, glycolytic flux was diminished in primary hepatocytes from Sirt5(-/-) compared to WT mice. Substitution of malonylated lysine residue 184 in glyceraldehyde 3-phosphate dehydrogenase with glutamic acid, a malonyllysine mimic, suppressed its enzymatic activity. Comparison with our previous reports on acylation reveals that malonylation targets a different set of proteins than acetylation and succinylation. These data demonstrate that SIRT5 is a global regulator of lysine malonylation and provide a mechanism for regulation of energetic flux through glycolysis.
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Affiliation(s)
- Yuya Nishida
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew J Rardin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Chris Carrico
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wenjuan He
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexandria K Sahu
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Philipp Gut
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rami Najjar
- Cell Signaling Technology, Inc, 3 Trask Lane, Danvers, MA 01923, USA
| | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; KineMed, Inc., Emeryville, CA 94608, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
| | - Eric Verdin
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA 94158, USA.
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433
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Karkashon S, Raghupathy R, Bhatia H, Dutta A, Hess S, Higgs J, Tifft CJ, Little JA. Intermediaries of branched chain amino acid metabolism induce fetal hemoglobin, and repress SOX6 and BCL11A, in definitive erythroid cells. Blood Cells Mol Dis 2015; 55:161-7. [PMID: 26142333 DOI: 10.1016/j.bcmd.2015.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 05/25/2015] [Indexed: 01/19/2023]
Abstract
High levels of fetal hemoglobin (HbF) can ameliorate human β-globin gene disorders. The short chain fatty acid butyrate is the paradigmatic metabolic intermediary that induces HbF. Inherited disorders of branched-chain amino acid (BCAA) metabolism have been associated with supranormal HbF levels beyond infancy, e.g., propionic acidemia (PA) and methylmalonic acidemia (MMA). We tested intermediaries of BCAA metabolism for their effects on definitive erythropoiesis. Like butyrate, the elevated BCAA intermediaries isovalerate, isobutyrate, and propionate, induce fetal globin gene expression in murine EryD in vitro, are associated with bulk histone H3 hyperacylation, and repress the transcription of key gamma globin regulatory factors, notably BCL11A and SOX6. Metabolic intermediaries that are elevated in Maple Syrup Urine Disease (MSUD) affect none of these processes. Percent HbF and gamma (γ) chain isoforms were also measured in non-anemic, therapeutically optimized subjects with MSUD (Group I, n=6) or with Isovaleric Acidemia (IVA), MMA, or PA (Group II, n=5). Mean HbF was 0.24 ± 0.15% in Group I and 0.87 ± 0.13% in Group II (p=.01); only the Gγ isoform was detected. We conclude that a family of biochemically related intermediaries of branched chain amino acid metabolism induces fetal hemoglobin during definitive erythropoiesis, with mechanisms that mirror those so far identified for butyrate.
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Affiliation(s)
- Shay Karkashon
- Division of Hematology, Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, 1300 Morris Park Blvd., Bronx, NY 10461, United States
| | - Radha Raghupathy
- Division of Hematology, Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, 1300 Morris Park Blvd., Bronx, NY 10461, United States
| | - Himanshu Bhatia
- Division of Hematology, Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, 1300 Morris Park Blvd., Bronx, NY 10461, United States
| | - Amrita Dutta
- Division of Hematology, Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, 1300 Morris Park Blvd., Bronx, NY 10461, United States
| | - Sonja Hess
- California Institute of Technology, Beckman Institute, Proteome Exploration Laboratory, 1200 E California Blvd, MC139-74, Pasadena, CA 91125, United States
| | - Jaimie Higgs
- Division of Genetics and Metabolism, Center for Hospital-based Specialties, Children's National Medical Center, 111 Michigan Ave. N.W., Washington, DC 20010-2970, United States
| | - Cynthia J Tifft
- Division of Genetics and Metabolism, Center for Hospital-based Specialties, Children's National Medical Center, 111 Michigan Ave. N.W., Washington, DC 20010-2970, United States
| | - Jane A Little
- Division of Hematology, Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, 1300 Morris Park Blvd., Bronx, NY 10461, United States.
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434
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Knight WA, Cropp TA. Genetic encoding of the post-translational modification 2-hydroxyisobutyryl-lysine. Org Biomol Chem 2015; 13:6479-81. [PMID: 25999185 DOI: 10.1039/c5ob00283d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the synthesis and genetic encoding of a recently discovered post-translational modification, 2-hydroxyisobutyryl-lysine, to the genetic code of E. coli. The production of homogeneous proteins containing this amino acid will facilitate the study of modification in full-length proteins.
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Affiliation(s)
- William A Knight
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, USA.
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435
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Signalling functions of coenzyme A and its derivatives in mammalian cells. Biochem Soc Trans 2015; 42:1056-62. [PMID: 25110002 DOI: 10.1042/bst20140146] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In all living organisms, CoA (coenzyme A) is synthesized in a highly conserved process that requires pantothenic acid (vitamin B5), cysteine and ATP. CoA is uniquely designed to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. The role of CoA and its thioester derivatives, including acetyl-CoA, malonyl-CoA and HMG-CoA (3-hydroxy-3-methylglutaryl-CoA), in the regulation of cellular metabolism has been extensively studied and documented. The main purpose of the present review is to summarize current knowledge on extracellular and intracellular signalling functions of CoA/CoA thioesters and to speculate on future developments in this area of research.
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436
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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437
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Wilkins BJ, Hahn LE, Heitmüller S, Frauendorf H, Valerius O, Braus GH, Neumann H. Genetically encoding lysine modifications on histone H4. ACS Chem Biol 2015; 10:939-44. [PMID: 25590375 DOI: 10.1021/cb501011v] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Post-translational modifications of proteins are important modulators of protein function. In order to identify the specific consequences of individual modifications, general methods are required for homogeneous production of modified proteins. The direct installation of modified amino acids by genetic code expansion facilitates the production of such proteins independent of the knowledge and availability of the enzymes naturally responsible for the modification. The production of recombinant histone H4 with genetically encoded modifications has proven notoriously difficult in the past. Here, we present a general strategy to produce histone H4 with acetylation, propionylation, butyrylation, and crotonylation on lysine residues. We produce homogeneous histone H4 containing up to four simultaneous acetylations to analyze the impact of the modifications on chromatin array compaction. Furthermore, we explore the ability of antibodies to discriminate between alternative lysine acylations by incorporating these modifications in recombinant histone H4.
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Affiliation(s)
- Bryan J. Wilkins
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Liljan E. Hahn
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Svenja Heitmüller
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Holm Frauendorf
- Institute
for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Oliver Valerius
- Institute
for Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Gerhard H. Braus
- Institute
for Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Heinz Neumann
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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438
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Sabari BR, Tang Z, Huang H, Yong-Gonzalez V, Molina H, Kong HE, Dai L, Shimada M, Cross JR, Zhao Y, Roeder RG, Allis CD. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol Cell 2015; 58:203-15. [PMID: 25818647 PMCID: PMC4501262 DOI: 10.1016/j.molcel.2015.02.029] [Citation(s) in RCA: 435] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 12/29/2014] [Accepted: 02/20/2015] [Indexed: 01/30/2023]
Abstract
Acetylation of histones at DNA regulatory elements plays a critical role in transcriptional activation. Histones are also modified by other acyl moieties, including crotonyl, yet the mechanisms that govern acetylation versus crotonylation and the functional consequences of this "choice" remain unclear. We show that the coactivator p300 has both crotonyltransferase and acetyltransferase activities, and that p300-catalyzed histone crotonylation directly stimulates transcription to a greater degree than histone acetylation. Levels of histone crotonylation are regulated by the cellular concentration of crotonyl-CoA, which can be altered through genetic and environmental perturbations. In a cell-based model of transcriptional activation, increasing or decreasing the cellular concentration of crotonyl-CoA leads to enhanced or diminished gene expression, respectively, which correlates with the levels of histone crotonylation flanking the regulatory elements of activated genes. Our findings support a general principle wherein differential histone acylation (i.e., acetylation versus crotonylation) couples cellular metabolism to the regulation of gene expression.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Ha Eun Kong
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Lunzhi Dai
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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439
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Morceau F, Chateauvieux S, Orsini M, Trécul A, Dicato M, Diederich M. Natural compounds and pharmaceuticals reprogram leukemia cell differentiation pathways. Biotechnol Adv 2015; 33:785-97. [PMID: 25886879 DOI: 10.1016/j.biotechadv.2015.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/18/2015] [Accepted: 03/29/2015] [Indexed: 12/22/2022]
Abstract
In addition to apoptosis resistance and cell proliferation capacities, the undifferentiated state also characterizes most cancer cells, especially leukemia cells. Cell differentiation is a multifaceted process that depends on complex regulatory networks that involve transcriptional, post-transcriptional and epigenetic regulation of gene expression. The time- and spatially-dependent expression of lineage-specific genes and genes that control cell growth and cell death is implicated in the process of maturation. The induction of cancer cell differentiation is considered an alternative approach to elicit cell death and proliferation arrest. Differentiation therapy has mainly been developed to treat acute myeloid leukemia, notably with all-trans retinoic acid (ATRA). Numerous molecules from diverse natural or synthetic origins are effective alone or in association with ATRA in both in vitro and in vivo experiments. During the last two decades, pharmaceuticals and natural compounds with various chemical structures, including alkaloids, flavonoids and polyphenols, were identified as potential differentiating agents of hematopoietic pathways and osteogenesis.
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Affiliation(s)
- Franck Morceau
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Sébastien Chateauvieux
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Marion Orsini
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Anne Trécul
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Marc Diederich
- College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
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440
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Rousseaux S, Khochbin S. Histone Acylation beyond Acetylation: Terra Incognita in Chromatin Biology. CELL JOURNAL 2015; 17:1-6. [PMID: 25870829 PMCID: PMC4393657 DOI: 10.22074/cellj.2015.506] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 12/24/2014] [Indexed: 12/16/2022]
Abstract
Histone acetylation, one of the first and best studied histone post-translational modifications (PTMs), as well as the factors involved in its deposition (writers), binding (readers) and removal (erasers), have been shown to act at the heart of regulatory circuits controlling essential cellular functions. The identification of a variety of competing histone lysine-modifying acyl groups including propionyl, butyryl, 2-hydroxyisobutyryl, crotonyl, malonyl, succinyl and glutaryl, raises numerous questions on their functional significance, the molecular systems that manage their establishment, removal and interplay with the well-known acetylation-based mechanisms. Detailed and large-scale investigations of two of these new histone PTMs, crotonylation and 2-hydroxyisobutyrylation, along with histone acetylation, in the context of male genome programming, where stage-specific gene expression programs are switched on and off in turn, have shed light on their functional contribution to the epigenome for the first time. These initial investigations fired many additional questions, which remain to be explored. This review surveys the major results taken from these two new histone acylations and discusses the new biology that is emerging based on the diversity of histone lysine acylations.
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Affiliation(s)
| | - Saadi Khochbin
- INSERMU823University Grenoble-AlpesInstitute Albert BonniotGrenobleF-38700France
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441
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Ourailidou ME, Dockerty P, Witte M, Poelarends GJ, Dekker FJ. Metabolic alkene labeling and in vitro detection of histone acylation via the aqueous oxidative Heck reaction. Org Biomol Chem 2015; 13:3648-53. [PMID: 25672493 PMCID: PMC4871226 DOI: 10.1039/c4ob02502d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The detection of protein lysine acylations remains a challenge due to lack of specific antibodies for acylations with various chain lengths. This problem can be addressed by metabolic labeling techniques using carboxylates with reactive functionalities. Subsequent chemoselective reactions with a complementary moiety connected to a detection tag enable the visualization and quantification of the protein lysine acylome. In this study, we present EDTA-Pd(II) as a novel catalyst for the oxidative Heck reaction on protein-bound alkenes, which allows employment of fully aqueous reaction conditions. We used this reaction to monitor histone lysine acylation in vitro after metabolic incorporation of olefinic carboxylates as chemical reporters.
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Affiliation(s)
- Maria E Ourailidou
- Pharmaceutical Gene Modulation, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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442
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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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443
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Benjamin R Sabari
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10021, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10021, USA
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
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444
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Chemical proteomics approaches to examine novel histone posttranslational modifications. Curr Opin Chem Biol 2015; 24:80-90. [DOI: 10.1016/j.cbpa.2014.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023]
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445
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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: 114] [Impact Index Per Article: 11.4] [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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446
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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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447
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Zhang K, Li L, Zhu M, Wang G, Xie J, Zhao Y, Fan E, Xu L, Li E. Comparative analysis of histone H3 and H4 post-translational modifications of esophageal squamous cell carcinoma with different invasive capabilities. J Proteomics 2015; 112:180-9. [PMID: 25234497 DOI: 10.1016/j.jprot.2014.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/28/2014] [Accepted: 09/04/2014] [Indexed: 02/05/2023]
Abstract
UNLABELLED Eukaryotic DNA is packaged into a chromatin with the help of four core histones (H2A, H2B, H3, and H4). Diverse histone post-translational modifications (PTMs) are hence involved in the regulation of gene transcription. However, how this regulation does work is still poorly understood and lacks details. Here we used the mass spectrometry-based proteomics approach to perform a comparative analysis of histone marks at a global level in two phenotypes of esophageal squamous cell carcinoma (ESCC) with different invasiveness. We obtained a comprehensive profiling of histone H3 and H4 PTMs including lysine methylation, acetylation and novel butyrylation. The correlation between histone marks and cancer invasive capabilities was further characterized and one distinguishable PTM, H4K79me2 was discovered and verified in this study. Immunohistochemistry analysis suggests that abnormal level of H4K79me2 may be related to poor survival of ESCC patients. Our results enrich the dataset of the feature pattern of global histone PTMs in ESCC cell lines. BIOLOGICAL SIGNIFICANCE Core histone proteins, decorated by multiple biological significant protein post-translational modifications (PTMs) such as lysine acetylation and lysine methylation, are considered to regulate gene transcription and be associated with the development of cancer. Recent studies have further shown that global level of histone modifications is the potential hallmark of cancer to predict the clinical outcomes of human cancers. However, the regulation mechanism is largely unknown. Here we used the mass spectrometry based proteomics coupled with stable isotope labeling with amino acids in cell culture (SILAC) to characterize the global levels of histone marks in two phenotypes of esophageal squamous cell carcinoma (ESCC) cell lines with different invasive capabilities. To the best of our knowledge, it is the first report about the comparative analysis for histone marks of the different invasive ESCC cell lines. A significantly differential level of histone modification, H4K79me2, was determined and verified. Immunohistochemistry analysis further suggests that abnormal level of H4K79me2 may be related to poor survival of ESCC patients. Our results could contribute to understanding the different expressions of global histone PTMs in different invasive ESCC cell lines.
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Affiliation(s)
- Kai Zhang
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Department of Biochemistry and Molecular Biology, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Medicinal Chemical Biology, Department of Chemistry, Nankai University, Tianjin 300071, China.
| | - Liyan Li
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China
| | - Mengxiao Zhu
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China
| | - Guojuan Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Jianjun Xie
- Department of Biochemistry and Molecular Biology, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Yunlong Zhao
- State Key Laboratory of Medicinal Chemical Biology, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Enguo Fan
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Liyan Xu
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
| | - Enmin Li
- Department of Biochemistry and Molecular Biology, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
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448
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Sadakierska-Chudy A, Filip M. A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res 2014; 27:172-97. [PMID: 25516120 PMCID: PMC4300421 DOI: 10.1007/s12640-014-9508-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/31/2022]
Abstract
The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.
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Affiliation(s)
- Anna Sadakierska-Chudy
- Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343, Kraków, Poland,
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449
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Wu Z, Cheng Z, Sun M, Wan X, Liu P, He T, Tan M, Zhao Y. A chemical proteomics approach for global analysis of lysine monomethylome profiling. Mol Cell Proteomics 2014; 14:329-39. [PMID: 25505155 DOI: 10.1074/mcp.m114.044255] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases.
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Affiliation(s)
- Zhixiang Wu
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Zhongyi Cheng
- §Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, P.R. China
| | - Mingwei Sun
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Xuelian Wan
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Ping Liu
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Tieming He
- §Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, P.R. China
| | - Minjia Tan
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China;
| | - Yingming Zhao
- From the ‡The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, P.R. China; ¶Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois
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450
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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: 15] [Impact Index Per Article: 1.4] [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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