1
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Koudelka A, Buchan GJ, Cechova V, O'Brien JP, Liu H, Woodcock SR, Mullett SJ, Zhang C, Freeman BA, Gelhaus SL. Lipoxin A 4 yields an electrophilic 15-oxo metabolite that mediates FPR2 receptor-independent anti-inflammatory signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579101. [PMID: 38370667 PMCID: PMC10871244 DOI: 10.1101/2024.02.06.579101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The enzymatic oxidation of arachidonic acid is proposed to yield trihydroxytetraene species (termed lipoxins) that resolve inflammation via ligand activation of the formyl peptide receptor, FPR2. While cell and murine models activate signaling responses to synthetic lipoxins, primarily 5S,6R,15S-trihydroxy-7E,9E,11Z,13E-eicosatetraenoic acid (lipoxin A4, LXA4), there are expanding concerns about the biological formation, detection and signaling mechanisms ascribed to LXA4 and related di- and tri-hydroxy ω-6 and ω-3 fatty acids. Herein, the generation and actions of LXA4 and its primary 15-oxo metabolite were assessed in control, LPS-activated and arachidonic acid supplemented RAW 264.7 macrophages. Despite protein expression of all enzymes required for LXA4 synthesis, both LXA4 and its 15-oxo-LXA4 metabolite were undetectable. Moreover, synthetic LXA4 and the membrane permeable 15-oxo-LXA4 methyl ester that is rapidly de-esterified to 15-oxo-LXA4, displayed no ligand activity for the putative LXA4 receptor FPR2, as opposed to the FPR2 ligand WKYMVm. Alternatively, 15-oxo-LXA4, an electrophilic α,β-unsaturated ketone, alkylates nucleophilic amino acids such as cysteine to modulate redox-sensitive transcriptional regulatory protein and enzyme function. 15-oxo-LXA4 activated nuclear factor (erythroid related factor 2)-like 2 (Nrf2)-regulated gene expression of anti-inflammatory and repair genes and inhibited nuclear factor (NF)-κB-regulated pro-inflammatory mediator expression. LXA4 did not impact these macrophage anti-inflammatory and repair responses. In summary, these data show an absence of macrophage LXA4 formation and receptor-mediated signaling actions. Rather, if LXA4 were present in sufficient concentrations, this, and other more abundant mono- and poly-hydroxylated unsaturated fatty acids can be readily oxidized to electrophilic α,β-unsaturated ketone products that modulate the redox-sensitive cysteine proteome via G-protein coupled receptor-independent mechanisms.
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Affiliation(s)
- Adolf Koudelka
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Gregory J Buchan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Veronika Cechova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - James P O'Brien
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Steven R Woodcock
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Steven J Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
- Health Sciences Mass Spectrometry Core, University of Pittsburgh (Pittsburgh, PA 15213)
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
| | - Stacy L Gelhaus
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine (Pittsburgh, PA 15213)
- Health Sciences Mass Spectrometry Core, University of Pittsburgh (Pittsburgh, PA 15213)
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2
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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3
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Swenson CS, Pillai KS, Carlos AJ, Moellering RE. Spatial Chemoproteomics for Mapping the Active Proteome. Isr J Chem 2023; 63:e202200104. [PMID: 38046285 PMCID: PMC10688764 DOI: 10.1002/ijch.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 01/06/2023]
Abstract
Functional regulation of cell signaling through dynamic changes in protein activity state as well as spatial organization represent two dynamic, complex, and conserved phenomena in biology. Seemingly separate areas of -omics method development have focused on building tools that can detect and quantify protein activity states, as well as map sub-cellular and intercellular protein organization. Integration of these efforts, through the development of chemical tools and platforms that enable detection and quantification of protein functional states with spatial resolution provide opportunities to better understand heterogeneity in the proteome within cell organelles, multi-cellular tissues, and whole organisms. This review provides an overview of and considerations for major classes of chemical proteomic probes and technologies that enable protein activity mapping from sub-cellular compartments to live animals.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Kavya Smitha Pillai
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Anthony J Carlos
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
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4
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Tang KC, Maddox SM, Backus KM, Raj M. Tunable heteroaromatic azoline thioethers (HATs) for cysteine profiling. Chem Sci 2022; 13:763-774. [PMID: 35173941 PMCID: PMC8768877 DOI: 10.1039/d1sc04139h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
Here we report a new series of hydrolytically stable chemotype heteroaromatic azoline thioethers (HATs) to achieve highly selective, rapid, and efficient covalent labeling of cysteine under physiological conditions. Although the resulting cysteine-azoline conjugate is stable, we highlight traceless decoupling of the conjugate to afford unmodified starting components in response to reducing conditions. We demonstrated that HAT probes reverse the reactivity of nucleophilic cysteine to electrophilic dehydroalanine (Dha) under mild basic conditions. We demonstrated the umpolung capability of HAT probes for the modification of cysteine on peptides and proteins with various nucleophiles. We demonstrated that HAT probes increase the mass sensitivity of the modified peptides and proteins by 100 fold as compared to the classical methods. Finally, we extended the application of HAT probes for specific modification of cysteines in a complex cell lysate mixture.
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Affiliation(s)
- Kuei C Tang
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Sean M Maddox
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA Los Angeles CA 90095 USA.,Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA Los Angeles CA 90095 USA
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA Los Angeles CA 90095 USA.,Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA Los Angeles CA 90095 USA
| | - Monika Raj
- Department of Chemistry, Emory University Atlanta GA 30322 USA
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5
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Abegg D, Tomanik M, Qiu N, Pechalrieu D, Shuster A, Commare B, Togni A, Herzon SB, Adibekian A. Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway. J Am Chem Soc 2021; 143:20332-20342. [PMID: 34817176 DOI: 10.1021/jacs.1c09724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemoproteomic profiling of cysteines has emerged as a powerful method for screening the proteome-wide targets of cysteine-reactive fragments, drugs, and natural products. Herein, we report the development and an in-depth evaluation of a tetrafluoroalkyl benziodoxole (TFBX) as a cysteine-selective chemoproteomic probe. We show that this probe features numerous key improvements compared to the traditionally used cysteine-reactive probes, including a superior target occupancy, faster labeling kinetics, and broader proteomic coverage, thus enabling profiling of cysteines directly in live cells. In addition, the fluorine "signature" of probe 7 constitutes an additional advantage resulting in a more confident adduct-amino acid site assignment in mass-spectrometry-based identification workflows. We demonstrate the utility of our new probe for proteome-wide target profiling by identifying the cellular targets of (-)-myrocin G, an antiproliferative fungal natural product with a to-date unknown mechanism of action. We show that this natural product and a simplified analogue target the X-ray repair cross-complementing protein 5 (XRCC5), an ATP-dependent DNA helicase that primes DNA repair machinery for nonhomologous end joining (NHEJ) upon DNA double-strand breaks, making them the first reported inhibitors of this biomedically highly important protein. We further demonstrate that myrocins disrupt the interaction of XRCC5 with DNA leading to sensitization of cancer cells to the chemotherapeutic agent etoposide as well as UV-light-induced DNA damage. Altogether, our next-generation cysteine-reactive probe enables broader and deeper profiling of the cysteinome, rendering it a highly attractive tool for elucidation of targets of electrophilic small molecules.
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Affiliation(s)
- Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Martin Tomanik
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Nan Qiu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Dany Pechalrieu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Anton Shuster
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruno Commare
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Antonio Togni
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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6
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Parkinson E, Aleksic M, Kukic P, Bailey A, Cubberley R, Skipp P. Proteomic analysis of the cellular response to a potent sensitiser unveils the dynamics of haptenation in living cells. Toxicology 2020; 445:152603. [DOI: 10.1016/j.tox.2020.152603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/09/2023]
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7
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Stucki D, Stahl W. Carbon monoxide – beyond toxicity? Toxicol Lett 2020; 333:251-260. [DOI: 10.1016/j.toxlet.2020.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022]
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8
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McConnell EW, Smythers AL, Hicks LM. Maleimide-Based Chemical Proteomics for Quantitative Analysis of Cysteine Reactivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1697-1705. [PMID: 32573231 DOI: 10.1021/jasms.0c00116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cysteine is the most intrinsically nucleophilic residue in proteins and serves as a mediator against increasing reactive oxygen species (ROS) via reversible thiol oxidation. Despite the importance of cysteine oxidation in understanding biological stress response, cysteine sites most reactive toward ROS remain largely unknown and are a major analytical challenge. Herein, a chemical proteomic method to quantify site-specific cysteine reactivity using a maleimide-activated, thiol-reactive probe (N-propargylmaleimide, NPM) is described. Implementation of a gel-based approach via conjugation of rhodamine-azide to NPM-labeled cysteine residues by copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry allowed simple and highly sensitive fluorescence profiling. Relative quantification of >1500 unique cysteine sites from greater than 800 proteins was achieved by conjugating dialkoxydiphenylsilane (DADPS) biotin-azide by the CuAAC reaction and subsequently performing biotin-streptavidin affinity purification and mass-spectrometry-based proteomics. Taken together, this work defines a novel role for the NPM probe in chemical proteomics and presents a robust method for determination of cysteine reactivity during oxidative stress response.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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9
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Poganik JR, Aye Y. Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals. Front Aging Neurosci 2020; 12:1. [PMID: 32116644 PMCID: PMC7019031 DOI: 10.3389/fnagi.2020.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
With a lipid-rich environment and elevated oxygen consumption, the central nervous system (CNS) is subject to intricate regulation by lipid-derived electrophiles (LDEs). Investigations into oxidative damage and chronic LDE generation in neural disorders have spurred the development of tools that can detect and catalog the gamut of LDE-adducted proteins. Despite these advances, deconstructing the precise consequences of individual protein-specific LDE modifications remained largely impossible until recently. In this perspective, we first overview emerging toolsets that can decode electrophile-signaling events in a protein/context-specific manner, and how the accumulating mechanistic insights brought about by these tools have begun to offer new means to modulate pathways relevant to multiple sclerosis (MS). By surveying the latest data surrounding the blockbuster MS drug dimethyl fumarate that functions through LDE-signaling-like mechanisms, we further provide a vision for how chemical biology tools probing electrophile signaling may be leveraged toward novel interventions in CNS disease.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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10
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Slowly Reducible Genetically Encoded Green Fluorescent Indicator for In Vivo and Ex Vivo Visualization of Hydrogen Peroxide. Int J Mol Sci 2019; 20:ijms20133138. [PMID: 31252566 PMCID: PMC6650888 DOI: 10.3390/ijms20133138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) plays an important role in modulating cell signaling and homeostasis in live organisms. The HyPer family of genetically encoded indicators allows the visualization of H2O2 dynamics in live cells within a limited field of view. The visualization of H2O2 within a whole organism with a single cell resolution would benefit from a slowly reducible fluorescent indicator that integrates the H2O2 concentration over desired time scales. This would enable post hoc optical readouts in chemically fixed samples. Herein, we report the development and characterization of NeonOxIrr, a genetically encoded green fluorescent indicator, which rapidly increases fluorescence brightness upon reaction with H2O2, but has a low reduction rate. NeonOxIrr is composed of circularly permutated mNeonGreen fluorescent protein fused to the truncated OxyR transcription factor isolated from E. coli. When compared in vitro to a standard in the field, HyPer3 indicator, NeonOxIrr showed 5.9-fold higher brightness, 15-fold faster oxidation rate, 5.9-fold faster chromophore maturation, similar intensiometric contrast (2.8-fold), 2-fold lower photostability, and significantly higher pH stability both in reduced (pKa of 5.9 vs. ≥7.6) and oxidized states (pKa of 5.9 vs.≥ 7.9). When expressed in the cytosol of HEK293T cells, NeonOxIrr demonstrated a 2.3-fold dynamic range in response to H2O2 and a 44 min reduction half-time, which were 1.4-fold lower and 7.6-fold longer than those for HyPer3. We also demonstrated and characterized the NeonOxIrr response to H2O2 when the sensor was targeted to the matrix and intermembrane space of the mitochondria, nucleus, cell membranes, peroxisomes, Golgi complex, and endoplasmic reticulum of HEK293T cells. NeonOxIrr could reveal endogenous reactive oxygen species (ROS) production in HeLa cells induced with staurosporine but not with thapsigargin or epidermal growth factor. In contrast to HyPer3, NeonOxIrr could visualize optogenetically produced ROS in HEK293T cells. In neuronal cultures, NeonOxIrr preserved its high 3.2-fold dynamic range to H2O2 and slow 198 min reduction half-time. We also demonstrated in HeLa cells that NeonOxIrr preserves a 1.7-fold ex vivo dynamic range to H2O2 upon alkylation with N-ethylmaleimide followed by paraformaldehyde fixation. The same alkylation-fixation procedure in the presence of NP-40 detergent allowed ex vivo detection of H2O2 with 1.5-fold contrast in neuronal cultures and in the cortex of the mouse brain. The slowly reducible H2O2 indicator NeonOxIrr can be used for both the in vivo and ex vivo visualization of ROS. Expanding the family of fixable indicators may be a promising strategy to visualize biological processes at a single cell resolution within an entire organism.
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11
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Aranda-Caño L, Sánchez-Calvo B, Begara-Morales JC, Chaki M, Mata-Pérez C, Padilla MN, Valderrama R, Barroso JB. Post-Translational Modification of Proteins Mediated by Nitro-Fatty Acids in Plants: Nitroalkylation. PLANTS 2019; 8:plants8040082. [PMID: 30934982 PMCID: PMC6524050 DOI: 10.3390/plants8040082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/28/2022]
Abstract
Nitrate fatty acids (NO₂-FAs) are considered reactive lipid species derived from the non-enzymatic oxidation of polyunsaturated fatty acids by nitric oxide (NO) and related species. Nitrate fatty acids are powerful biological electrophiles which can react with biological nucleophiles such as glutathione and certain protein⁻amino acid residues. The adduction of NO₂-FAs to protein targets generates a reversible post-translational modification called nitroalkylation. In different animal and human systems, NO₂-FAs, such as nitro-oleic acid (NO₂-OA) and conjugated nitro-linoleic acid (NO₂-cLA), have cytoprotective and anti-inflammatory influences in a broad spectrum of pathologies by modulating various intracellular pathways. However, little knowledge on these molecules in the plant kingdom exists. The presence of NO₂-OA and NO₂-cLA in olives and extra-virgin olive oil and nitro-linolenic acid (NO₂-Ln) in Arabidopsis thaliana has recently been detected. Specifically, NO₂-Ln acts as a signaling molecule during seed and plant progression and beneath abiotic stress events. It can also release NO and modulate the expression of genes associated with antioxidant responses. Nevertheless, the repercussions of nitroalkylation on plant proteins are still poorly known. In this review, we demonstrate the existence of endogenous nitroalkylation and its effect on the in vitro activity of the antioxidant protein ascorbate peroxidase.
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Affiliation(s)
- Lorena Aranda-Caño
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, Faculty of Experimental Sciences, University Campus Las Lagunillas, University of Jaén, E-23071 Jaén, Spain.
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12
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Vickers AEM, Ulyanov AV, Fisher RL. Progression of Repair and Injury in Human Liver Slices. Int J Mol Sci 2018; 19:ijms19124130. [PMID: 30572671 PMCID: PMC6321528 DOI: 10.3390/ijms19124130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022] Open
Abstract
Human liver slice function was stressed by daily dosing of acetaminophen (APAP) or diclofenac (DCF) to investigate injury and repair. Initially, untreated human liver and kidney slices were evaluated with the global human U133A array to assess the extended culture conditions. Then, drug induced injury and signals of repair in human liver slices exposed to APAP or DCF (1 mM) were evaluated via specific gene expression arrays. In culture, the untreated human liver and kidney slices remained differentiated and gene expression indicated that repair pathways were activated in both tissues. Morphologically the human liver slices exhibited evidence of repair and regeneration, while kidney slices did not. APAP and DCF exposure caused a direct multi-factorial response. APAP and DCF induced gene expression changes in transporters, oxidative stress and mitochondria energy. DCF caused a greater effect on heat shock and endoplasmic reticulum (ER) stress gene expression. Concerning wound repair, APAP caused a mild repression of gene expression; DCF suppressed the expression of matrix collagen genes, the remodeling metalloproteases, cell adhesion integrins, indicating a greater hinderance to wound repair than APAP. Thus, human liver slices are a relevant model to investigate the mechanisms of drug-induced injury and repair.
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Affiliation(s)
| | - Anatoly V Ulyanov
- Inova Translational Medicine Institute, Inova Hospital, Fairfax VA 22031, USA.
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13
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Abstract
The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology and Toxicology, College of
Pharmacy, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Jesse R. Poganik
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
- Department of Biochemistry, Weill Cornell Medicine, New
York, New York, 10065, USA
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14
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Hauck AK, Zhou T, Hahn W, Petegrosso R, Kuang R, Chen Y, Bernlohr DA. Obesity-induced protein carbonylation in murine adipose tissue regulates the DNA-binding domain of nuclear zinc finger proteins. J Biol Chem 2018; 293:13464-13476. [PMID: 30012885 DOI: 10.1074/jbc.ra118.003469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/20/2018] [Indexed: 11/06/2022] Open
Abstract
In obesity-linked insulin resistance, oxidative stress in adipocytes leads to lipid peroxidation and subsequent carbonylation of proteins by diffusible lipid electrophiles. Reduction in oxidative stress attenuates protein carbonylation and insulin resistance, suggesting that lipid modification of proteins may play a role in metabolic disease, but the mechanisms remain incompletely understood. Herein, we show that in vivo, diet-induced obesity in mice surprisingly results in preferential carbonylation of nuclear proteins by 4-hydroxy-trans-2,3-nonenal (4-HNE) or 4-hydroxy-trans-2,3-hexenal (4-HHE). Proteomic and structural analyses revealed that residues in or around the sites of zinc coordination of zinc finger proteins, such as those containing the C2H2 or MATRIN, RING, C3H1, or N4-type DNA-binding domains, are particularly susceptible to carbonylation by lipid aldehydes. These observations strongly suggest that carbonylation functionally disrupts protein secondary structure supported by metal coordination. Analysis of one such target, the nuclear protein estrogen-related receptor γ (ERR-γ), showed that ERR-γ is modified by 4-HHE in the obese state. In vitro carbonylation decreased the DNA-binding capacity of ERR-γ and correlated with the obesity-linked down-regulation of many key genes promoting mitochondrial bioenergetics. Taken together, these findings reveal a novel mechanistic connection between oxidative stress and metabolic dysfunction arising from carbonylation of nuclear zinc finger proteins, such as the transcriptional regulator ERR-γ.
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Affiliation(s)
- Amy K Hauck
- From the Departments of Biochemistry, Molecular Biology, and Biophysics and
| | - Tong Zhou
- From the Departments of Biochemistry, Molecular Biology, and Biophysics and
| | - Wendy Hahn
- From the Departments of Biochemistry, Molecular Biology, and Biophysics and
| | - Raphael Petegrosso
- Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455
| | - Rui Kuang
- Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455
| | - Yue Chen
- From the Departments of Biochemistry, Molecular Biology, and Biophysics and
| | - David A Bernlohr
- From the Departments of Biochemistry, Molecular Biology, and Biophysics and
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15
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Embaby AM, Schoffelen S, Kofoed C, Meldal M, Diness F. Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712589] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ahmed M. Embaby
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Sanne Schoffelen
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Christian Kofoed
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Frederik Diness
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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Embaby AM, Schoffelen S, Kofoed C, Meldal M, Diness F. Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification. Angew Chem Int Ed Engl 2018; 57:8022-8026. [DOI: 10.1002/anie.201712589] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ahmed M. Embaby
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Sanne Schoffelen
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Christian Kofoed
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Frederik Diness
- Center for Evolutionary Chemical BiologyDepartment of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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17
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Hoch DG, Abegg D, Adibekian A. Cysteine-reactive probes and their use in chemical proteomics. Chem Commun (Camb) 2018; 54:4501-4512. [PMID: 29645055 DOI: 10.1039/c8cc01485j] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteomic profiling using bioorthogonal chemical probes that selectively react with certain amino acids is now a widely used method in life sciences to investigate enzymatic activities, study posttranslational modifications and discover novel covalent inhibitors. Over the past two decades, researchers have developed selective probes for several different amino acids, including lysine, serine, cysteine, threonine, tyrosine, aspartate and glutamate. Among these amino acids, cysteines are particularly interesting due to their highly diverse and complex biochemical role in our cells. In this feature article, we focus on the chemical probes and methods used to study cysteines in complex proteomes.
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Affiliation(s)
- Dominic G Hoch
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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18
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Proteomic profiling of oxidized cysteine and methionine residues by hydroxyl radicals in myosin of pork. Food Chem 2018; 243:277-284. [DOI: 10.1016/j.foodchem.2017.09.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/11/2017] [Accepted: 09/14/2017] [Indexed: 11/22/2022]
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Abstract
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.
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20
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Bak DW, Pizzagalli MD, Weerapana E. Identifying Functional Cysteine Residues in the Mitochondria. ACS Chem Biol 2017; 12:947-957. [PMID: 28157297 DOI: 10.1021/acschembio.6b01074] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The mitochondria are dynamic organelles that regulate oxidative metabolism and mediate cellular redox homeostasis. Proteins within the mitochondria are exposed to large fluxes in the surrounding redox environment. In particular, cysteine residues within mitochondrial proteins sense and respond to these redox changes through oxidative modifications of the cysteine thiol group. These oxidative modifications result in a loss in cysteine reactivity, which can be monitored using cysteine-reactive chemical probes and quantitative mass spectrometry (MS). Analysis of cell lysates treated with cysteine-reactive probes enable the identification of hundreds of cysteine residues, however, the mitochondrial proteome is poorly represented (<10% of identified peptides), due to the low abundance of mitochondrial proteins and suppression of mitochondrial peptide MS signals by highly abundant cytosolic peptides. Here, we apply a mitochondrial isolation and purification protocol to substantially increase coverage of the mitochondrial cysteine proteome. Over 1500 cysteine residues from ∼450 mitochondrial proteins were identified, thereby enabling interrogation of an unprecedented number of mitochondrial cysteines. Specifically, these mitochondrial cysteines were ranked by reactivity to identify hyper-reactive cysteines with potential catalytic and regulatory functional roles. Furthermore, analyses of mitochondria exposed to nitrosative stress revealed previously uncharacterized sites of protein S-nitrosation on mitochondrial proteins. Together, the mitochondrial cysteine enrichment strategy presented herein enables detailed characterization of protein modifications that occur within the mitochondria during (patho)physiological fluxes in the redox environment.
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Affiliation(s)
- Daniel W. Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mattia D. Pizzagalli
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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21
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Slawik C, Rickmeyer C, Brehm M, Böhme A, Schüürmann G. Glutathione Adduct Patterns of Michael-Acceptor Carbonyls. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4018-4026. [PMID: 28225253 DOI: 10.1021/acs.est.6b04981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Glutathione (GSH) has so far been considered to facilitate detoxification of soft organic electrophiles through covalent binding at its cysteine (Cys) thiol group, followed by stepwise catalyzed degradation and eventual elimination along the mercapturic acid pathway. Here we show that in contrast to expectation from HSAB theory, Michael-acceptor ketones, aldehydes and esters may form also single, double and triple adducts with GSH involving β-carbon attack at the much harder N-terminus of the γ-glutamyl (Glu) unit of GSH. In particular, formation of the GSH-N single adduct contradicts the traditional view that S alkylation always forms the initial reaction of GSH with Michael-acceptor carbonyls. To this end, chemoassay analyses of the adduct formation of GSH with nine α,β-unsaturated carbonyls employing high performance liquid chromatography and tandem mass spectrometry have been performed. Besides enriching the GSH adductome and potential biomarker applications, electrophilic N-terminus functionalization is likely to impair GSH homeostasis substantially through blocking the γ-glutamyl transferase catalysis of the first breakdown step of modified GSH, and thus its timely reconstitution. The discussion includes a comparison with cyclic adducts of GSH and furan metabolites as reported in literature, and quantum chemically calculated thermodynamics of hard-hard, hard-soft, and soft-soft adducts.
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Affiliation(s)
- Christian Slawik
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | - Christiane Rickmeyer
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin Brehm
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
| | - Alexander Böhme
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
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22
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Long MJC, Poganik JR, Ghosh S, Aye Y. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology. ACS Chem Biol 2017; 12:586-600. [PMID: 28068059 DOI: 10.1021/acschembio.6b01148] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.
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Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jesse R. Poganik
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Souradyuti Ghosh
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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23
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Liver Effects of Clinical Drugs Differentiated in Human Liver Slices. Int J Mol Sci 2017; 18:ijms18030574. [PMID: 28272341 PMCID: PMC5372590 DOI: 10.3390/ijms18030574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 02/06/2023] Open
Abstract
Drugs with clinical adverse effects are compared in an ex vivo 3-dimensional multi-cellular human liver slice model. Functional markers of oxidative stress and mitochondrial function, glutathione GSH and ATP levels, were affected by acetaminophen (APAP, 1 mM), diclofenac (DCF, 1 mM) and etomoxir (ETM, 100 μM). Drugs targeting mitochondria more than GSH were dantrolene (DTL, 10 μM) and cyclosporin A (CSA, 10 μM), while GSH was affected more than ATP by methimazole (MMI, 500 μM), terbinafine (TBF, 100 μM), and carbamazepine (CBZ 100 μM). Oxidative stress genes were affected by TBF (18%), CBZ, APAP, and ETM (12%–11%), and mitochondrial genes were altered by CBZ, APAP, MMI, and ETM (8%–6%). Apoptosis genes were affected by DCF (14%), while apoptosis plus necrosis were altered by APAP and ETM (15%). Activation of oxidative stress, mitochondrial energy, heat shock, ER stress, apoptosis, necrosis, DNA damage, immune and inflammation genes ranked CSA (75%), ETM (66%), DCF, TBF, MMI (61%–60%), APAP, CBZ (57%–56%), and DTL (48%). Gene changes in fatty acid metabolism, cholestasis, immune and inflammation were affected by DTL (51%), CBZ and ETM (44%–43%), APAP and DCF (40%–38%), MMI, TBF and CSA (37%–35%). This model advances multiple dosing in a human ex vivo model, plus functional markers and gene profile markers of drug induced human liver side-effects.
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Electrophilic Nitro-Fatty Acids: Nitric Oxide and Nitrite-Derived Metabolic and Inflammatory Signaling Mediators. Nitric Oxide 2017. [DOI: 10.1016/b978-0-12-804273-1.00016-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
SIGNIFICANCE The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. RECENT ADVANCES Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. CRITICAL ISSUES Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. FUTURE DIRECTIONS Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.
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Affiliation(s)
- Dean P Jones
- 1 Department of Medicine, Emory University , Atlanta, Georgia
| | - Helmut Sies
- 2 Institute for Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf , Düsseldorf, Germany .,3 Leibniz Research Institute for Environmental Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
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26
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Iwakiri Y, Kim MY. Nitric oxide in liver diseases. Trends Pharmacol Sci 2015; 36:524-36. [PMID: 26027855 PMCID: PMC4532625 DOI: 10.1016/j.tips.2015.05.001] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 02/06/2023]
Abstract
Nitric oxide (NO) and its derivatives play important roles in the physiology and pathophysiology of the liver. Despite its diverse and complicated roles, certain patterns of the effect of NO on the pathogenesis and progression of liver diseases are observed. In general, NO derived from endothelial NO synthase (eNOS) in liver sinusoidal endothelial cells (LSECs) is protective against disease development, while inducible NOS (iNOS)-derived NO contributes to pathological processes. This review addresses the roles of NO in the development of various liver diseases with a focus on recently published articles. We present here two recent advances in understanding NO-mediated signaling - nitrated fatty acids (NO2-FAs) and S-guanylation - and conclude with suggestions for future directions in NO-related studies on the liver.
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Affiliation(s)
- Yasuko Iwakiri
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Moon Young Kim
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
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27
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Abegg D, Frei R, Cerato L, Prasad Hari D, Wang C, Waser J, Adibekian A. Proteome-Wide Profiling of Targets of Cysteine reactive Small Molecules by Using Ethynyl Benziodoxolone Reagents. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505641] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Abegg D, Frei R, Cerato L, Prasad Hari D, Wang C, Waser J, Adibekian A. Proteome-Wide Profiling of Targets of Cysteine reactive Small Molecules by Using Ethynyl Benziodoxolone Reagents. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201505641] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Abstract
The cysteine (Cys) proteome is a major component of the adaptive interface between the genome and the exposome. The thiol moiety of Cys undergoes a range of biologic modifications enabling biological switching of structure and reactivity. These biological modifications include sulfenylation and disulfide formation, formation of higher oxidation states, S-nitrosylation, persulfidation, metalation, and other modifications. Extensive knowledge about these systems and their compartmentalization now provides a foundation to develop advanced integrative models of Cys proteome regulation. In particular, detailed understanding of redox signaling pathways and sensing networks is becoming available to allow the discrimination of network structures. This research focuses attention on the need for atlases of Cys modifications to develop systems biology models. Such atlases will be especially useful for integrative studies linking the Cys proteome to imaging and other omics platforms, providing a basis for improved redox-based therapeutics. Thus, a framework is emerging to place the Cys proteome as a complement to the quantitative proteome in the omics continuum connecting the genome to the exposome.
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Affiliation(s)
- Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Joshua D Chandler
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA.
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Abo M, Weerapana E. A Caged Electrophilic Probe for Global Analysis of Cysteine Reactivity in Living Cells. J Am Chem Soc 2015; 137:7087-90. [DOI: 10.1021/jacs.5b04350] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Masahiro Abo
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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31
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Shannon DA, Weerapana E. Covalent protein modification: the current landscape of residue-specific electrophiles. Curr Opin Chem Biol 2015; 24:18-26. [DOI: 10.1016/j.cbpa.2014.10.021] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
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Chattoraj S, Chowdhury R, Dey SK, Jana SS, Bhattacharyya K. Role of Red-Ox Cycle in Structural Oscillations and Solvation Dynamics in the Mitochondria of a Live Cell. J Phys Chem B 2014; 119:8842-51. [DOI: 10.1021/jp503808z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shyamtanu Chattoraj
- Department of Physical Chemistry and ‡Department of Biological Chemistry, Indian Association For The Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Rajdeep Chowdhury
- Department of Physical Chemistry and ‡Department of Biological Chemistry, Indian Association For The Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Sumit Kumar Dey
- Department of Physical Chemistry and ‡Department of Biological Chemistry, Indian Association For The Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Siddhartha Sankar Jana
- Department of Physical Chemistry and ‡Department of Biological Chemistry, Indian Association For The Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry and ‡Department of Biological Chemistry, Indian Association For The Cultivation of Science, Jadavpur, Kolkata 700
032, India
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Codreanu SG, Ullery JC, Zhu J, Tallman KA, Beavers WN, Porter NA, Marnett LJ, Zhang B, Liebler DC. Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics 2014; 13:849-59. [PMID: 24429493 PMCID: PMC3945913 DOI: 10.1074/mcp.m113.032953] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions.
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Affiliation(s)
- Simona G Codreanu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Rahaman MM, Sawa T, Ahtesham AK, Khan S, Inoue H, Irie A, Fujii S, Akaike T. S-guanylation proteomics for redox-based mitochondrial signaling. Antioxid Redox Signal 2014; 20:295-307. [PMID: 22978631 PMCID: PMC3887461 DOI: 10.1089/ars.2012.4606] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIMS 8-nitroguanosine 3',5'-cyclic monophosphate (8-Nitro-cGMP) is a nitrated derivative of cGMP that is formed via cross-talk of reactive oxygen species formed by NADPH oxidase 2 and mitochondria. This nitrated nucleotide can function as a unique electrophilic second messenger in regulation of redox signaling by inducing a post-translational modification of protein thiols via cGMP adduction (protein S-guanylation). With S-guanylation proteomics, we investigated endogenous mitochondrial protein S-guanylation. RESULTS We developed a new mass spectrometry (MS)-based proteomic method-S-guanylation proteomics-which comprised two approaches: (i) direct protein digestion followed by immunoaffinity capture of S-guanylated peptides that were subjected to liquid chromatography-tandem MS (LC-MS/MS); and (ii) two-dimensional (2D)-gel electrophoretic separation of S-guanylated proteins that were subjected to in-gel digestion, followed by LC-MS/MS. We thereby identified certain mitochondrial proteins that are S-guanylated endogenously during immunological stimulation, including mortalin and 60-kDa heat-shock protein (HSP60). Mortalin and HSP60 were recently reported to regulate mitochondrial permeability-transition pore (mPTP) opening, at least partly, by interacting with cyclophilin D, an mPTP component. Our data revealed that immunological stimulation and 8-nitro-cGMP treatment induced mPTP opening in a cyclophilin D-dependent manner. INNOVATION AND CONCLUSION Our S-guanylation proteomic method determined that mitochondrial HSPs may be novel targets for redox modification via protein S-guanylation that participates in mPTP regulation and mitochondrial redox signaling.
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Affiliation(s)
- Md Mizanur Rahaman
- 1 Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University , Kumamoto, Japan
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Affiliation(s)
- Shengwen Shen
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - William R. Cullen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver,
British Columbia, Canada, V6T 1Z1
| | - Michael Weinfeld
- Department of Oncology, Cross
Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada, T6G 1Z2
| | - X. Chris Le
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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36
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Detection of electrophile-sensitive proteins. Biochim Biophys Acta Gen Subj 2013; 1840:913-22. [PMID: 24021887 DOI: 10.1016/j.bbagen.2013.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/22/2013] [Accepted: 09/03/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND Redox signaling is an important emerging mechanism of cellular function. Dysfunctional redox signaling is increasingly implicated in numerous pathologies, including atherosclerosis, diabetes, and cancer. The molecular messengers in this type of signaling are reactive species which can mediate the post-translational modification of specific groups of proteins, thereby effecting functional changes in the modified proteins. Electrophilic compounds comprise one class of reactive species which can participate in redox signaling. Electrophiles modulate cell function via formation of covalent adducts with proteins, particularly cysteine residues. SCOPE OF REVIEW This review will discuss the commonly used methods of detection for electrophile-sensitive proteins, and will highlight the importance of identifying these proteins for studying redox signaling and developing novel therapeutics. MAJOR CONCLUSIONS There are several methods which can be used to detect electrophile-sensitive proteins. These include the use of tagged model electrophiles, as well as derivatization of endogenous electrophile-protein adducts. GENERAL SIGNIFICANCE In order to understand the mechanisms by which electrophiles mediate redox signaling, it is necessary to identify electrophile-sensitive proteins and quantitatively assess adduct formation. Strengths and limitations of these methods will be discussed. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Salvatore SR, Vitturi DA, Baker PRS, Bonacci G, Koenitzer JR, Woodcock SR, Freeman BA, Schopfer FJ. Characterization and quantification of endogenous fatty acid nitroalkene metabolites in human urine. J Lipid Res 2013; 54:1998-2009. [PMID: 23620137 DOI: 10.1194/jlr.m037804] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The oxidation and nitration of unsaturated fatty acids transforms cell membrane and lipoprotein constituents into mediators that regulate signal transduction. The formation of 9-NO2-octadeca-9,11-dienoic acid and 12-NO2-octadeca-9,11-dienoic acid stems from peroxynitrite- and myeloperoxidase-derived nitrogen dioxide reactions as well as secondary to nitrite disproportionation under the acidic conditions of digestion. Broad anti-inflammatory and tissue-protective responses are mediated by nitro-fatty acids. It is now shown that electrophilic fatty acid nitroalkenes are present in the urine of healthy human volunteers (9.9 ± 4.0 pmol/mg creatinine); along with electrophilic 16- and 14-carbon nitroalkenyl β-oxidation metabolites. High resolution mass determinations and coelution with isotopically-labeled metabolites support renal excretion of cysteine-nitroalkene conjugates. These products of Michael addition are in equilibrium with the free nitroalkene pool in urine and are displaced by thiol reaction with mercury chloride. This reaction increases the level of free nitroalkene fraction >10-fold and displays a K(D) of 7.5 × 10(-6) M. In aggregate, the data indicates that formation of Michael adducts by electrophilic fatty acids is favored under biological conditions and that reversal of these addition reactions is critical for detecting both parent nitroalkenes and their metabolites. The measurement of this class of mediators can constitute a sensitive noninvasive index of metabolic and inflammatory status.
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Affiliation(s)
- Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Go YM, Duong DM, Peng J, Jones DP. Protein Cysteines Map to Functional Networks According to Steady-state Level of Oxidation. ACTA ACUST UNITED AC 2013; 4:196-209. [PMID: 22605892 DOI: 10.4172/jpb.1000190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The cysteine (Cys) proteome serves critical roles in protein structure, function and regulation, and includes key targets in oxidative mechanisms of disease. Thioredoxins maintain Cys residues in thiol forms, and previous research shows that the redox potential of thioredoxin in mitochondria and nuclei is more reduced than cytoplasm, suggesting that proteins in these compartments may have different steady-state oxidation. This study measured fractional oxidation of 641 peptidyl Cys residues from 333 proteins in HT29 cells by mass spectrometry. Average oxidation of cytoplasmic, nuclear and mitochondrial proteins was similar (15.8, 15.5, 14%, respectively). Pathway analysis showed that more reduced cytoplasmic Cys were in proteins associated with the cytoskeleton, more reduced nuclear Cys with Ran signaling and RNA post-transcriptional modifcation, and more reduced mitochondrial Cys with energy metabolism, cell growth and cell proliferation. More oxidized cytoplasmic Cys included associations with PI3/Akt, Myc-mediated apoptosis and 14-3-3-mediated signaling. Weaker associations of oxidized nuclear and mitochondrial Cys occurred with granzyme B signaling and intermediary metabolism, respectively. Thus, steady-state peptidyl Cys oxidation is associated with functional pathways rather than simply with organellar distribution. This suggests that oxidative mechanisms of disease could target functional pathways or networks rather than individual proteins or subcellular compartments.
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Affiliation(s)
- Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory Proteomics Service Center, Emory University, Atlanta, Georgia 30322 USA
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Higdon AN, Landar A, Barnes S, Darley-Usmar VM. The electrophile responsive proteome: integrating proteomics and lipidomics with cellular function. Antioxid Redox Signal 2012; 17:1580-9. [PMID: 22352679 PMCID: PMC3448939 DOI: 10.1089/ars.2012.4523] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
SIGNIFICANCE The process of lipid peroxidation is emerging as an important mechanism that mediates the post-translational modification of proteins. Through advanced analytical techniques, lipidomics is now emerging as a critical factor in our understanding of the pathology of a broad range of diseases. RECENT ADVANCES During enzymatic or nonenzymatic lipid peroxidation, the simple structure of an unsaturated fatty acid is converted to an oxylipidome, many members of which are electrophilic and form the reactive lipid species (RLS). This aspect of lipid biology is particularly important, as it directly connects lipidomics with proteomics through the post-translational modification of a sub-proteome in the cell. This arises, because the electrophilic members of the oxylipidome react with proteins at nucleophilic amino-acid residues and so change their structure and function to form electrophile-responsive proteomes (ERP). CRITICAL ISSUES Biological systems have relatively few but well-defined and mechanistically distinct pro-oxidant pathways generating RLS. Defining the ERPs and the mechanisms underlying their formation and action has been a major focus for the field of lipidomics and redox signaling. FUTURE DIRECTIONS We propose that a unique oxylipidome can be defined for specific oxidants and will predict the biological responses through the reaction with proteins to form a specific ERP. In this review, we will describe the ERPs that modulate antioxidant and anti-inflammatory protective pathways, including the activation of Keap1/Nrf2 and the promotion of cell death through interactions with mitochondria.
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Affiliation(s)
- Ashlee N Higdon
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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40
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Vickers AEM, Fisher RL. Evaluation of drug-induced injury and human response in precision-cut tissue slices. Xenobiotica 2012; 43:29-40. [PMID: 23094640 DOI: 10.3109/00498254.2012.732714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
1.Drug induced organ injury is multifaceted, encompassing a spectrum of cell types and numerous networks reflecting cell-cell and cell-matrix interactions. Characterization of drug induced side effects and human response can be addressed in organ slice models. 2.The application of human tissue to various organ slice models including liver, intestine, kidney, liver-blood co-cultures and thyroid enhances our ability to focus on the clinical relevance of side effects identified in animal studies for human, and to evaluate potential biomarkers of the side effects. Dose-response relationships can help discern drug concentrations which alter organ function or affect morphology, to identify drug concentrationswhich could pose a risk for humans. 3.Insight into pathways of organ injury, by incorporating gene and protein expression profiling, with functional measurements and morphology, aid to define species differences and sensitivity. 4.Human organ slice studies are valuable for bridging the extrapolation of animal derived data and for identifying mechanisms relevant for humans, thereby expanding the scope of translational research for drug safety assessment.
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Abstract
The process of lipid peroxidation is widespread in biology and is mediated through both enzymatic and non-enzymatic pathways. A significant proportion of the oxidized lipid products are electrophilic in nature, the RLS (reactive lipid species), and react with cellular nucleophiles such as the amino acids cysteine, lysine and histidine. Cell signalling by electrophiles appears to be limited to the modification of cysteine residues in proteins, whereas non-specific toxic effects involve modification of other nucleophiles. RLS have been found to participate in several physiological pathways including resolution of inflammation, cell death and induction of cellular antioxidants through the modification of specific signalling proteins. The covalent modification of proteins endows some unique features to this signalling mechanism which we have termed the ‘covalent advantage’. For example, covalent modification of signalling proteins allows for the accumulation of a signal over time. The activation of cell signalling pathways by electrophiles is hierarchical and depends on a complex interaction of factors such as the intrinsic chemical reactivity of the electrophile, the intracellular domain to which it is exposed and steric factors. This introduces the concept of electrophilic signalling domains in which the production of the lipid electrophile is in close proximity to the thiol-containing signalling protein. In addition, we propose that the role of glutathione and associated enzymes is to insulate the signalling domain from uncontrolled electrophilic stress. The persistence of the signal is in turn regulated by the proteasomal pathway which may itself be subject to redox regulation by RLS. Cell death mediated by RLS is associated with bioenergetic dysfunction, and the damaged proteins are probably removed by the lysosome-autophagy pathway.
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Irving RM, Elfarra AA. Role of reactive metabolites in the circulation in extrahepatic toxicity. Expert Opin Drug Metab Toxicol 2012; 8:1157-72. [PMID: 22681489 DOI: 10.1517/17425255.2012.695347] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Reactive metabolite-mediated toxicity is frequently limited to the organ where the electrophilic metabolites are generated. Some reactive metabolites, however, might have the ability to translocate from their site of formation. This suggests that for these reactive metabolites, investigations into the role of organs other than the one directly affected could be relevant to understanding the mechanism of toxicity. AREAS COVERED The authors discuss the physiological and biochemical factors that can enable reactive metabolites to cause toxicity in an organ distal from the site of generation. Furthermore, the authors present a case study which describes studies that demonstrate that S-(1,2-dichlorovinyl)-L-cysteine sulfoxide (DCVCS) and N-acetyl-S-(1,2-dichlorovinyl-L-cysteine sulfoxide (N-AcDCVCS), reactive metabolites of the known trichloroethylene metabolites S-(1,2-dichlorovinyl)-L-cysteine (DCVC), and N-acetyl-S-(1,2-dichlorovinyl)-L-cysteine (N-AcDCVC), are generated in the liver and translocate through the circulation to the kidney to cause nephrotoxicity. EXPERT OPINION The ability of reactive metabolites to translocate could be important to consider when investigating mechanisms of toxicity. A mechanistic approach, similar to the one described for DCVCS and N-AcDCVCS, could be useful in determining the role of circulating reactive metabolites in extrahepatic toxicity of drugs and other chemicals. If this is the case, intervention strategies that would not otherwise be feasible might be effective for reducing extrahepatic toxicity.
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Affiliation(s)
- Roy M Irving
- University of Wisconsin-Madison, School of Veterinary Medicine, Department of Comparative Biosciences and Molecular and Environmental Toxicology Center, Madison, WI 53706, USA
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Nadtochiy SM, Zhu QM, Zhu Q, Urciuoli W, Rafikov R, Black SM, Brookes PS. Nitroalkenes confer acute cardioprotection via adenine nucleotide translocase 1. J Biol Chem 2011; 287:3573-80. [PMID: 22158628 DOI: 10.1074/jbc.m111.298406] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Electrophilic nitrated lipids (nitroalkenes) are emerging as an important class of protective cardiovascular signaling molecules. Although species such as nitro-linoleate (LNO(2)) and nitro-oleate can confer acute protection against cardiac ischemic injury, their mechanism of action is unclear. Mild uncoupling of mitochondria is known to be cardioprotective, and adenine nucleotide translocase 1 (ANT1) is a key mediator of mitochondrial uncoupling. ANT1 also contains redox-sensitive cysteines that may be targets for modification by nitroalkenes. Therefore, in this study we tested the hypothesis that nitroalkenes directly modify ANT1 and that nitroalkene-mediated cardioprotection requires ANT1. Using biotin-tagged LNO(2) infused into intact perfused hearts, we obtained mass spectrometric (MALDI-TOF-TOF) evidence for direct modification (nitroalkylation) of ANT1 on cysteine 57. Furthermore, in a cell model of ischemia-reperfusion injury, siRNA knockdown of ANT1 inhibited the cardioprotective effect of LNO(2). Although the molecular mechanism linking ANT1-Cys(57) nitroalkylation and uncoupling is not yet known, these data suggest that ANT1-mediated uncoupling may be a mechanism for nitroalkene-induced cardioprotection.
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Affiliation(s)
- Sergiy M Nadtochiy
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, New York 14642, USA
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Irving RM, Brownfield MS, Elfarra AA. N-biotinyl-S-(1,2-dichlorovinyl)-L-cysteine sulfoxide as a potential model for S-(1,2-dichlorovinyl)-L-cysteine sulfoxide: characterization of stability and reactivity with glutathione and kidney proteins in vitro. Chem Res Toxicol 2011; 24:1915-23. [PMID: 21988407 DOI: 10.1021/tx200263n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-(1,2-Dichlorovinyl)-L-cysteine sulfoxide (DCVCS) is a reactive and potent nephrotoxic metabolite of the human trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC). Because DCVCS covalent binding to kidney proteins likely plays a role in its nephrotoxicity, in this study biotin-tagged DCVCS, N-biotinyl-DCVCS (NB-DCVCS), was synthesized, and its stability in buffer alone and in the presence of rat blood or plasma was characterized in vitro. In addition, reactivity toward GSH and covalent binding to selected model enzymes and isolated kidney proteins were characterized. The half-lives of NB-DCVCS (39.6 min) and the DCVCS (diastereomer 1, 14.4 min; diastereomer 2, 6 min) in the presence of GSH were comparable. Incubating the model enzymes glutathione reductase and malate dehydrogenase with 10 μM NB-DCVCS for 3 h at 37 °C followed by immunoblotting using antibiotin antibodies demonstrated that glutathione reductase and malate dehydrogenase were extensively modified by NB-DCVCS. When rat kidney cytosol (6 μg/μL) was incubated with NB-DCVCS (312.5 nM to 5 μM) for 3 h at 37 °C followed by immunoblotting, a concentration-dependent increase in signal with multiple proteins with different molecular weights was observed, suggesting that NB-DCVCS binds to multiple kidney proteins with different selectivity. Incubating rat kidney cytosol with DCVCS (10-100 μM) prior to the addition of NB-DCVCS (2.5 μM) reduced the immunoblotting signal, suggesting that NB-DCVCS and DCVCS compete for the same binding sites. A comparison of the stability of NB-DCVCS and DCVCS in rat blood and plasma was determined in vitro, and NB-DCVCS exhibited higher stability than DCVCS in both media. Collectively, these results suggest that NB-DCVCS shows sufficient stability, reactivity, and selectivity to warrant further investigations into its possible use as a tool for future characterization of the role of covalent modification of renal proteins by DCVCS in nephrotoxicity.
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Affiliation(s)
- Roy M Irving
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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45
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Schopfer FJ, Cipollina C, Freeman BA. Formation and signaling actions of electrophilic lipids. Chem Rev 2011; 111:5997-6021. [PMID: 21928855 PMCID: PMC3294277 DOI: 10.1021/cr200131e] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francisco J. Schopfer
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Chiara Cipollina
- Fondazione Ri.MED, Piazza Sett’Angeli 10, 90134 Palermo, Italy
- Institute of Biomedicine and Molecular Immunology, Italian National Research Council, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Bruce A. Freeman
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
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Modulatory profiling identifies mechanisms of small molecule-induced cell death. Proc Natl Acad Sci U S A 2011; 108:E771-80. [PMID: 21896738 DOI: 10.1073/pnas.1106149108] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cell death is a complex process that plays a vital role in development, homeostasis, and disease. Our understanding of and ability to control cell death is impeded by an incomplete characterization of the full range of cell death processes that occur in mammalian systems, especially in response to exogenous perturbations. We present here a general approach to address this problem, which we call modulatory profiling. Modulatory profiles are composed of the changes in potency and efficacy of lethal compounds produced by a second cell death-modulating agent in human cell lines. We show that compounds with the same characterized mechanism of action have similar modulatory profiles. Furthermore, clustering of modulatory profiles revealed relationships not evident when clustering lethal compounds based on gene expression profiles alone. Finally, modulatory profiling of compounds correctly predicted three previously uncharacterized compounds to be microtubule-destabilizing agents, classified numerous compounds that act nonspecifically, and identified compounds that cause cell death through a mechanism that is morphologically and biochemically distinct from previously established ones.
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47
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Mammalian metallothionein in toxicology, cancer, and cancer chemotherapy. J Biol Inorg Chem 2011; 16:1087-101. [PMID: 21822976 DOI: 10.1007/s00775-011-0823-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/20/2011] [Indexed: 12/16/2022]
Abstract
The present paper centers on mammalian metallothionein 1 and 2 in relationship to cell and tissue injury beginning with its reaction with Cd²⁺ and then considering its role in the toxicology and chemotherapy of both metals and non-metal electrophiles and oxidants. Intertwined is a consideration of MTs role in tumor cell Zn²⁺ metabolism. The paper updates and expands on our recent review by Petering et al. (Met Ions Life Sci 5:353-398, 2009).
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48
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Hewitt M, Cronin MTD, Rowe PH, Schultz TW. Repeatability analysis of the Tetrahymena pyriformis population growth impairment assay. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:621-637. [PMID: 21830879 DOI: 10.1080/1062936x.2011.604100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Assessments necessary to ensure the safety of both humans and the environment are challenged by the sheer number of chemicals in use today. Chemical legislation, such as REACH, aims to use alternative methods to reduce the reliance on in vivo animal testing. Consequently, databases such as the TETRATOX database, containing data from the Tetrahymena pyriformis population growth impairment assay, have been used extensively to develop computational models which aid in priority setting and initial hazard assessments. To use any toxicological data, an assessment of quality is required. One important aspect of quality is the repeatability of the assay. This study considered TETRATOX assay data for 85 structurally and mechanistically diverse compounds. The repeatability of replicate determinations was assessed and factors relating to repeatability are discussed. Despite the majority of compounds demonstrating excellent repeatability, it was found that the mechanism of action is likely to be a modulating factor, with compounds acting via electrophilic mechanisms being more likely to exhibit reduced repeatability than those acting via narcotic mechanisms. It is evident from this study that the TETRATOX assay is a robust and highly repeatable assay, suitable for use in toxicological modelling studies and priority setting.
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Affiliation(s)
- M Hewitt
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
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49
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Lindahl M, Mata-Cabana A, Kieselbach T. The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance. Antioxid Redox Signal 2011; 14:2581-642. [PMID: 21275844 DOI: 10.1089/ars.2010.3551] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ten years ago, proteomics techniques designed for large-scale investigations of redox-sensitive proteins started to emerge. The proteomes, defined as sets of proteins containing reactive cysteines that undergo oxidative post-translational modifications, have had a particular impact on research concerning the redox regulation of cellular processes. These proteomes, which are hereafter termed "disulfide proteomes," have been studied in nearly all kingdoms of life, including animals, plants, fungi, and bacteria. Disulfide proteomics has been applied to the identification of proteins modified by reactive oxygen and nitrogen species under stress conditions. Other studies involving disulfide proteomics have addressed the functions of thioredoxins and glutaredoxins. Hence, there is a steadily growing number of proteins containing reactive cysteines, which are probable targets for redox regulation. The disulfide proteomes have provided evidence that entire pathways, such as glycolysis, the tricarboxylic acid cycle, and the Calvin-Benson cycle, are controlled by mechanisms involving changes in the cysteine redox state of each enzyme implicated. Synthesis and degradation of proteins are processes highly represented in disulfide proteomes and additional biochemical data have established some mechanisms for their redox regulation. Thus, combined with biochemistry and genetics, disulfide proteomics has a significant potential to contribute to new discoveries on redox regulation and signaling.
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Affiliation(s)
- Marika Lindahl
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Centro de Investigaciones Científicas Isla de la Cartuja, Seville, Spain
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50
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Chavez JD, Wu J, Bisson W, Maier CS. Site-specific proteomic analysis of lipoxidation adducts in cardiac mitochondria reveals chemical diversity of 2-alkenal adduction. J Proteomics 2011; 74:2417-29. [PMID: 21513823 DOI: 10.1016/j.jprot.2011.03.031] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/30/2011] [Accepted: 03/30/2011] [Indexed: 12/31/2022]
Abstract
The modification of proteins by lipid peroxidation products has been linked to numerous diseases and age-related disorders. Here we report on the identification of endogenous protein targets of electrophilic 2-alkenals in cardiac mitochondria. An aldehyde/keto-specific chemical labeling and affinity strategy in combination with LC-MS/MS resulted in 39 unique lipoxidation sites on 27 proteins. Several of the target sites were modified by a variety of 2-alkenal products including acrolein, β-hydroxyacrolein, crotonaldehyde, 4-hydroxy-2-hexenal, 4-hydroxy-2-nonenal and 4-oxo-2-nonenal. Many of the adduction sites are implicated in the catalytic function of key mitochondrial enzymes suggesting potential impact on pathways and overall mitochondrial function.
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Affiliation(s)
- Juan D Chavez
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
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