1
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Differential regulation of cysteine oxidative post-translational modifications in high and low aerobic capacity. Sci Rep 2018; 8:17772. [PMID: 30538258 PMCID: PMC6289973 DOI: 10.1038/s41598-018-35728-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
Given the association between high aerobic capacity and the prevention of metabolic diseases, elucidating the mechanisms by which high aerobic capacity regulates whole-body metabolic homeostasis is a major research challenge. Oxidative post-translational modifications (Ox-PTMs) of proteins can regulate cellular homeostasis in skeletal and cardiac muscles, but the relationship between Ox-PTMs and intrinsic components of oxidative energy metabolism is still unclear. Here, we evaluated the Ox-PTM profile in cardiac and skeletal muscles of rats bred for low (LCR) and high (HCR) intrinsic aerobic capacity. Redox proteomics screening revealed different cysteine (Cys) Ox-PTM profile between HCR and LCR rats. HCR showed a higher number of oxidized Cys residues in skeletal muscle compared to LCR, while the opposite was observed in the heart. Most proteins with differentially oxidized Cys residues in the skeletal muscle are important regulators of oxidative metabolism. The most oxidized protein in the skeletal muscle of HCR rats was malate dehydrogenase (MDH1). HCR showed higher MDH1 activity compared to LCR in skeletal, but not cardiac muscle. These novel findings indicate a clear association between Cys Ox-PTMs and aerobic capacity, leading to novel insights into the role of Ox-PTMs as an essential signal to maintain metabolic homeostasis.
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2
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Morales-Prieto N, Ruiz-Laguna J, Abril N. Dietary Se supplementation partially restores the REDOX proteomic map of M. spretus liver exposed to p,p ′-DDE. Food Chem Toxicol 2018; 114:292-301. [DOI: 10.1016/j.fct.2018.02.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/14/2018] [Accepted: 02/21/2018] [Indexed: 12/29/2022]
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3
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Izquierdo-Álvarez A, Tello D, Cabrera-García JD, Martínez-Ruiz A. Identification of S-Nitrosylated and Reversibly Oxidized Proteins by Fluorescence Switch and Complementary Techniques. Methods Mol Biol 2018; 1747:73-87. [PMID: 29600452 DOI: 10.1007/978-1-4939-7695-9_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
S-nitrosylation and other reversible oxidative posttranslational modifications of proteins are part of the nonclassical mechanisms of nitric oxide signaling. The biotin switch technique for specifically labeling S-nitrosylated proteins opened the way to proteomic identification of these modifications. Since then, several variations and adaptations of the original method have been applied.We describe here the protocols of several techniques that can be used for the proteomic identification of these modifications, as well as for the detailed characterization of the modification of individual proteins. The fluorescence switch technique allows the proteomic identification of S-nitrosylated proteins based on their fluorescent labeling coupled to electrophoretic separation, as well as the comparison of the overall modification in different samples. The redox fluorescence switch is an adaptation to detect all the proteins reversibly oxidized in cysteine residues. We also describe the protocols of complementary techniques that allow comparing the extent of modification of individual proteins in several conditions by biotin switch, and the identification of modified residues by differential labeling adapted for mass spectrometry identification.
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Affiliation(s)
- Alicia Izquierdo-Álvarez
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain
- Biomechanics Section, KU Leuven, Leuven, Belgium
| | - Daniel Tello
- Unidad de Investigación, Hospital Santa Cristina, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - J Daniel Cabrera-García
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain
| | - Antonio Martínez-Ruiz
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
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4
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Morales-Prieto N, Abril N. REDOX proteomics reveals energy metabolism alterations in the liver of M. spretus mice exposed to p, p'-DDE. CHEMOSPHERE 2017; 186:848-863. [PMID: 28826133 DOI: 10.1016/j.chemosphere.2017.08.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/27/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
The toxicity induced by the pesticide 2,2-bis(p-chlorophenyl)-1,1,1,-trichloroethane (DDT) and its derivative 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (p,p'-DDE) has been associated with mitochondrial dysfunction, uncoupling of oxidative phosphorylation and respiratory chain electron transport, intracellular ion imbalance, generation of reactive oxygen species and impairment of the antioxidant defense system. A disruption in the cellular redox status causes protein Cys-based regulatory shifts that influence the activity of many proteins and trigger signal transduction alterations. Here, we analyzed the ability of p,p'-DDE to alter the activities of hepatic antioxidants and glycolytic enzymes to investigate the oxidative stress generation in the liver of p,p'-DDE-fed M. spretus mice. We also determined the consequences of the treatment on the redox status in the thiol Cys groups. The data indicate that the liver of p,p'-DDE exposed mice lacks certain protective enzymes, and p,p'-DDE caused a metabolic reprogramming that increased the glycolytic rate and disturbed the metabolism of lipids. Our results suggested that the overall metabolism of the liver was altered because important signaling pathways are controlled by p,p'-DDE-deregulated proteins. The histological data support the proposed metabolic consequences of the p,p'-DDE exposure.
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Affiliation(s)
- Noelia Morales-Prieto
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, España, Spain
| | - Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, España, Spain.
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5
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Santofimia-Castaño P, Izquierdo-Alvarez A, Plaza-Davila M, Martinez-Ruiz A, Fernandez-Bermejo M, Mateos-Rodriguez JM, Salido GM, Gonzalez A. Ebselen impairs cellular oxidative state and induces endoplasmic reticulum stress and activation of crucial mitogen-activated protein kinases in pancreatic tumour AR42J cells. J Cell Biochem 2017; 119:1122-1133. [PMID: 28703940 DOI: 10.1002/jcb.26280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/11/2017] [Indexed: 12/25/2022]
Abstract
Ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) is an organoselenium radical scavenger compound, which has strong antioxidant and anti-inflammatory effects. However, evidence suggests that this compound could exert deleterious actions on cell physiology. In this study, we have analyzed the effect of ebselen on rat pancreatic AR42J cells. Cytosolic free-Ca2+ concentration ([Ca2+ ]c ), cellular oxidative status, setting of endoplasmic reticulum stress, and phosphorylation of major mitogen-activated protein kinases were analyzed. Our results show that ebselen evoked a concentration-dependent increase in [Ca2+ ]c . The compound induced an increase in the generation of reactive oxygen species in the mitochondria. We also observed an increase in global cysteine oxidation in the presence of ebselen. In the presence of ebselen an impairment of cholecystokinin-evoked amylase release was noted. Moreover, involvement of the unfolded protein response markers, ER chaperone and signaling regulator GRP78/BiP, eukaryotic translation initiation factor 2α and X-box binding protein 1 was detected. Finally, increases in the phosphorylation of SAPK/JNK, p38 MAPK, and p44/42 MAPK in the presence of ebselen were also observed. Our results provide evidences for an impairment of cellular oxidative state and enzyme secretion, the induction of endoplasmic reticulum stress and the activation of crucial mitogen-activated protein kinases in the presence of ebselen. As a consequence ebselen exerts a potential toxic effect on AR42J cells.
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Affiliation(s)
| | - Alicia Izquierdo-Alvarez
- Servicio de Inmunologia, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain
| | - María Plaza-Davila
- Department of Physiology (Cell Physiology Research Group), University of Extremadura, Caceres, Spain
| | - Antonio Martinez-Ruiz
- Servicio de Inmunologia, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain.,Centro de Investigacion Biomedica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Miguel Fernandez-Bermejo
- Department of Physiology (Cell Physiology Research Group), University of Extremadura, Caceres, Spain.,Department of Gastroenterology, San Pedro de Alcantara Hospital, Caceres, Spain
| | | | - Gines M Salido
- Department of Physiology (Cell Physiology Research Group), University of Extremadura, Caceres, Spain
| | - Antonio Gonzalez
- Department of Physiology (Cell Physiology Research Group), University of Extremadura, Caceres, Spain
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6
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Delobel J, Prudent M, Crettaz D, ElHajj Z, Riederer BM, Tissot JD, Lion N. Cysteine redox proteomics of the hemoglobin-depleted cytosolic fraction of stored red blood cells. Proteomics Clin Appl 2017; 10:883-93. [PMID: 27377365 DOI: 10.1002/prca.201500132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/02/2016] [Accepted: 06/30/2016] [Indexed: 01/17/2023]
Abstract
PURPOSE Erythrocyte concentrates (ECs) represent the most transfused labile blood products. They are stored at 4°C in additive solutions for up to 56 days. Protein oxidation is a marker of oxidative stress and cysteine residues, whose oxidations are required for physiological cell functions, are highly prone to such modification. EXPERIMENTAL DESIGN Five ECs from independent donations were followed. Soluble protein extracts were prepared at days 6, 27, and 41, and cysteines were alkylated, reduced, and labeled with infrared dyes. Samples were mixed two by two (day 6 as reference) and analyzed by 2D-DIGE. Detection of labeled cysteines allows quantitative comparison of oxidative status. Spots of interest were analyzed by proteomics. RESULTS Thirty-two spots containing 43 proteins were classified as increasing, decreasing, or exhibiting a peak of expression during storage. Proteins having catalytic and antioxidant activities were particularly affected during storage, for example, peroxiredoxin-1 and DJ-1 were reversibly oxidized and catalase was irreversibly oxidized. These proteins could be used to evaluate different storage strategies to maintain proper protein function during the overall storage period. CONCLUSIONS AND CLINICAL RELEVANCE This redox-DIGE approach brings new quantitative data on oxidized proteins in stored red blood cells. As previously reported on carbonylation, the oxidative damages differently affect protein functions.
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Affiliation(s)
- Julien Delobel
- Laboratoire de Recherche sur les Produits Sanguins, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Michel Prudent
- Laboratoire de Recherche sur les Produits Sanguins, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - David Crettaz
- Laboratoire de Recherche sur les Produits Sanguins, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Zeinab ElHajj
- Centre des Neurosciences Psychiatriques, Hôpital de Cery-CHUV, Prilly, Switzerland
| | - Beat M Riederer
- Centre des Neurosciences Psychiatriques, Hôpital de Cery-CHUV, Prilly, Switzerland
| | - Jean-Daniel Tissot
- Laboratoire de Recherche sur les Produits Sanguins, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Niels Lion
- Laboratoire de Recherche sur les Produits Sanguins, Transfusion Interrégionale CRS, Epalinges, Switzerland
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Huang H, Haar Petersen M, Ibañez-Vea M, Lassen PS, Larsen MR, Palmisano G. Simultaneous Enrichment of Cysteine-containing Peptides and Phosphopeptides Using a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) in Combination with titanium dioxide (TiO2) Chromatography. Mol Cell Proteomics 2016; 15:3282-3296. [PMID: 27281782 PMCID: PMC5054350 DOI: 10.1074/mcp.m115.054551] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 12/13/2022] Open
Abstract
Cysteine is a rare and conserved amino acid involved in most cellular functions. The thiol group of cysteine can be subjected to diverse oxidative modifications that regulate many physio-pathological states. In the present work, a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) was synthesized to selectively label cysteine-containing peptides (Cys peptides) followed by their enrichment with titanium dioxide (TiO2) and subsequent mass spectrometric analysis. The CysPAT strategy was developed using a synthetic peptide, a standard protein and subsequently the strategy was applied to protein lysates from Hela cells, achieving high specificity and enrichment efficiency. In particular, for Cys proteome analysis, the method led to the identification of 7509 unique Cys peptides from 500 μg of HeLa cell lysate starting material. Furthermore, the method was developed to simultaneously enrich Cys peptides and phosphorylated peptides. This strategy was applied to SILAC labeled Hela cells subjected to 5 min epidermal growth factor (EGF) stimulation. In total, 10440 unique reversibly modified Cys peptides (3855 proteins) and 7339 unique phosphopeptides (2234 proteins) were simultaneously identified from 250 μg starting material. Significant regulation was observed in both phosphorylation and reversible Cys modification of proteins involved in EGFR signaling. Our data indicates that EGF stimulation can activate the well-known phosphorylation of EGFR and downstream signaling molecules, such as mitogen-activated protein kinases (MAPK1 and MAPK3), however, it also leads to substantial modulation of reversible cysteine modifications in numerous proteins. Several protein tyrosine phosphatases (PTPs) showed a reduction of the catalytic Cys site in the conserved putative phosphatase HC(X)5R motif indicating an activation and subsequent de-phosphorylation of proteins involved in the EGF signaling pathway. Overall, the CysPAT strategy is a straight forward, easy and promising method for studying redox proteomics and the simultaneous enrichment strategy offers an excellent solution for characterization of cross-talk between phosphorylation and redox induced reversible cysteine modifications.
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Affiliation(s)
- Honggang Huang
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark; §The Danish Diabetes Academy, Odense, Denmark
| | - Martin Haar Petersen
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark; ¶Institute of Molecular Medicine, Cancer & Inflammation Research, University of Southern Denmark
| | - Maria Ibañez-Vea
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark
| | - Pernille S Lassen
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark
| | - Martin R Larsen
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark
| | - Giuseppe Palmisano
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark; ‖Department of Parasitology, ICB, University of São Paulo, Brazil
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8
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Ebselen alters cellular oxidative status and induces endoplasmic reticulum stress in rat hippocampal astrocytes. Toxicology 2016; 357-358:74-84. [DOI: 10.1016/j.tox.2016.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/08/2023]
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9
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Gunnoo SB, Madder A. Chemical Protein Modification through Cysteine. Chembiochem 2016; 17:529-53. [DOI: 10.1002/cbic.201500667] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Smita B. Gunnoo
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
| | - Annemieke Madder
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
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10
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11
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Söveges B, Imre T, Szende T, Póti ÁL, Cserép GB, Hegedűs T, Kele P, Németh K. A systematic study of protein labeling by fluorogenic probes using cysteine targeting vinyl sulfone-cyclooctyne tags. Org Biomol Chem 2016; 14:6071-8. [DOI: 10.1039/c6ob00810k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein labeling by cycloocytynylated vinyl sulfone linkers is fast and thiol-selective, and subsequent click reaction with fluorogenic azides generates intensive fluorescence.
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Affiliation(s)
- B. Söveges
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - T. Imre
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- MS Metabolomics Research Group
- Hungary
| | - T. Szende
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - Á. L. Póti
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Enzymology
- Protein Research Group
- Hungary
| | - G. B. Cserép
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - T. Hegedűs
- MTA-SE Molecular Biophysics Research Group
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto u. 37-47
- H-1094 Budapest
| | - P. Kele
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - K. Németh
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
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12
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Görlach A, Dimova EY, Petry A, Martínez-Ruiz A, Hernansanz-Agustín P, Rolo AP, Palmeira CM, Kietzmann T. Reactive oxygen species, nutrition, hypoxia and diseases: Problems solved? Redox Biol 2015; 6:372-385. [PMID: 26339717 PMCID: PMC4565025 DOI: 10.1016/j.redox.2015.08.016] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/21/2015] [Accepted: 08/25/2015] [Indexed: 02/06/2023] Open
Abstract
Within the last twenty years the view on reactive oxygen species (ROS) has changed; they are no longer only considered to be harmful but also necessary for cellular communication and homeostasis in different organisms ranging from bacteria to mammals. In the latter, ROS were shown to modulate diverse physiological processes including the regulation of growth factor signaling, the hypoxic response, inflammation and the immune response. During the last 60–100 years the life style, at least in the Western world, has changed enormously. This became obvious with an increase in caloric intake, decreased energy expenditure as well as the appearance of alcoholism and smoking; These changes were shown to contribute to generation of ROS which are, at least in part, associated with the occurrence of several chronic diseases like adiposity, atherosclerosis, type II diabetes, and cancer. In this review we discuss aspects and problems on the role of intracellular ROS formation and nutrition with the link to diseases and their problematic therapeutical issues. Oxidative stress is linked to overnutrition, obesity and associated diseases or cancer. Reactive oxygen species (ROS) are crucially involved in modulation of signaling cascades. NOX proteins and hypoxia contribute to formation of ROS under different nutrient regimes. ROS are powerful post-transcriptional and epigenetic regulators. Treatment of obesity with antioxidants requires more, larger, and better monitored clinical trials.
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Affiliation(s)
- Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Andreas Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Antonio Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
| | - Pablo Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Anabela P Rolo
- Department of Life Sciences, University of Coimbra and Center for Neurosciences and Cell Biology, University of Coimbra, Portugal
| | - Carlos M Palmeira
- Department of Life Sciences, University of Coimbra and Center for Neurosciences and Cell Biology, University of Coimbra, Portugal
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland.
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13
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Boronat S, García-Santamarina S, Hidalgo E. Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation. Free Radic Res 2015; 49:494-510. [PMID: 25782062 DOI: 10.3109/10715762.2015.1009053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.
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Affiliation(s)
- S Boronat
- Departament de Ciències Experimentals i de la Salut, Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , C/Dr. Aiguader 88, E-08003 Barcelona , Spain
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14
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Addepalli B. Detection of disulfide linkage by chemical derivatization and mass spectrometry. Methods Mol Biol 2015; 1255:117-126. [PMID: 25487208 DOI: 10.1007/978-1-4939-2175-1_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The location of disulfide linkage(s) or status of unpaired cysteines is a critical structural feature required for the characterization of three-dimensional structure of a protein and for the correlation of protein structure-function relationships. Cysteine, with its reactive thiol group, can undergo enzymatic or oxidative posttranslational modification in response to changing redox conditions to signal a cascade of downstream reactions. In such a situation, it becomes even more critical to obtain the information on the pair of cysteines involved in such a redox switch operation. Here, a method involving chemical derivatization and liquid chromatography-mass spectrometry (LC-MS) is described to determine the cysteine residues involved in disulfide bond formation for a protein containing multiple cysteines in its sequence.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 312 College Dr, Cincinnati, OH, 45221, USA,
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15
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Couvertier SM, Zhou Y, Weerapana E. Chemical-proteomic strategies to investigate cysteine posttranslational modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2315-30. [PMID: 25291386 DOI: 10.1016/j.bbapap.2014.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023]
Abstract
The unique combination of nucleophilicity and redox-sensitivity that is characteristic of cysteine residues results in a variety of posttranslational modifications (PTMs), including oxidation, nitrosation, glutathionylation, prenylation, palmitoylation and Michael adducts with lipid-derived electrophiles (LDEs). These PTMs regulate the activity of diverse protein families by modulating the reactivity of cysteine nucleophiles within active sites of enzymes, and governing protein localization between soluble and membrane-bound forms. Many of these modifications are highly labile, sensitive to small changes in the environment, and dynamic, rendering it difficult to detect these modified species within a complex proteome. Several chemical-proteomic platforms have evolved to study these modifications and enable a better understanding of the diversity of proteins that are regulated by cysteine PTMs. These platforms include: (1) chemical probes to selectively tag PTM-modified cysteines; (2) differential labeling platforms that selectively reveal and tag PTM-modified cysteines; (3) lipid, isoprene and LDE derivatives containing bioorthogonal handles; and (4) cysteine-reactivity profiling to identify PTM-induced decreases in cysteine nucleophilicity. Here, we will provide an overview of these existing chemical-proteomic strategies and their effectiveness at identifying PTM-modified cysteine residues within native biological systems.
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Affiliation(s)
| | - Yani Zhou
- Boston College, Chestnut Hill, MA 02467, USA
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16
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Santos AI, Martínez-Ruiz A, Araújo IM. S-nitrosation and neuronal plasticity. Br J Pharmacol 2014; 172:1468-78. [PMID: 24962517 DOI: 10.1111/bph.12827] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/08/2014] [Accepted: 06/09/2014] [Indexed: 12/22/2022] Open
Abstract
Nitric oxide (NO) has long been recognized as a multifaceted participant in brain physiology. Despite the knowledge that was gathered over many years regarding the contribution of NO to neuronal plasticity, for example the ability of the brain to change in response to new stimuli, only in recent years have we begun to understand how NO acts on the molecular and cellular level to orchestrate such important phenomena as synaptic plasticity (modification of the strength of existing synapses) or the formation of new synapses (synaptogenesis) and new neurons (neurogenesis). Post-translational modification of proteins by NO derivatives or reactive nitrogen species is a non-classical mechanism for signalling by NO. S-nitrosation is a reversible post-translational modification of thiol groups (mainly on cysteines) that may result in a change of function of the modified protein. S-nitrosation of key target proteins has emerged as a main regulatory mechanism by which NO can influence several levels of brain plasticity, which are reviewed in this work. Understanding how S-nitrosation contributes to neural plasticity can help us to better understand the physiology of these processes, and to better address pathological changes in plasticity that are involved in the pathophysiology of several neurological diseases.
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Affiliation(s)
- A I Santos
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal; IBB - Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine, University of Algarve, Faro, Portugal; Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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17
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Guo J, Nguyen AY, Dai Z, Su D, Gaffrey MJ, Moore RJ, Jacobs JM, Monroe ME, Smith RD, Koppenaal DW, Pakrasi HB, Qian WJ. Proteome-wide light/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics. Mol Cell Proteomics 2014; 13:3270-85. [PMID: 25118246 DOI: 10.1074/mcp.m114.041160] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in photosynthetic organisms. Herein, we present proteome-wide quantitative and site-specific profiling of in vivo thiol oxidation modulated by light/dark in the cyanobacterium Synechocystis sp. PCC 6803, an oxygenic photosynthetic prokaryote, using a resin-assisted thiol enrichment approach. Our proteomic approach integrates resin-assisted enrichment with isobaric tandem mass tag labeling to enable site-specific and quantitative measurements of reversibly oxidized thiols. The redox dynamics of ∼2,100 Cys-sites from 1,060 proteins under light, dark, and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (a photosystem II inhibitor) conditions were quantified. In addition to relative quantification, the stoichiometry or percentage of oxidation (reversibly oxidized/total thiols) for ∼1,350 Cys-sites was also quantified. The overall results revealed broad changes in thiol oxidation in many key biological processes, including photosynthetic electron transport, carbon fixation, and glycolysis. Moreover, the redox sensitivity along with the stoichiometric data enabled prediction of potential functional Cys-sites for proteins of interest. The functional significance of redox-sensitive Cys-sites in NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin (AhpC/TSA family protein Sll1621), and glucose 6-phosphate dehydrogenase was further confirmed with site-specific mutagenesis and biochemical studies. Together, our findings provide significant insights into the broad redox regulation of photosynthetic organisms.
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Affiliation(s)
- Jia Guo
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Amelia Y Nguyen
- ¶Department of Biology, Washington University, St. Louis, Missouri, 63130
| | - Ziyu Dai
- ‖Energy and Efficiency Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Dian Su
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Matthew J Gaffrey
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Ronald J Moore
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Jon M Jacobs
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Matthew E Monroe
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Richard D Smith
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352; ‡‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - David W Koppenaal
- ‡‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Himadri B Pakrasi
- ¶Department of Biology, Washington University, St. Louis, Missouri, 63130
| | - Wei-Jun Qian
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352;
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18
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Moreno ML, Escobar J, Izquierdo-Álvarez A, Gil A, Pérez S, Pereda J, Zapico I, Vento M, Sabater L, Marina A, Martínez-Ruiz A, Sastre J. Disulfide stress: a novel type of oxidative stress in acute pancreatitis. Free Radic Biol Med 2014; 70:265-77. [PMID: 24456905 DOI: 10.1016/j.freeradbiomed.2014.01.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/26/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
Abstract
Glutathione oxidation and protein glutathionylation are considered hallmarks of oxidative stress in cells because they reflect thiol redox status in proteins. Our aims were to analyze the redox status of thiols and to identify mixed disulfides and targets of redox signaling in pancreas in experimental acute pancreatitis as a model of acute inflammation associated with glutathione depletion. Glutathione depletion in pancreas in acute pancreatitis is not associated with any increase in oxidized glutathione levels or protein glutathionylation. Cystine and homocystine levels as well as protein cysteinylation and γ-glutamyl cysteinylation markedly rose in pancreas after induction of pancreatitis. Protein cysteinylation was undetectable in pancreas under basal conditions. Targets of disulfide stress were identified by Western blotting, diagonal electrophoresis, and proteomic methods. Cysteinylated albumin was detected. Redox-sensitive PP2A and tyrosine protein phosphatase activities diminished in pancreatitis and this loss was abrogated by N-acetylcysteine. According to our findings, disulfide stress may be considered a specific type of oxidative stress in acute inflammation associated with protein cysteinylation and γ-glutamylcysteinylation and oxidation of the pair cysteine/cystine, but without glutathione oxidation or changes in protein glutathionylation. Two types of targets of disulfide stress were identified: redox buffers, such as ribonuclease inhibitor or albumin, and redox-signaling thiols, which include thioredoxin 1, APE1/Ref1, Keap1, tyrosine and serine/threonine phosphatases, and protein disulfide isomerase. These targets exhibit great relevance in DNA repair, cell proliferation, apoptosis, endoplasmic reticulum stress, and inflammatory response. Disulfide stress would be a specific mechanism of redox signaling independent of glutathione redox status involved in inflammation.
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Affiliation(s)
- Mari-Luz Moreno
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Javier Escobar
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain; Division of Neonatology, University Hospital Materno-Infantil La Fe, 46026 Valencia, Spain
| | - Alicia Izquierdo-Álvarez
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - Anabel Gil
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Salvador Pérez
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Javier Pereda
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Inés Zapico
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain; Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid, Spain
| | - Máximo Vento
- Division of Neonatology, University Hospital Materno-Infantil La Fe, 46026 Valencia, Spain
| | - Luis Sabater
- Department of Surgery, University Clinic Hospital, University of Valencia, 46010 Valencia, Spain
| | - Anabel Marina
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Martínez-Ruiz
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - Juan Sastre
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain.
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19
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Mermelekas G, Makridakis M, Koeck T, Vlahou A. Redox proteomics: from residue modifications to putative biomarker identification by gel- and LC-MS-based approaches. Expert Rev Proteomics 2014; 10:537-49. [DOI: 10.1586/14789450.2013.855611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Bleijerveld OB, Zhang YN, Beldar S, Hoefer IE, Sze SK, Pasterkamp G, de Kleijn DPV. Proteomics of plaques and novel sources of potential biomarkers for atherosclerosis. Proteomics Clin Appl 2013; 7:490-503. [DOI: 10.1002/prca.201200119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/07/2013] [Accepted: 03/30/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Onno B. Bleijerveld
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ya-Nan Zhang
- Surgery & Cardiovascular Research Institute; National University (NUS) & National University Hospital (NUH); Singapore
| | - Serap Beldar
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Imo E. Hoefer
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Siu K. Sze
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Dominique P. V. de Kleijn
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
- Surgery & Cardiovascular Research Institute; National University (NUS) & National University Hospital (NUH); Singapore
- Interuniversity Cardiology Institute of the Netherlands; Utrecht the Netherlands
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21
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Kroll K, Pähtz V, Kniemeyer O. Elucidating the fungal stress response by proteomics. J Proteomics 2013; 97:151-63. [PMID: 23756228 DOI: 10.1016/j.jprot.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
Abstract
Fungal species need to cope with stress, both in the natural environment and during interaction of human- or plant pathogenic fungi with their host. Many regulatory circuits governing the fungal stress response have already been discovered. However, there are still large gaps in the knowledge concerning the changes of the proteome during adaptation to environmental stress conditions. With the application of proteomic methods, particularly 2D-gel and gel-free, LC/MS-based methods, first insights into the composition and dynamic changes of the fungal stress proteome could be obtained. Here, we review the recent proteome data generated for filamentous fungi and yeasts. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Kristin Kroll
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany
| | - Vera Pähtz
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany.
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22
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Hernansanz-Agustín P, Izquierdo-Álvarez A, García-Ortiz A, Ibiza S, Serrador JM, Martínez-Ruiz A. Nitrosothiols in the immune system: signaling and protection. Antioxid Redox Signal 2013; 18:288-308. [PMID: 22746191 PMCID: PMC3518543 DOI: 10.1089/ars.2012.4765] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE In the immune system, nitric oxide (NO) has been mainly associated with antibacterial defenses exerted through oxidative, nitrosative, and nitrative stress and signal transduction through cyclic GMP-dependent mechanisms. However, S-nitrosylation is emerging as a post-translational modification (PTM) involved in NO-mediated cell signaling. RECENT ADVANCES Precise roles for S-nitrosylation in signaling pathways have been described both for innate and adaptive immunity. Denitrosylation may protect macrophages from their own S-nitrosylation, while maintaining nitrosative stress compartmentalized in the phagosomes. Nitrosothiols have also been shown to be beneficial in experimental models of autoimmune diseases, mainly through their role in modulating T-cell differentiation and function. CRITICAL ISSUES Relationship between S-nitrosylation, other thiol redox PTMs, and other NO-signaling pathways has not been always taken into account, particularly in the context of immune responses. Methods for assaying S-nitrosylation in individual proteins and proteomic approaches to study the S-nitrosoproteome are constantly being improved, which helps to move this field forward. FUTURE DIRECTIONS Integrated studies of signaling pathways in the immune system should consider whether S-nitrosylation/denitrosylation processes are among the PTMs influencing the activity of key signaling and adaptor proteins. Studies in pathophysiological scenarios will also be of interest to put these mechanisms into broader contexts. Interventions modulating nitrosothiol levels in autoimmune disease could be investigated with a view to developing new therapies.
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Affiliation(s)
- Pablo Hernansanz-Agustín
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
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23
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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24
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Differential redox proteomics allows identification of proteins reversibly oxidized at cysteine residues in endothelial cells in response to acute hypoxia. J Proteomics 2012; 75:5449-62. [PMID: 22800641 DOI: 10.1016/j.jprot.2012.06.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 06/13/2012] [Accepted: 06/26/2012] [Indexed: 11/21/2022]
Abstract
Adaptation to decreased oxygen availability (hypoxia) is crucial for proper cell function and survival. In metazoans, this is partly achieved through gene transcriptional responses mediated by hypoxia-inducible factors (HIFs). There is abundant evidence that production of reactive oxygen species (ROS) increases during hypoxia, which contributes to the activation of the HIF pathway. In addition to altering the cellular redox balance, leading to oxidative stress, ROS can transduce signals by reversibly modifying the redox state of cysteine residues in certain proteins. Using the "redox fluorescence switch" (RFS), a thiol redox proteomic technique that fluorescently labels reversibly oxidized cysteines, we analyzed endothelial cells subjected to acute hypoxia and subsequent reoxygenation. We observed a general increase in cysteine oxidation during hypoxia, which was reversed by reoxygenation, and two-dimensional electrophoresis revealed the differential oxidation of specific proteins. Using complementary derivatization techniques, we confirmed the modification of individual target proteins and identified specific cysteine residues that were oxidized in hypoxic conditions, thereby overcoming several limitations associated with fluorescence derivatization. These findings provide an important basis for future studies of the role of these modifications in HIF activation and in other acute adaptive responses to hypoxia.
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