1
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López-Rivera F, Chuang J, Spatt D, Gopalakrishnan R, Winston F. Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae. Genetics 2022; 222:iyac125. [PMID: 35977387 PMCID: PMC9526074 DOI: 10.1093/genetics/iyac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans as an integral member of the RNA polymerase II elongation complex. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated 8 suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA coactivator complex, Sgf73. The identification of these distinct groups suggests that there are multiple ways in which Spn1 bypass can occur, including changes in histone acetylation and alterations in other histone chaperones. Thus, Spn1 may function to overcome repressive chromatin by multiple mechanisms during transcription. Our results suggest that bypassing a subset of these functions allows viability in the absence of Spn1.
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Affiliation(s)
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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2
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Hsu KF, Wilkins SE, Hopkinson RJ, Sekirnik R, Flashman E, Kawamura A, McCullagh JS, Walport LJ, Schofield CJ. Hypoxia and hypoxia mimetics differentially modulate histone post-translational modifications. Epigenetics 2021; 16:14-27. [PMID: 32609604 PMCID: PMC7889154 DOI: 10.1080/15592294.2020.1786305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) to the tails of the core histone proteins are critically involved in epigenetic regulation. Hypoxia affects histone modifications by altering the activities of histone-modifying enzymes and the levels of hypoxia-inducible factor (HIF) isoforms. Synthetic hypoxia mimetics promote a similar response, but how accurately the hypoxia mimetics replicate the effects of limited oxygen availability on the levels of histone PTMs is uncertain. Here we report studies on the profiling of the global changes to PTMs on intact histones in response to hypoxia/hypoxia-related stresses using liquid chromatography-mass spectrometry (LC-MS). We demonstrate that intact protein LC-MS profiling is a relatively simple and robust method for investigating potential effects of drugs on histone modifications. The results provide insights into the profiles of PTMs associated with hypoxia and inform on the extent to which hypoxia and hypoxia mimetics cause similar changes to histones. These findings imply chemically-induced hypoxia does not completely replicate the substantial effects of physiological hypoxia on histone PTMs, highlighting that caution should be used in interpreting data from their use.
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Affiliation(s)
- Kuo-Feng Hsu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sarah E. Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, Leicester, UK
| | - Rok Sekirnik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Emily Flashman
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, UK
| | - James S.O. McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
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3
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Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Methods 2020; 184:86-92. [PMID: 32070774 PMCID: PMC7727281 DOI: 10.1016/j.ymeth.2020.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Middle-down proteomics has emerged as the method of choice to study combinatorial histone post translational modifications (PTMs). In the common bottom-up workflow, histones are digested into relatively short peptides (4-20 aa), separated using reversed-phase chromatography and analyzed using typical proteomics methods in mass spectrometry. In middle-down, histones are cleaved into longer polypeptides (50-60 aa) mostly corresponding to their N-terminal tails, resolved using weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) and analyzed with less conventional mass spectrometry, i.e. using Electron Transfer Dissociation (ETD) for analyte fragmentation. Middle-down is not nearly as utilized as bottom-up for PTM analysis, partially due to its limited reproducibility and robustness. This has also limited the establishment of rigorous benchmarks to discriminate good vs poor quality experiments. Here, we describe critical aspects of the middle-down workflow to assist the user in evaluating the presence of biased and misleading results. Specifically, we tested the use of porous graphitic carbon (PGC) during the desalting step, demonstrating that desalting using only C18 material leads to sample loss. We also tested different salts in the WCX-HILIC buffers for their effect on retention, selectivity, and reproducibility of analysis of variants of histone tail fragments, in particular replacing ammonium ion with ethylenediammonium ion in buffer A. These substitutions had marked effects on selectivity and retention. Our results provide a streamlined way to evaluate middle-down performance to identify and quantify combinatorial histone PTMs.
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Affiliation(s)
- Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariel R Mendoza
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Congcong Lu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Plymire DA, Wing CE, Robinson DE, Patrie SM. Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12030-12038. [PMID: 29016107 DOI: 10.1021/acs.analchem.7b02426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Myelin basic protein (MBP) plays an important structural and functional role in the neuronal myelin sheath. Translated MBP exhibits extreme microheterogeneity with numerous alternative splice variants (ASVs) and post-translational modifications (PTMs) reportedly tied to central nervous system maturation, myelin stability, and the pathobiology of various de- and dys-myelinating disorders. Conventional bioanalytical tools cannot efficiently examine ASV and PTM events simultaneously, which limits understanding of the role of MBP microheterogeneity in human physiology and disease. To address this need, we report on a top-down proteomics pipeline that combines superficially porous reversed-phase liquid chromatography (SPLC), Fourier transform mass spectrometry (FTMS), data-independent acquisition (DIA) with nozzle-skimmer dissociation (NSD), and aligned data processing resources to rapidly characterize abundant MBP proteoforms within murine tissue. The three-tier proteoform identification and characterization workflow resolved four known MBP ASVs and hundreds of differentially modified states from a single 90 min SPLC-FTMS run on ∼0.5 μg of material. This included 323 proteoforms for the 14.1 kDa ASV alone. We also identified two novel ASVs from an alternative transcriptional start site (ATSS) of the MBP gene as well as a never before characterized S-acylation event linking palmitic acid, oleic acid, and stearic acid at C78 of the 17.125 kDa ASV.
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Affiliation(s)
- Daniel A Plymire
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Casey E Wing
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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5
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Zheng S, Sun M, Zhang K, Gu J, Guo Z, Tian S, Zhai G, He X, Jin Y, Zhang Y. Profiling post-translational modifications of histones in neural differentiation of embryonic stem cells using liquid chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1017-1018:36-44. [PMID: 26945132 DOI: 10.1016/j.jchromb.2016.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/10/2016] [Accepted: 02/14/2016] [Indexed: 12/21/2022]
Abstract
The neural differentiation of embryonic stem cells (ESCs) is of great significance for understanding of the mechanism of diseases. Histone post-translational modifications (HPTMs) play a key role in the regulation of ESCs differentiation. Here, we combined the stable isotope chemical derivatization with nano-HPLC-mass spectrometry (MS) for comprehensive analysis and quantification of histone post-translational modifications (HPTMs) in mouse embryonic stem cells (mESCs) and neural progenitor cells (mNPCs) that was derived from ESCs. We identified 85 core HPTM sites in ESCs and 78HPTM sites in NPCs including some novel lysine modifications. Our quantitative analysis results further revealed the changes of HPTMs from ESCs to NPCs and suggested effect of combinational HPTMs in the differentiation. This study demonstrates that HPLC-MS-based quantitative proteomics has a considerable advantage on quantification of combinational PTMs and expands our understanding of HPTMs in the differentiation.
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Affiliation(s)
- Shuzhen Zheng
- Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Ming Sun
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kai Zhang
- Department of Chemistry, Nankai University, Tianjin 300071, China; 2011Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070 Tianjin, China.
| | - Junjie Gu
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhenchang Guo
- 2011Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070 Tianjin, China
| | - Shanshan Tian
- 2011Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070 Tianjin, China
| | - Guijin Zhai
- 2011Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070 Tianjin, China
| | - Xiwen He
- Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Ying Jin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yukui Zhang
- Department of Chemistry, Nankai University, Tianjin 300071, China; National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, China
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6
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Chen J, Liu Z, Wang F, Mao J, Zhou Y, Liu J, Zou H, Zhang Y. Enhancing the performance of LC-MS for intact protein analysis by counteracting the signal suppression effects of trifluoroacetic acid during electrospray. Chem Commun (Camb) 2015; 51:14758-60. [DOI: 10.1039/c5cc06072a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop an acidic vapor assisted electrospray ionization strategy within an enclosed electrospray ionization source to counteract the ion suppression effects caused by trifluoroacetic acid.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Zheyi Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Fangjun Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Jiawei Mao
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Ye Zhou
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Jing Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
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7
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Ntai I, Kim K, Fellers RT, Skinner OS, Smith A, Early BP, Savaryn JP, LeDuc RD, Thomas PM, Kelleher NL. Applying label-free quantitation to top down proteomics. Anal Chem 2014; 86:4961-8. [PMID: 24807621 PMCID: PMC4033644 DOI: 10.1021/ac500395k] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/28/2014] [Indexed: 01/16/2023]
Abstract
With the prospect of resolving whole protein molecules into their myriad proteoforms on a proteomic scale, the question of their quantitative analysis in discovery mode comes to the fore. Here, we demonstrate a robust pipeline for the identification and stringent scoring of abundance changes of whole protein forms <30 kDa in a complex system. The input is ~100-400 μg of total protein for each biological replicate, and the outputs are graphical displays depicting statistical confidence metrics for each proteoform (i.e., a volcano plot and representations of the technical and biological variation). A key part of the pipeline is the hierarchical linear model that is tailored to the original design of the study. Here, we apply this new pipeline to measure the proteoform-level effects of deleting a histone deacetylase (rpd3) in S. cerevisiae. Over 100 proteoform changes were detected above a 5% false positive threshold in WT vs the Δrpd3 mutant, including the validating observation of hyperacetylation of histone H4 and both H2B isoforms. Ultimately, this approach to label-free top down proteomics in discovery mode is a critical technical advance for testing the hypothesis that whole proteoforms can link more tightly to complex phenotypes in cell and disease biology than do peptides created in shotgun proteomics.
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Affiliation(s)
- Ioanna Ntai
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Kyunggon Kim
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Ryan T. Fellers
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Owen S. Skinner
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Archer
D. Smith
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Bryan P. Early
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - John P. Savaryn
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Richard D. LeDuc
- National
Center for Genome Analysis
Support, Indiana University, 2709 E. 10th Street, Bloomington, Indiana 47408, United States
| | - Paul M. Thomas
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
| | - Neil L. Kelleher
- Departments
of Chemistry, Molecular Biosciences and
the Proteomics Center of Excellence, 2145 N. Sheridan Road, Evanston, Illinois 60208, United
States
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8
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Catherman AD, Skinner OS, Kelleher NL. Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun 2014; 445:683-93. [PMID: 24556311 PMCID: PMC4103433 DOI: 10.1016/j.bbrc.2014.02.041] [Citation(s) in RCA: 319] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/10/2014] [Indexed: 12/29/2022]
Abstract
The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
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Affiliation(s)
- Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
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9
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Li M, Durbin KR, Sweet SMM, Tipton JD, Zheng Y, Kelleher NL. Oncogene-induced cellular senescence elicits an anti-Warburg effect. Proteomics 2013; 13:2585-96. [PMID: 23798001 DOI: 10.1002/pmic.201200298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 05/04/2013] [Accepted: 06/12/2013] [Indexed: 11/06/2022]
Abstract
Cellular senescence, an irreversible cell cycle arrest induced by a diversity of stimuli, has been considered as an innate tumor suppressing mechanism with implications and applications in cancer therapy. Using a targeted proteomics approach, we show that fibroblasts induced into senescence by expression of oncogenic Ras exhibit a decrease of global acetylation on all core histones, consistent with formation of senescence-associated heterochromatic foci. We also detected clear increases in repressive markers (e.g. >50% elevation of H3K27me2/3) along with decreases in histone marks associated with increased transcriptional expression/elongation (e.g. H3K36me2/3). Despite the increases in repressive marks of chromatin, 179 loci (of 2206 total) were found to be upregulated by global quantitative proteomics. The changes in the cytosolic proteome indicated an upregulation of mitochondrial proteins and downregulation of proteins involved in glycolysis. These alterations in primary metabolism are opposite to the well-known Warburg effect observed in cancer cells. This study significantly improves our understanding of stress-induced senescence and provides a potential application for triggering it in antiproliferative strategies that target the primary metabolism in cancer cells.
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Affiliation(s)
- Mingxi Li
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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10
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Hersman E, Nelson DM, Griffith WP, Jelinek C, Cotter RJ. Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 312:5-16. [PMID: 22389584 PMCID: PMC3289288 DOI: 10.1016/j.ijms.2011.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The in vitro deuteroacetylation of histones obtained from biological sources has been used previously in bottom-up mass spectrometry analyses to quantitate the percent of endogenous acetylation of specific lysine sites and/or peptides. In this report, derivatization of unmodified lysine residues on histones is used in combination with high performance mass spectrometry, including combined HPLC MS/MS, to distinguish and quantitate endogenously acetylated isoforms occurring within the same tryptic peptide sequence and to extend this derivatization strategy to other post-translational modifications, specifically methylation, dimethylation and trimethylation. The in vitro deuteroacetylation of monomethylated lysine residues is observed, though dimethylated or trimethylated residues are not derivatised. Comparison of the relative intensities ascribed to the deuteroacetylated and monomethylated species with the deuteroacetylated but unmethylated analog, provides an opportunity to estimate the percent of methylation at that site. In addition to the observed fragmentation patterns, the very high mass accuracy available on the Orbitrap mass spectrometer can be used to confirm the structural isoforms, and in particular to distinguish between trimethylated and acetylated species.
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Affiliation(s)
- Elisabeth Hersman
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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11
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Affiliation(s)
- Feng Xian
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
| | - Christopher L. Hendrickson
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800
East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Alan G. Marshall
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800
East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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12
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Roth MJ, Plymire DA, Chang AN, Kim J, Maresh EM, Larson SE, Patrie SM. Sensitive and Reproducible Intact Mass Analysis of Complex Protein Mixtures with Superficially Porous Capillary Reversed-Phase Liquid Chromatography Mass Spectrometry. Anal Chem 2011; 83:9586-92. [DOI: 10.1021/ac202339x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Michael J. Roth
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Daniel A. Plymire
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Audrey N. Chang
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Jaekuk Kim
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Erica M. Maresh
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Shane E. Larson
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Steven M. Patrie
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
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13
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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14
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Young NL, Dimaggio PA, Garcia BA. The significance, development and progress of high-throughput combinatorial histone code analysis. Cell Mol Life Sci 2010; 67:3983-4000. [PMID: 20683756 PMCID: PMC11115713 DOI: 10.1007/s00018-010-0475-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 07/05/2010] [Accepted: 07/20/2010] [Indexed: 01/18/2023]
Abstract
The physiological state of eukaryotic DNA is chromatin. Nucleosomes, which consist of DNA in complex with histones, are the fundamental unit of chromatin. The post-translational modifications (PTMs) of histones play a critical role in the control of gene transcription, epigenetics and other DNA-templated processes. It has been known for several years that these PTMs function in concert to allow for the storage and transduction of highly specific signals through combinations of modifications. This code, the combinatorial histone code, functions much like a bar code or combination lock providing the potential for massive information content. The capacity to directly measure these combinatorial histone codes has mostly been laborious and challenging, thus limiting efforts often to one or two samples. Recently, progress has been made in determining such information quickly, quantitatively and sensitively. Here we review both the historical and recent progress toward routine and rapid combinatorial histone code analysis.
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Affiliation(s)
- Nicolas L Young
- Department of Molecular Biology, Princeton University, 415 Schultz Laboratory, Princeton, NJ 08544, USA
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15
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Gurard-Levin ZA, Kilian KA, Kim J, Bähr K, Mrksich M. Peptide arrays identify isoform-selective substrates for profiling endogenous lysine deacetylase activity. ACS Chem Biol 2010; 5:863-73. [PMID: 20849068 PMCID: PMC2941244 DOI: 10.1021/cb100088g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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This paper reports the development of a class of isoform-selective peptide substrates for measuring endogenous lysine deacetylase (KDAC) activities in cell culture. The peptides were first identified by comparing the substrate specificity profiles of the four KDAC isoforms KDAC2, KDAC3, KDAC8, and sirtuin 1 (SIRT1) on a 361-member hexapeptide array wherein the two C-terminal residues to the acetylated lysine were varied. The arrays were prepared by immobilizing the peptides to a self-assembled monolayer of alkanethiolates on gold and could therefore be analyzed by a mass spectrometry technique termed SAMDI (self-assembled monolayers for matrix assisted laser desorption/ionization time-of-flight mass spectrometry). Arrays presenting the selective substrates were treated with nuclear extracts from HeLa, Jurkat, and smooth muscle cells and analyzed to measure endogenous deacetylase activities. We then use the arrays to profile KDAC activity through the HeLa cell cycle. We find that the activity profile of the KDAC3 selective peptide closely mirrors the changing acetylation state of the H4 histone, suggesting a role for this enzyme in cell cycle regulation. This work is significant because it describes a general route for identifying selective substrates that can be used to understand the differential roles of members of the deacetylase enzyme family in complex biological processes and further because the label-free approach avoids perturbation of enzyme activity that has plagued fluorescence-based assays.
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Affiliation(s)
- Zachary A. Gurard-Levin
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Kristopher A. Kilian
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Joohoon Kim
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Katinka Bähr
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Milan Mrksich
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
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16
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Contrepois K, Ezan E, Mann C, Fenaille F. Ultra-High Performance Liquid Chromatography−Mass Spectrometry for the Fast Profiling of Histone Post-Translational Modifications. J Proteome Res 2010; 9:5501-9. [DOI: 10.1021/pr100497a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Kévin Contrepois
- CEA, iBiTecS, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM) and Service de Pharmacologie et d’Immunoanalyse (SPI), F-91191 Gif Sur Yvette, France
| | - Eric Ezan
- CEA, iBiTecS, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM) and Service de Pharmacologie et d’Immunoanalyse (SPI), F-91191 Gif Sur Yvette, France
| | - Carl Mann
- CEA, iBiTecS, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM) and Service de Pharmacologie et d’Immunoanalyse (SPI), F-91191 Gif Sur Yvette, France
| | - François Fenaille
- CEA, iBiTecS, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM) and Service de Pharmacologie et d’Immunoanalyse (SPI), F-91191 Gif Sur Yvette, France
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17
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Dal Piaz F, Tosco A, Eletto D, Piccinelli AL, Moltedo O, Franceschelli S, Sbardella G, Remondelli P, Rastrelli L, Vesci L, Pisano C, De Tommasi N. The identification of a novel natural activator of p300 histone acetyltranferase provides new insights into the modulation mechanism of this enzyme. Chembiochem 2010; 11:818-27. [PMID: 20373302 DOI: 10.1002/cbic.200900721] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many severe human pathologies are related to alterations of the fine balance between histone acetylation and deacetylation; because not all such diseases involve hypoacetylation, but also hyperacetylation, compounds able to enhance or repress the activities of histone acetyltransferases (HATs) could be promising therapeutic agents. We evaluated in vitro and in cell the ability of eleven natural polyisoprenylated benzophenone derivatives to modulate the HAT activity of p300/CBP, an enzyme that plays a pivotal role in a variety of cellular processes. Some of the tested compounds bound efficiently to the p300/CBP protein: in particular, guttiferone A, guttiferone E and clusianone inhibit its HAT activity, whereas nemorosone showed a surprising ability to activate the enzyme. The ability of nemorosone to penetrate cell membranes and modulate histone acetylation into the cell together with its high affinity for the p300/CBP enzyme made this compound a suitable lead for the design of optimized anticancer drugs. Besides, the studies performed at a cellular and molecular level on both the inhibitors and the activator provided new insights into the modulation mechanism of p300/CBP by small molecules.
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Affiliation(s)
- Fabrizio Dal Piaz
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Salerno, Via Ponte Don Melillo 1, 84084 Fisciano, SA, Italy.
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