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Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
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2
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Justinić I, Katić A, Uršičić D, Ćurko-Cofek B, Blagović B, Čanadi Jurešić G. Combining proteomics and lipid analysis to unravel Confidor stress response in Saccharomyces cerevisiae. ENVIRONMENTAL TOXICOLOGY 2020; 35:346-358. [PMID: 31696623 DOI: 10.1002/tox.22870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
The yeast Saccharomyces cerevisiae is a useful model for studying the influence of different stress factors on eukaryotic cells. In this work we used the pesticide imidacloprid, in the Confidor formulation, as the stress factor and analyzed its influence on the metabolic activity, proteome and lipid content and composition of Saccharomyces cerevisiae yeast. During the cultivation of yeast, the lowest recommended application dose of Confidor (0.025%, v/v) was added to the growth media and its influence on the mitochondria, cytosol with microsomes, and the whole yeast cells was monitored. The results show that under the stress provoked by the toxic effects of Confidor, yeast cells density significantly decreased and the percentage of metabolically disturbed cells significantly increased comparing with untreated control. Also, there was a downregulation of majority of glycolytic, gluconeogenesis, and TCA cycle enzymes (Fba1, Adh1, Hxk2, Tal1, Tdh1,Tdh3, Eno1) thus providing enough acetyl-CoA for the lipid restructuring and accumulation mechanism since we have found the changes in the cell and mitochondrial lipid content and FA composition. This data suggest that lipids could be the molecules that orchestrate the answer of the cells in the stress response to the Confidor treatment.
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Affiliation(s)
- Iva Justinić
- Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ana Katić
- Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Deni Uršičić
- Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Božena Ćurko-Cofek
- Department of Physiology, Immunology and Patophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Branka Blagović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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3
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Alcock LJ, Langini M, Stühler K, Remke M, Perkins MV, Bernardes GJL, Chalker JM. Proteome‐Wide Survey of Cysteine Oxidation by Using a Norbornene Probe. Chembiochem 2020; 21:1329-1334. [DOI: 10.1002/cbic.201900729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Lisa J. Alcock
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
| | - Maike Langini
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Molecular Medicine University Hospital Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Michael V. Perkins
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
| | - Gonçalo J. L. Bernardes
- University of Cambridge Department of Chemistry Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Justin M. Chalker
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
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4
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Abstract
Introduction: Protein thiols are susceptible to oxidation in health and disease. Redox proteomics methods facilitate the identification, quantification, and rationalization of oxidation processes including those involving protein thiols. These residues are crucial to understanding redox homeostasis underpinning normal cell functioning and regulation as well as novel biomarkers of pathology and promising novel drug targets.Areas covered: This article reviews redox proteomic approaches to study of protein thiols in some important human pathologies and assesses the clinical potential of individual Cys residues as novel biomarkers for disease detection and as targets for novel treatments.Expert commentary: Although protein thiols are not as routinely used as redox biomarkers as some other lesions such as carbonylation, there has been growing recent interest in their potential. Driven largely by developments in high-resolution mass spectrometry it is possible now to identify proteins that are redox modified at thiol groups or that interact with regulatory oxidoreductases. Thiols that are specifically susceptible to modification by reactive oxygen species can be routinely identified now and quantitative MS can be used to quantify the proportion of a protein that is redox modified.
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Affiliation(s)
- David Sheehan
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
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5
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Sousa BC, Ahmed T, Dann WL, Ashman J, Guy A, Durand T, Pitt AR, Spickett CM. Short-chain lipid peroxidation products form covalent adducts with pyruvate kinase and inhibit its activity in vitro and in breast cancer cells. Free Radic Biol Med 2019; 144:223-233. [PMID: 31173844 DOI: 10.1016/j.freeradbiomed.2019.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
Pyruvate kinase catalyses the last step in glycolysis and has been suggested to contribute to the regulation of aerobic glycolysis in cancer cells. It can be inhibited by oxidation of cysteine residues in vitro and in vivo, which is relevant to the more pro-oxidant state in cancer and proliferating tissues. These conditions also favour lipid peroxidation and the formation of electrophilic fragmentation products, including short-chain aldehydes that can covalently modify proteins. However, as yet few studies have investigated their interactions with pyruvate kinase, so we investigated the effects of three different aldehydes, acrolein, malondialdehyde and 4-hydroxy-2(E)-hexenal (HHE), on the structure and activity of the enzyme. Analysis by LC-MS/MS showed unique modification profiles for each aldehyde, but Cys152, Cys423 and Cys474 were the residues most susceptible to electrophilic modification. Analysis of enzymatic activity under these conditions showed that acrolein was the strongest inhibitor, and at incubation times longer than 2 h, pathophysiological concentrations induced significant effects. Treatment of MCF-7 cells with the aldehydes caused similar losses of pyruvate kinase activity to those observed in vitro, and at lower concentrations than those required to cause cell death, with time and dose-dependent effects; acrolein adducts on Cys152 and Cys358 were detected. Cys358 and Cys474 are located at or near the allosteric or active sites, and formation of adducts on these residues probably contributes to loss of activity at low treatment concentrations. This study provides the first detailed analysis of the structure-activity relationship of C3 and C6 aldehydes with pyruvate kinase, and suggests that reactive short-chain aldehydes generated in diseases with an oxidative aetiology or from environmental exposure such as smoking could be involved in the metabolic alterations observed in cancer cells, through alteration of pyruvate kinase activity.
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Affiliation(s)
- Bebiana C Sousa
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Tanzim Ahmed
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - William L Dann
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Jed Ashman
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK.
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6
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Castro-Torres E, Jiménez-Sandoval P, Romero-Romero S, Fuentes-Pascacio A, López-Castillo LM, Díaz-Quezada C, Fernández-Velasco DA, Torres-Larios A, Brieba LG. Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:950-964. [PMID: 31034710 DOI: 10.1111/tpj.14375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Reactive oxidative species (ROS) and S-glutathionylation modulate the activity of plant cytosolic triosephosphate isomerases (cTPI). Arabidopsis thaliana cTPI (AtcTPI) is subject of redox regulation at two reactive cysteines that function as thiol switches. Here we investigate the role of these residues, AtcTPI-Cys13 and At-Cys218, by substituting them with aspartic acid that mimics the irreversible oxidation of cysteine to sulfinic acid and with amino acids that mimic thiol conjugation. Crystallographic studies show that mimicking AtcTPI-Cys13 oxidation promotes the formation of inactive monomers by reposition residue Phe75 of the neighboring subunit, into a conformation that destabilizes the dimer interface. Mutations in residue AtcTPI-Cys218 to Asp, Lys, or Tyr generate TPI variants with a decreased enzymatic activity by creating structural modifications in two loops (loop 7 and loop 6) whose integrity is necessary to assemble the active site. In contrast with mutations in residue AtcTPI-Cys13, mutations in AtcTPI-Cys218 do not alter the dimeric nature of AtcTPI. Therefore, modifications of residues AtcTPI-Cys13 and AtcTPI-Cys218 modulate AtcTPI activity by inducing the formation of inactive monomers and by altering the active site of the dimeric enzyme, respectively. The identity of residue AtcTPI-Cys218 is conserved in the majority of plant cytosolic TPIs, this conservation and its solvent-exposed localization make it the most probable target for TPI regulation upon oxidative damage by reactive oxygen species. Our data reveal the structural mechanisms by which S-glutathionylation protects AtcTPI from irreversible chemical modifications and re-routes carbon metabolism to the pentose phosphate pathway to decrease oxidative stress.
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Affiliation(s)
- Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Pedro Jiménez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Sergio Romero-Romero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Laura M López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - D Alejandro Fernández-Velasco
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, México City, 04510, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
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7
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Ulrich K, Jakob U. The role of thiols in antioxidant systems. Free Radic Biol Med 2019; 140:14-27. [PMID: 31201851 PMCID: PMC7041647 DOI: 10.1016/j.freeradbiomed.2019.05.035] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/04/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
Abstract
The sulfur biochemistry of the thiol group endows cysteines with a number of highly specialized and unique features that enable them to serve a variety of different functions in the cell. Typically highly conserved in proteins, cysteines are predominantly found in functionally or structurally crucial regions, where they act as stabilizing, catalytic, metal-binding and/or redox-regulatory entities. As highly abundant low molecular weight thiols, cysteine thiols and their oxidized disulfide counterparts are carefully balanced to maintain redox homeostasis in various cellular compartments, protect organisms from oxidative and xenobiotic stressors and partake actively in redox-regulatory and signaling processes. In this review, we will discuss the role of protein thiols as scavengers of hydrogen peroxide in antioxidant enzymes, use thiol peroxidases to exemplify how protein thiols contribute to redox signaling, provide an overview over the diverse set of low molecular weight thiol-based redox systems found in biology, and illustrate how thiol-based redox systems have evolved not only to protect against but to take full advantage of a world full of molecular oxygen.
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Affiliation(s)
- Kathrin Ulrich
- Department of Molecular, Cellular, and Developmental Biology, University of Michgan, Ann Arbor, MI, 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michgan, Ann Arbor, MI, 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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8
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Saccharomyces cerevisiae Cytosolic Thioredoxins Control Glycolysis, Lipid Metabolism, and Protein Biosynthesis under Wine-Making Conditions. Appl Environ Microbiol 2019; 85:AEM.02953-18. [PMID: 30683739 DOI: 10.1128/aem.02953-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/15/2019] [Indexed: 01/17/2023] Open
Abstract
Thioredoxins are small proteins that regulate the cellular redox state, prevent oxidative damage, and play an active role in cell repair. Oxidative stress has proven to be of much relevance in biotechnological processes when the metabolism of Saccharomyces cerevisiae is mainly respiratory. During wine yeast starter production, active dry yeast cytosolic thioredoxin Trx2p is a key player in protecting metabolic enzymes from being oxidized by carbonylation. Less is known about the role of redox control during grape juice fermentation. A mutant strain that lacked both cytosolic thioredoxins, Trx1p and Trx2p, was tested for grape juice fermentation. Its growth and sugar consumption were greatly impaired, which indicates the system's relevance under fermentative conditions. A proteomic analysis indicated that deletion of the genes TRX1 and TRX2 caused a reduction in the ribosomal proteins and factors involved in translation elongation in addition to enzymes for glycolysis and amino acid biosynthesis. A metabolomic analysis of the trx1Δ trx2Δ mutant showed an increase in most proteogenic amino acids, phospholipids, and sphingolipids and higher fatty acid desaturase Ole1p content. Low glycolytic activity was behind the reduced growth and fermentative capacity of the thioredoxin deletion strain. All three hexokinases were downregulated in the mutant strain, but total hexokinase activity remained, probably due to posttranslational regulation. Pyruvate kinase Cdc19p presented an early level of aggregation in the trx1Δ trx2Δ mutant, which may contribute to a diminished hexose metabolism and trigger regulatory mechanisms that could influence the level of glycolytic enzymes.IMPORTANCE Oxidative stress is a common hazardous condition that cells have to face in their lifetime. Oxidative damage may diminish cell vitality and viability by reducing metabolism and eventually leading to aging and ultimate death. Wine yeast Saccharomyces cerevisiae also faces oxidative attack during its biotechnological uses. One of the main yeast antioxidant systems involves two small proteins called thioredoxins. When these two proteins are removed, wine yeast shows diminished growth, protein synthesis, and sugar metabolism under wine-making conditions, and amino acid and lipid metabolism are also affected. Altogether, our results indicate that proper redox regulation is a key factor for metabolic adaptations during grape juice fermentation.
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9
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Cobley JN, Sakellariou GK, Husi H, McDonagh B. Proteomic strategies to unravel age-related redox signalling defects in skeletal muscle. Free Radic Biol Med 2019; 132:24-32. [PMID: 30219702 DOI: 10.1016/j.freeradbiomed.2018.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/22/2018] [Accepted: 09/12/2018] [Indexed: 01/06/2023]
Abstract
Increased oxidative damage and disrupted redox signalling are consistently associated with age-related loss of skeletal muscle mass and function. Redox signalling can directly regulate biogenesis and degradation pathways and indirectly via activation of key transcription factors. Contracting skeletal muscle fibres endogenously generate free radicals (e.g. superoxide) and non-radical derivatives (e.g. hydrogen peroxide). Exercise induced redox signalling can promote beneficial adaptive responses that are disrupted by age-related redox changes. Identifying and quantifying the redox signalling pathways responsible for successful adaptation to exercise makes skeletal muscle an attractive physiological model for redox proteomic approaches. Site specific identification of the redox modification and quantification of site occupancy in the context of protein abundance remains a crucial concept for redox proteomics approaches. Notwithstanding, the technical limitations associated with skeletal muscle for proteomic analysis, we discuss current approaches for the identification and quantification of transient and stable redox modifications that have been employed to date in ageing research. We also discuss recent developments in proteomic approaches in skeletal muscle and potential implications and opportunities for investigating disrupted redox signalling in skeletal muscle ageing.
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Affiliation(s)
- James N Cobley
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | | | - Holger Husi
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, NUI Galway, Ireland.
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10
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Erdős G, Mészáros B, Reichmann D, Dosztányi Z. Large-Scale Analysis of Redox-Sensitive Conditionally Disordered Protein Regions Reveals Their Widespread Nature and Key Roles in High-Level Eukaryotic Processes. Proteomics 2019; 19:e1800070. [PMID: 30628183 DOI: 10.1002/pmic.201800070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/13/2018] [Indexed: 12/17/2022]
Abstract
Recently developed quantitative redox proteomic studies enable the direct identification of redox-sensing cysteine residues that regulate the functional behavior of target proteins in response to changing levels of reactive oxygen species. At the molecular level, redox regulation can directly modify the active sites of enzymes, although a growing number of examples indicate the importance of an additional underlying mechanism that involves conditionally disordered proteins. These proteins alter their functional behavior by undergoing a disorder-to-order transition in response to changing redox conditions. However, the extent to which this mechanism is used in various proteomes is currently unknown. Here, a recently developed sequence-based prediction tool incorporated into the IUPred2A web server is used to estimate redox-sensitive conditionally disordered regions at a large scale. It is shown that redox-sensitive conditional disorder is fairly widespread in various proteomes and that its presence strongly correlates with the expansion of specific domains in multicellular organisms that largely rely on extra stability provided by disulfide bonds or zinc ion binding. The analyses of yeast redox proteomes and human disease data further underlie the significance of this phenomenon in the regulation of a wide range of biological processes, as well as its biomedical importance.
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Affiliation(s)
- Gábor Erdős
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Bálint Mészáros
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
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11
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Fernando U, Chatur S, Joshi M, Thomas Bonner C, Fan T, Hubbard K, Chabot D, Rowland O, Wang L, Subramaniam R, Rampitsch C. Redox signalling from NADPH oxidase targets metabolic enzymes and developmental proteins in Fusarium graminearum. MOLECULAR PLANT PATHOLOGY 2019; 20:92-106. [PMID: 30113774 PMCID: PMC6430467 DOI: 10.1111/mpp.12742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
NADPH oxidase (NOX) is one of the sources of reactive oxygen species (ROS) that modulates the activity of proteins through modifications of their cysteine residues. In a previous study, we demonstrated the importance of NOX in both the development and pathogenicity of the phytopathogen Fusarium graminearum. In this article, comparative proteomics between the wild-type and a Nox mutant of F. graminearum was used to identify active cysteine residues on candidate redox-sensing proteins. A two-dimensional gel approach based on labelling with monobromobimane (mBBR) identified 19 candidate proteins, and was complemented with a gel-free shotgun approach based on a biotin switch method, which yielded 99 candidates. The results indicated that, in addition to temporal regulation, a large number of primary metabolic enzymes are potentially targeted by NoxAB-generated ROS. Targeted disruption of these metabolic genes showed that, although some are dispensable, others are essential. In addition to metabolic enzymes, developmental proteins, such as the Woronin body major protein (FGSG_08737) and a glycosylphosphatidylinositol (GPI)-anchored protein (FGSG_10089), were also identified. Deletion of either of these genes reduced the virulence of F. graminearum. Furthermore, changing the redox-modified cysteine (Cys325 ) residue in FGSG_10089 to either serine or phenylalanine resulted in a similar phenotype to the FGSG_10089 knockout strain, which displayed reduced virulence and altered cell wall morphology; this underscores the importance of Cys325 to the function of the protein. Our results indicate that NOX-generated ROS act as intracellular signals in F. graminearum and modulate the activity of proteins affecting development and virulence in planta.
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Affiliation(s)
- Ursla Fernando
- Agriculture and Agrifood Canada, Morden Research & Development CentreMordenR6M 1Y5MBCanada
| | - Salima Chatur
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Manisha Joshi
- Agriculture and Agrifood Canada, Morden Research & Development CentreMordenR6M 1Y5MBCanada
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Christopher Thomas Bonner
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
- Department of BiologyCarleton UniversityOttawaK1S 5B6ONCanada
| | - Tao Fan
- Agriculture and Agrifood Canada, Morden Research & Development CentreMordenR6M 1Y5MBCanada
| | - Keith Hubbard
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Denise Chabot
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Owen Rowland
- Department of BiologyCarleton UniversityOttawaK1S 5B6ONCanada
| | - Li Wang
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Rajagopal Subramaniam
- Agriculture and Agrifood Canada, Ottawa Research & Development CentreOttawaK1A 0C6ONCanada
| | - Christof Rampitsch
- Agriculture and Agrifood Canada, Morden Research & Development CentreMordenR6M 1Y5MBCanada
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12
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Castro-Torres E, Jimenez-Sandoval P, Fernández-de Gortari E, López-Castillo M, Baruch-Torres N, López-Hidalgo M, Peralta-Castro A, Díaz-Quezada C, Sotelo-Mundo RR, Benitez-Cardoza CG, Espinoza-Fonseca LM, Ochoa-Leyva A, Brieba LG. Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic Bacteria Synechocystis. Front Mol Biosci 2018; 5:103. [PMID: 30538993 PMCID: PMC6277545 DOI: 10.3389/fmolb.2018.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 11/05/2018] [Indexed: 11/18/2022] Open
Abstract
In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria Synechocystis (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α)8 fold. We found that oxidizing agents diamide (DA) and H2O2, as well as thiol-conjugating agents such as oxidized glutathione (GSSG) and methyl methanethiosulfonate (MMTS), do not inhibit the catalytic activity of SyTPI at concentrations required to inactivate plastidic and cytosolic TPIs from the plant model Arabidopsis thaliana (AtpdTPI and AtcTPI, respectively). The crystal structure of SyTPI revealed that each monomer contains three cysteines, C47, C127, and C176; however only the thiol group of C176 is solvent exposed. While AtcTPI and AtpdTPI are redox-regulated by chemical modifications of their accessible and reactive cysteines, we found that C176 of SyTPI is not sensitive to redox modification in vitro. Our data let us postulate that SyTPI was replaced by a eukaryotic TPI, because the latter contains redox-sensitive cysteines that may be subject to post-translational modifications required for modulating TPI's enzymatic activity.
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Affiliation(s)
- Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Eli Fernández-de Gortari
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States
| | - Margarita López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico
| | - L Michel Espinoza-Fonseca
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
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López-Grueso MJ, González-Ojeda R, Requejo-Aguilar R, McDonagh B, Fuentes-Almagro CA, Muntané J, Bárcena JA, Padilla CA. Thioredoxin and glutaredoxin regulate metabolism through different multiplex thiol switches. Redox Biol 2018; 21:101049. [PMID: 30639960 PMCID: PMC6327914 DOI: 10.1016/j.redox.2018.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/08/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to define the role of Trx and Grx on metabolic thiol redox regulation and identify their protein and metabolite targets. The hepatocarcinoma-derived HepG2 cell line under both normal and oxidative/nitrosative conditions by overexpression of NO synthase (NOS3) was used as experimental model. Grx1 or Trx1 silencing caused conspicuous changes in the redox proteome reflected by significant changes in the reduced/oxidized ratios of specific Cys's including several glycolytic enzymes. Cys91 of peroxiredoxin-6 (PRDX6) and Cys153 of phosphoglycerate mutase-1 (PGAM1), that are known to be involved in progression of tumor growth, are reported here for the first time as specific targets of Grx1. A group of proteins increased their CysRED/CysOX ratio upon Trx1 and/or Grx1 silencing, including caspase-3 Cys163, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) Cys247 and triose-phosphate isomerase (TPI) Cys255 likely by enhancement of NOS3 auto-oxidation. The activities of several glycolytic enzymes were also significantly affected. Glycolysis metabolic flux increased upon Trx1 silencing, whereas silencing of Grx1 had the opposite effect. Diversion of metabolic fluxes toward synthesis of fatty acids and phospholipids was observed in siRNA-Grx1 treated cells, while siRNA-Trx1 treated cells showed elevated levels of various sphingomyelins and ceramides and signs of increased protein degradation. Glutathione synthesis was stimulated by both treatments. These data indicate that Trx and Grx have both, common and specific protein Cys redox targets and that down regulation of either redoxin has markedly different metabolic outcomes. They reflect the delicate sensitivity of redox equilibrium to changes in any of the elements involved and the difficulty of forecasting metabolic responses to redox environmental changes. Trx1 and Grx1 Cys redox targets are abundant among Glycolytic enzymes. PRDX6-Cys91 and PGAM-Cys153 are specific targets of Grx1. Down regulation of thioredoxin and glutaredoxin have different metabolic outcomes. Glutathione synthesis and membrane lipid composition are sensitive to Trx1 and Grx1 down regulation. Redoxins down regulation also induce target Cys reductive changes under NOS3 overexpression.
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Affiliation(s)
- M J López-Grueso
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - R González-Ojeda
- Institute of Biomedicine of Seville (IBIS), IBiS/"Virgen del Rocío" University Hospital/CSIC/University of Seville, Seville, Spain
| | - R Requejo-Aguilar
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - B McDonagh
- Dept. of Physiology, School of Medicine, NUI Galway, Ireland
| | | | - J Muntané
- Dept. of Physiology, School of Medicine, NUI Galway, Ireland
| | - J A Bárcena
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
| | - C A Padilla
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
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Redox regulation of pyruvate kinase M2 by cysteine oxidation and S-nitrosation. Biochem J 2018; 475:3275-3291. [PMID: 30254098 PMCID: PMC6208296 DOI: 10.1042/bcj20180556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/09/2023]
Abstract
We show here that the M2 isoform of human pyruvate kinase (M2PYK) is susceptible to nitrosation and oxidation, and that these modifications regulate enzyme activity by preventing the formation of the active tetrameric form. The biotin-switch assay carried out on M1 and M2 isoforms showed that M2PYK is sensitive to nitrosation and that Cys326 is highly susceptible to redox modification. Structural and enzymatic studies have been carried out on point mutants for three cysteine residues (Cys424, Cys358, and Cys326) to characterise their potential roles in redox regulation. Nine cysteines are conserved between M2PYK and M1PYK. Cys424 is the only cysteine unique to M2PYK. C424S, C424A, and C424L showed a moderate effect on enzyme activity with 80, 100, and 140% activity, respectively, compared with M2PYK. C358 had been previously identified from in vivo studies to be the favoured target for oxidation. Our characterised mutant showed that this mutation stabilises tetrameric M2PYK, suggesting that the in vivo resistance to oxidation for the Cys358Ser mutation is due to stabilisation of the tetrameric form of the enzyme. In contrast, the Cys326Ser mutant exists predominantly in monomeric form. A biotin-switch assay using this mutant also showed a significant reduction in biotinylation of M2PYK, confirming that this is a major target for nitrosation and probably oxidation. Our results show that the sensitivity of M2PYK to oxidation and nitrosation is regulated by its monomer–tetramer equilibrium. In the monomer state, residues (in particular C326) are exposed to oxidative modifications that prevent reformation of the active tetrameric form.
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15
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Dumont S, Bykova NV, Khaou A, Besserour Y, Dorval M, Rivoal J. Arabidopsis thaliana alcohol dehydrogenase is differently affected by several redox modifications. PLoS One 2018; 13:e0204530. [PMID: 30252897 PMCID: PMC6155552 DOI: 10.1371/journal.pone.0204530] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
In plant cells, many stresses, including low oxygen availability, result in a higher production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These molecules can lead to redox-dependent post-translational modification of proteins Cys residues. Here, we studied the effect of different redox modifications on alcohol dehydrogenase (ADH) from Arabidopsis thaliana. ADH catalyzes the last step of the ethanol fermentation pathway used by plants to cope with energy deficiency during hypoxic stress. Arabidopsis suspension cell cultures showed decreased ADH activity upon exposure to H2O2, but not to the thiol oxidizing agent diamide. We purified recombinant ADH and observed a significant decrease in the enzyme activity by treatments with H2O2 and diethylamine NONOate (DEA/NO). Treatments leading to the formation of a disulfide bond between ADH and glutathione (protein S-glutathionylation) had no negative effect on the enzyme activity. LC-MS/MS analysis showed that Cys47 and Cys243 could make a stable disulfide bond with glutathione, suggesting redox sensitivity of these residues. Mutation of ADH Cys47 to Ser caused an almost complete loss of the enzyme activity while the Cys243 to Ser mutant had increased specific activity. Incubation of ADH with NAD+ or NADH prevented inhibition of the enzyme by H2O2 or DEA/NO. These results suggest that binding of ADH with its cofactors may limit availability of Cys residues to redox modifications. Our study demonstrates that ADH from A. thaliana is subject to different redox modifications. Implications of ADH sensitivity to ROS and RNS during hypoxic stress conditions are discussed.
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Affiliation(s)
- Sébastien Dumont
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Natalia V. Bykova
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Alexia Khaou
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Yasmine Besserour
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Maude Dorval
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Ulrich K, Finkenzeller C, Merker S, Rojas F, Matthews K, Ruppert T, Krauth-Siegel RL. Stress-Induced Protein S-Glutathionylation and S-Trypanothionylation in African Trypanosomes-A Quantitative Redox Proteome and Thiol Analysis. Antioxid Redox Signal 2017; 27:517-533. [PMID: 28338335 PMCID: PMC5567454 DOI: 10.1089/ars.2016.6947] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIMS Trypanosomatids have a unique trypanothione-based thiol redox metabolism. The parasite-specific dithiol is synthesized from glutathione and spermidine, with glutathionylspermidine as intermediate catalyzed by trypanothione synthetase. In this study, we address the oxidative stress response of African trypanosomes with special focus on putative protein S-thiolation. RESULTS Challenging bloodstream Trypanosoma brucei with diamide, H2O2 or hypochlorite results in distinct levels of reversible overall protein S-thiolation. Quantitative proteome analyses reveal 84 proteins oxidized in diamide-stressed parasites. Fourteen of them, including several essential thiol redox proteins and chaperones, are also enriched when glutathione/glutaredoxin serves as a reducing system indicating S-thiolation. In parasites exposed to H2O2, other sets of proteins are modified. Only three proteins are S-thiolated under all stress conditions studied in accordance with a highly specific response. H2O2 causes primarily the formation of free disulfides. In contrast, in diamide-treated cells, glutathione, glutathionylspermidine, and trypanothione are almost completely protein bound. Remarkably, the total level of trypanothione is decreased, whereas those of glutathione and glutathionylspermidine are increased, indicating partial hydrolysis of protein-bound trypanothione. Depletion of trypanothione synthetase exclusively induces protein S-glutathionylation. Total mass analyses of a recombinant peroxidase treated with T(SH)2 and either diamide or hydrogen peroxide verify protein S-trypanothionylation as stable modification. INNOVATION Our data reveal for the first time that trypanosomes employ protein S-thiolation when exposed to exogenous and endogenous oxidative stresses and trypanothione, despite its dithiol character, forms protein-mixed disulfides. CONCLUSION The stress-specific responses shown here emphasize protein S-trypanothionylation and S-glutathionylation as reversible protection mechanism in these parasites. Antioxid. Redox Signal. 27, 517-533.
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Affiliation(s)
- Kathrin Ulrich
- 1 Biochemie-Zentrum der Universität Heidelberg (BZH) , Heidelberg, Germany
| | | | - Sabine Merker
- 2 Zentrum für Molekularbiologie der Universität Heidelberg (ZMBH) , Heidelberg, Germany
| | - Federico Rojas
- 3 Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh , Edinburgh, United Kingdom
| | - Keith Matthews
- 3 Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh , Edinburgh, United Kingdom
| | - Thomas Ruppert
- 2 Zentrum für Molekularbiologie der Universität Heidelberg (ZMBH) , Heidelberg, Germany
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Biological and Chemical Adaptation to Endogenous Hydrogen Peroxide Production in Streptococcus pneumoniae D39. mSphere 2017; 2:mSphere00291-16. [PMID: 28070562 PMCID: PMC5214746 DOI: 10.1128/msphere.00291-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/04/2016] [Indexed: 12/29/2022] Open
Abstract
Adaptation to endogenous oxidative stress is an integral aspect of Streptococcus pneumoniae colonization and virulence. In this work, we identify key transcriptomic and proteomic features of the pneumococcal endogenous oxidative stress response. The thiol peroxidase TpxD plays a critical role in adaptation to endogenous H2O2 and serves to limit protein sulfenylation of glycolytic, capsule, and nucleotide biosynthesis enzymes in S. pneumoniae. The catalase-negative, facultative anaerobe Streptococcus pneumoniae D39 is naturally resistant to hydrogen peroxide (H2O2) produced endogenously by pyruvate oxidase (SpxB). Here, we investigate the adaptive response to endogenously produced H2O2. We show that lactate oxidase, which converts lactate to pyruvate, positively impacts pyruvate flux through SpxB and that ΔlctO mutants produce significantly lower H2O2. In addition, both the SpxB pathway and a candidate pyruvate dehydrogenase complex (PDHC) pathway contribute to acetyl coenzyme A (acetyl-CoA) production during aerobic growth, and the pyruvate format lyase (PFL) pathway is the major acetyl-CoA pathway during anaerobic growth. Microarray analysis of the D39 strain cultured under aerobic versus strict anaerobic conditions shows upregulation of spxB, a gene encoding a rhodanese-like protein (locus tag spd0091), tpxD, sodA, piuB, piuD, and an Fe-S protein biogenesis operon under H2O2-producing conditions. Proteome profiling of H2O2-induced sulfenylation reveals that sulfenylation levels correlate with cellular H2O2 production, with endogenous sulfenylation of ≈50 proteins. Deletion of tpxD increases cellular sulfenylation 5-fold and has an inhibitory effect on ATP generation. Two major targets of protein sulfenylation are glyceraldehyde-3-phosphate dehydrogenase (GapA) and SpxB itself, but targets also include pyruvate kinase, LctO, AdhE, and acetate kinase (AckA). Sulfenylation of GapA is inhibitory, while the effect on SpxB activity is negligible. Strikingly, four enzymes of capsular polysaccharide biosynthesis are sulfenylated, as are enzymes associated with nucleotide biosynthesis via ribulose-5-phosphate. We propose that LctO/SpxB-generated H2O2 functions as a signaling molecule to downregulate capsule production and drive altered flux through sugar utilization pathways. IMPORTANCE Adaptation to endogenous oxidative stress is an integral aspect of Streptococcus pneumoniae colonization and virulence. In this work, we identify key transcriptomic and proteomic features of the pneumococcal endogenous oxidative stress response. The thiol peroxidase TpxD plays a critical role in adaptation to endogenous H2O2 and serves to limit protein sulfenylation of glycolytic, capsule, and nucleotide biosynthesis enzymes in S. pneumoniae.
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Briehl MM. Oxygen in human health from life to death--An approach to teaching redox biology and signaling to graduate and medical students. Redox Biol 2015; 5:124-139. [PMID: 25912168 PMCID: PMC4412967 DOI: 10.1016/j.redox.2015.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023] Open
Abstract
In the absence of oxygen human life is measured in minutes. In the presence of oxygen, normal metabolism generates reactive species (ROS) that have the potential to cause cell injury contributing to human aging and disease. Between these extremes, organisms have developed means for sensing oxygen and ROS and regulating their cellular processes in response. Redox signaling contributes to the control of cell proliferation and death. Aberrant redox signaling underlies many human diseases. The attributes acquired by altered redox homeostasis in cancer cells illustrate this particularly well. This teaching review and the accompanying illustrations provide an introduction to redox biology and signaling aimed at instructors of graduate and medical students. The ability to sense oxygen and respond to oxidative stress is ancient. Chemical and kinetic properties of ROS are key to understanding redox signaling. Redox signaling participates in normal control of cell proliferation and death. Aberrant redox signaling contributes to the hallmarks of cancer. Novel redox-based chemotherapeutics are being developed.
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Affiliation(s)
- Margaret M Briehl
- Department of Pathology, University of Arizona, PO Box 24-5043, Tucson, AZ 85724-5043, USA.
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Correani V, Francesco LD, Cera I, Mignogna G, Giorgi A, Mazzanti M, Fumagalli L, Fabrizi C, Maras B, Schininà ME. Reversible redox modifications in the microglial proteome challenged by beta amyloid. MOLECULAR BIOSYSTEMS 2015; 11:1584-93. [DOI: 10.1039/c4mb00703d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reversible redox modifications of the microglial proteome contribute to switching of these neuronal sentinel cells toward a neuroinflammatory phenotype.
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Affiliation(s)
- Virginia Correani
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Laura Di Francesco
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Isabella Cera
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Giuseppina Mignogna
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Michele Mazzanti
- Dipartimento di Bioscienze
- Università degli Studi di Milano
- Milan
- Italy
| | - Lorenzo Fumagalli
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Cinzia Fabrizi
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Bruno Maras
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - M. Eugenia Schininà
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
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Chardonnet S, Sakr S, Cassier-Chauvat C, Le Maréchal P, Chauvat F, Lemaire SD, Decottignies P. First proteomic study of S-glutathionylation in cyanobacteria. J Proteome Res 2014; 14:59-71. [PMID: 25208982 DOI: 10.1021/pr500625a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glutathionylation, the reversible post-translational formation of a mixed disulfide between a cysteine residue and glutathione (GSH), is a crucial mechanism for signal transduction and regulation of protein function. Until now this reversible redox modification was studied mainly in eukaryotic cells. Here we report a large-scale proteomic analysis of glutathionylation in a photosynthetic prokaryote, the model cyanobacterium Synechocystis sp. PCC6803. Treatment of acellular extracts with N,N-biotinyl glutathione disulfide (BioGSSG) induced glutathionylation of numerous proteins, which were subsequently isolated by affinity chromatography on streptavidin columns and identified by nano LC-MS/MS analysis. Potential sites of glutathionylation were also determined for 125 proteins following tryptic cleavage, streptavidin-affinity purification, and mass spectrometry analysis. Taken together the two approaches allowed the identification of 383 glutathionylatable proteins that participate in a wide range of cellular processes and metabolic pathways such as carbon and nitrogen metabolisms, cell division, stress responses, and H2 production. In addition, the glutathionylation of two putative targets, namely, peroxiredoxin (Sll1621) involved in oxidative stress tolerance and 3-phosphoglycerate dehydrogenase (Sll1908) acting on amino acids metabolism, was confirmed by biochemical studies on the purified recombinant proteins. These results suggest that glutathionylation constitutes a major mechanism of global regulation of the cyanobacterial metabolism under oxidative stress conditions.
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McDonagh B, Sakellariou GK, Smith NT, Brownridge P, Jackson MJ. Differential cysteine labeling and global label-free proteomics reveals an altered metabolic state in skeletal muscle aging. J Proteome Res 2014; 13:5008-21. [PMID: 25181601 PMCID: PMC4227305 DOI: 10.1021/pr5006394] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The
molecular mechanisms underlying skeletal muscle aging and associated
sarcopenia have been linked to an altered oxidative status of redox-sensitive
proteins. Reactive oxygen and reactive nitrogen species (ROS/RNS)
generated by contracting skeletal muscle are necessary for optimal
protein function, signaling, and adaptation. To investigate the redox
proteome of aging gastrocnemius muscles from adult and old male mice,
we developed a label-free quantitative proteomic approach that includes
a differential cysteine labeling step. The approach allows simultaneous
identification of up- and downregulated proteins between samples in
addition to the identification and relative quantification of the
reversible oxidation state of susceptible redox cysteine residues.
Results from muscles of adult and old mice indicate significant changes
in the content of chaperone, glucose metabolism, and cytoskeletal
regulatory proteins, including Protein DJ-1, cAMP-dependent protein
kinase type II, 78 kDa glucose regulated protein, and a reduction
in the number of redox-responsive proteins identified in muscle of
old mice. Results demonstrate skeletal muscle aging causes a reduction
in redox-sensitive proteins involved in the generation of precursor
metabolites and energy metabolism, indicating a loss in the flexibility
of the redox energy response. Data is available via ProteomeXchange
with identifier PXD001054.
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Affiliation(s)
- Brian McDonagh
- MRC-Arthritis Research UK Centre for Integrated Research into Musculoskeletal Aging (CIMA), Skeletal Muscle Pathophysiology Research Group, Institute of Ageing and Chronic Disease, ‡Protein Function Group, Institute of Integrative Biology, University of Liverpool , Liverpool L69 3GA, United Kingdom
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22
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Ilyas S, Rehman A, Varela AC, Sheehan D. Redox proteomics changes in the fungal pathogen Trichosporon asahii on arsenic exposure: identification of protein responses to metal-induced oxidative stress in an environmentally-sampled isolate. PLoS One 2014; 9:e102340. [PMID: 25062082 PMCID: PMC4111368 DOI: 10.1371/journal.pone.0102340] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/18/2014] [Indexed: 01/25/2023] Open
Abstract
Trichosporon asahii is a yeast pathogen implicated in opportunistic infections. Cultures of an isolate collected from industrial wastewater were exposed for 2 days to 100 mg/L sodium arsenite (NaAsO2) and cadmium (CdCl2). Both metals reduced glutathione transferase (GST) activity but had no effect on superoxide dismutase or catalase. NaAsO2 exposure increased glutathione reductase activity while CdCl2 had no effect. Protein thiols were labeled with 5-iodoacetamido fluorescein followed by one dimensional electrophoresis which revealed extensive protein thiol oxidation in response to CdCl2 treatment but thiol reduction in response to NaAsO2. Two dimensional electrophoresis analyses showed that the intensity of some protein spots was enhanced on treatment as judged by SameSpots image analysis software. In addition, some spots showed decreased IAF fluorescence suggesting thiol oxidation. Selected spots were excised and tryptic digested for identification by MALDI-TOF/TOF MS. Twenty unique T. asahii proteins were identified of which the following proteins were up-regulated in response to NaAsO2: 3-isopropylmalate dehydrogenase, phospholipase B, alanine-glyoxylate aminotransferase, ATP synthase alpha chain, 20S proteasome beta-type subunit Pre3p and the hypothetical proteins A1Q1_08001, A1Q2_03020, A1Q1_06950, A1Q1_06913. In addition, the following showed decreased thiol-associated fluorescence consistent with thiol oxidation; aconitase; aldehyde reductase I; phosphoglycerate kinase; translation elongation factor 2; heat shock protein 70 and hypothetical protein A1Q2_04745. Some proteins showed both increase in abundance coupled with decrease in IAF fluorescence; 3-hydroxyisobutyryl- CoA hydrolase; homoserine dehydrogenase Hom6 and hypothetical proteins A1Q2_03020 and A1Q1_00754. Targets implicated in redox response included 10 unique metabolic enzymes, heat shock proteins, a component of the 20S proteasome and translation elongation factor 2. These data suggest extensive proteomic alterations in response to metal-induced oxidative stress in T. asahii. Amino acid metabolism, protein folding and degradation are principally affected.
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Affiliation(s)
- Sidra Ilyas
- Dept. Of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Abdul Rehman
- Dept. Of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Ana Coelho Varela
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - David Sheehan
- Environmental Research Institute and School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- * E-mail:
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Rodríguez-Lombardero S, Rodríguez-Belmonte ME, González-Siso MI, Vizoso-Vázquez Á, Valdiglesias V, Laffón B, Cerdán ME. Proteomic analyses reveal that Sky1 modulates apoptosis and mitophagy in Saccharomyces cerevisiae cells exposed to cisplatin. Int J Mol Sci 2014; 15:12573-90. [PMID: 25029545 PMCID: PMC4139861 DOI: 10.3390/ijms150712573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 12/11/2022] Open
Abstract
Sky1 is the only member of the SR (Serine–Arginine) protein kinase family in Saccharomyces cerevisiae. When yeast cells are treated with the anti-cancer drug cisplatin, Sky1 kinase activity is necessary to produce the cytotoxic effect. In this study, proteome changes in response to this drug and/or SKY1 deletion have been evaluated in order to understand the role of Sky1 in the response of yeast cells to cisplatin. Results reveal differential expression of proteins previously related to the oxidative stress response, DNA damage, apoptosis and mitophagy. With these precedents, the role of Sky1 in apoptosis, necrosis and mitophagy has been evaluated by flow-cytometry, fluorescence microscopy, biosensors and fluorescence techniques. After cisplatin treatment, an apoptotic-like process diminishes in the ∆sky1 strain in comparison to the wild-type. The treatment does not affect mitophagy in the wild-type strain, while an increase is observed in the ∆sky1 strain. The increased resistance to cisplatin observed in the ∆sky1 strain may be attributable to a decrease of apoptosis and an increase of mitophagy.
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Affiliation(s)
- Silvia Rodríguez-Lombardero
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esther Rodríguez-Belmonte
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Isabel González-Siso
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Ángel Vizoso-Vázquez
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Vanessa Valdiglesias
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Blanca Laffón
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esperanza Cerdán
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
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Zaccarin M, Falda M, Roveri A, Bosello-Travain V, Bordin L, Maiorino M, Ursini F, Toppo S. Quantitative label-free redox proteomics of reversible cysteine oxidation in red blood cell membranes. Free Radic Biol Med 2014; 71:90-98. [PMID: 24642086 DOI: 10.1016/j.freeradbiomed.2014.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/01/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
Reversible oxidation of cysteine residues is a relevant posttranslational modification of proteins. However, the low activation energy and transitory nature of the redox switch and the intrinsic complexity of the analysis render quite challenging the aim of a rigorous high-throughput screening of the redox status of redox-sensitive cysteine residues. We describe here a quantitative workflow for redox proteomics, where the ratio between the oxidized forms of proteins in the control vs treated samples is determined by a robust label-free approach. We critically present the convenience of the procedure by specifically addressing the following aspects: (i) the accurate ratio, calculated from the whole set of identified peptides rather than just isotope-tagged fragments; (ii) the application of a robust analytical pipeline to frame the most consistent data averaged over the biological variability; (iii) the relevance of using stringent criteria of analysis, even at the cost of losing potentially interesting but statistically uncertain data. The pipeline has been assessed on red blood cell membrane challenged with diamide as a model of a mild oxidative condition. The cluster of identified proteins encompassed components of the cytoskeleton more oxidized. Indirectly, our analysis confirmed the previous observation that oxidized hemoglobin binds to membranes while oxidized peroxiredoxin 2 loses affinity.
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Affiliation(s)
- Mattia Zaccarin
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | - Marco Falda
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | - Antonella Roveri
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | | | - Luciana Bordin
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | - Matilde Maiorino
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | - Fulvio Ursini
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, via A. Gabelli, 63, I-35121 Padova, Italy.
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25
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Navarro P, Trevisan-Herraz M, Bonzon-Kulichenko E, Núñez E, Martínez-Acedo P, Pérez-Hernández D, Jorge I, Mesa R, Calvo E, Carrascal M, Hernáez ML, García F, Bárcena JA, Ashman K, Abian J, Gil C, Redondo JM, Vázquez J. General statistical framework for quantitative proteomics by stable isotope labeling. J Proteome Res 2014; 13:1234-47. [PMID: 24512137 DOI: 10.1021/pr4006958] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The combination of stable isotope labeling (SIL) with mass spectrometry (MS) allows comparison of the abundance of thousands of proteins in complex mixtures. However, interpretation of the large data sets generated by these techniques remains a challenge because appropriate statistical standards are lacking. Here, we present a generally applicable model that accurately explains the behavior of data obtained using current SIL approaches, including (18)O, iTRAQ, and SILAC labeling, and different MS instruments. The model decomposes the total technical variance into the spectral, peptide, and protein variance components, and its general validity was demonstrated by confronting 48 experimental distributions against 18 different null hypotheses. In addition to its general applicability, the performance of the algorithm was at least similar than that of other existing methods. The model also provides a general framework to integrate quantitative and error information fully, allowing a comparative analysis of the results obtained from different SIL experiments. The model was applied to the global analysis of protein alterations induced by low H₂O₂ concentrations in yeast, demonstrating the increased statistical power that may be achieved by rigorous data integration. Our results highlight the importance of establishing an adequate and validated statistical framework for the analysis of high-throughput data.
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Affiliation(s)
- Pedro Navarro
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM , 28049 Madrid, Spain
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26
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27
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Peinado J, López de Lerma N, Peralbo-Molina A, Priego-Capote F, de Castro C, McDonagh B. Sunlight exposure increases the phenolic content in postharvested white grapes. An evaluation of their antioxidant activity in Saccharomyces cerevisiae. J Funct Foods 2013. [DOI: 10.1016/j.jff.2013.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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28
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Thiol redox sensitivity of two key enzymes of heme biosynthesis and pentose phosphate pathways: uroporphyrinogen decarboxylase and transketolase. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:932472. [PMID: 23970950 PMCID: PMC3730168 DOI: 10.1155/2013/932472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/10/2013] [Accepted: 06/19/2013] [Indexed: 12/22/2022]
Abstract
Uroporphyrinogen decarboxylase (Hem12p) and transketolase (Tkl1p) are key mediators of two critical processes within the cell, heme biosynthesis, and the nonoxidative part of the pentose phosphate pathway (PPP). The redox properties of both Hem12p and Tkl1p from Saccharomyces cerevisiae were investigated using proteomic techniques (SRM and label-free quantification) and biochemical assays in cell extracts and in vitro with recombinant proteins. The in vivo analysis revealed an increase in oxidized Cys-peptides in the absence of Grx2p, and also after treatment with H2O2 in the case of Tkl1p, without corresponding changes in total protein, demonstrating a true redox response. Out of three detectable Cys residues in Hem12p, only the conserved residue Cys52 could be modified by glutathione and efficiently deglutathionylated by Grx2p, suggesting a possible redox control mechanism for heme biosynthesis. On the other hand, Tkl1p activity was sensitive to thiol redox modification and although Cys622 could be glutathionylated to a limited extent, it was not a natural substrate of Grx2p. The human orthologues of both enzymes have been involved in certain cancers and possess Cys residues equivalent to those identified as redox sensitive in yeast. The possible implication for redox regulation in the context of tumour progression is put forward.
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29
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López de Lerma N, Peinado J, Peinado RA. In vitro and in vivo antioxidant activity of musts and skin extracts from off-vine dried Vitis vinifera cv. “Tempranillo” grapes. J Funct Foods 2013. [DOI: 10.1016/j.jff.2013.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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30
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Antioxidant defence system during exponential and stationary growth phases of Phycomyces blakesleeanus: Response to oxidative stress by hydrogen peroxide. Fungal Biol 2013; 117:275-87. [DOI: 10.1016/j.funbio.2013.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/23/2022]
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31
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Paulech J, Solis N, Edwards AV, Puckeridge M, White MY, Cordwell SJ. Large-Scale Capture of Peptides Containing Reversibly Oxidized Cysteines by Thiol-Disulfide Exchange Applied to the Myocardial Redox Proteome. Anal Chem 2013; 85:3774-80. [DOI: 10.1021/ac400166e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jana Paulech
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Nestor Solis
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Alistair V.G. Edwards
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Max Puckeridge
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Melanie Y. White
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Stuart J. Cordwell
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
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32
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Identification of proteins containing redox-sensitive thiols after PRDX1, PRDX3 and GCLC silencing and/or glucose oxidase treatment in Hepa 1–6 cells. J Proteomics 2012; 77:262-79. [DOI: 10.1016/j.jprot.2012.08.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/07/2012] [Accepted: 08/22/2012] [Indexed: 12/20/2022]
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33
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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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Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:514847. [PMID: 22844595 PMCID: PMC3403169 DOI: 10.1155/2012/514847] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 04/30/2012] [Indexed: 11/18/2022]
Abstract
Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. Reversible cysteine modifications allow for potential redox regulation of proteins. Traditional measurement of the relative absolute quantity of a protein between two samples is not always necessarily proportional to the activity of the protein. We propose application of iTRAQ reagents in combination with a previous thiol selection method to relatively quantify the redox state of cysteines both within and between samples in a single analysis. Our method allows for the identification of the proteins, identification of redox-sensitive cysteines within proteins, and quantification of the redox status of individual cysteine-containing peptides. As a proof of principle, we applied this technique to yeast alcohol dehydrogenase-1 exposed in vitro to H2O2 and also in vivo to the complex proteome of the Gram-negative bacterium Bacillus subtilis.
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35
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Gregersen N, Hansen J, Palmfeldt J. Mitochondrial proteomics--a tool for the study of metabolic disorders. J Inherit Metab Dis 2012; 35:715-26. [PMID: 22526845 DOI: 10.1007/s10545-012-9480-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 12/14/2022]
Abstract
Mitochondria are important for a number of life and death processes, such as energy production, creation of reactive oxygen species, and elicitation of stress responses. These responses range from induction of protein quality control and antioxidant systems to mitochondria elimination and cell death. Mitochondrial dysfunctions are involved in pathologies associated with many diseases, for example metabolic disorders, diabetes, cancers, cardiovascular and neurodegenerative diseases as well as obesity and aging. Mitochondrial proteomics can be a powerful tool in the study of these diseases, especially since it can cover mitochondrial proteins from several metabolic pathways, such as the citric acid cycle, fatty acid oxidation, and respiratory chain, as well as protein networks involved in stress responses. The mitochondrial proteome can consist of more than 1,000 different proteins. However, it is difficult to define the precise number, since mitochondria are dynamic and difficult to purify, and because an unknown number of proteins possess dual or multiple localization, depending on cell type and physiological conditions. This review describes several quantitative studies of proteins from mitochondria isolated by centrifugation, separated by various methods (e.g., electrophoresis and nanoLC), and analyzed by advanced mass spectrometry. We illustrate the methods by showing that multiple pathways and networks are affected in cells from patients carrying gene variations affecting a mitochondrial protein. The study of cultured skin fibroblasts from patients with ethylmalonic aciduria associated with variations in the genes coding for short-chain acyl-CoA dehydrogenase (SCAD) or ETHE1 are two of the examples. The possibility of obtaining mitochondrial proteomics data from whole cell proteomics studies is also exemplified by the involvement of liver mitochondria in metabolic syndrome.
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Affiliation(s)
- Niels Gregersen
- Research Unit for Molecular Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
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36
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Martínez-Acedo P, Núñez E, Gómez FJS, Moreno M, Ramos E, Izquierdo-Álvarez A, Miró-Casas E, Mesa R, Rodriguez P, Martínez-Ruiz A, Dorado DG, Lamas S, Vázquez J. A novel strategy for global analysis of the dynamic thiol redox proteome. Mol Cell Proteomics 2012; 11:800-13. [PMID: 22647871 DOI: 10.1074/mcp.m111.016469] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nitroxidative stress in cells occurs mainly through the action of reactive nitrogen and oxygen species (RNOS) on protein thiol groups. Reactive nitrogen and oxygen species-mediated protein modifications are associated with pathophysiological states, but can also convey physiological signals. Identification of Cys residues that are modified by oxidative stimuli still poses technical challenges and these changes have never been statistically analyzed from a proteome-wide perspective. Here we show that GELSILOX, a method that combines a robust proteomics protocol with a new computational approach that analyzes variance at the peptide level, allows a simultaneous analysis of dynamic alterations in the redox state of Cys sites and of protein abundance. GELSILOX permits the characterization of the major endothelial redox targets of hydrogen peroxide in endothelial cells and reveals that hypoxia induces a significant increase in the status of oxidized thiols. GELSILOX also detected thiols that are redox-modified by ischemia-reperfusion in heart mitochondria and demonstrated that these alterations are abolished in ischemia-preconditioned animals.
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Affiliation(s)
- Pablo Martínez-Acedo
- Centro de Biología Molecular Severo Ochoa, Nicolás Cabrera 1, 28049 Madrid, Spain
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McDonagh B, Domínguez-Martín MA, Gómez-Baena G, López-Lozano A, Diez J, Bárcena JA, García Fernández JM. Nitrogen starvation induces extensive changes in the redox proteome of Prochlorococcus sp. strain SS120. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:257-267. [PMID: 23757281 DOI: 10.1111/j.1758-2229.2012.00329.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Very low nitrogen concentration is a critical limitation in the oligotrophic oceans inhabited by the cyanobacterium Prochlorococccus, one of the main primary producers on Earth. It is well known that nitrogen starvation affects redox homeostasis in cells. We have studied the effect of nitrogen starvation on the thiol redox proteome in the Prochlorococcus sp. SS120 strain, by using shotgun proteomic techniques to map the cysteine modified in each case and to quantify the ratio of reversibly oxidized/reduced species. We identified a number of proteins showing modified cysteines only under either control or N-starvation, including isocitrate dehydrogenase and ribulose phosphate 3-epimerase. We detected other key enzymes, such as glutamine synthetase, transporters and transaminases, showing that nitrogen-related pathways were deeply affected by nitrogen starvation. Reversibly oxidized cysteines were also detected in proteins of other important metabolic pathways, such as photosynthesis, phosphorus metabolism, ATP synthesis and nucleic acids metabolism. Our results demonstrate a wide effect of nitrogen limitation on the redox status of the Prochlorococcus proteome, suggesting that besides previously reported transcriptional changes, this cyanobacterium responds with post-translational redox changes to the lack of nitrogen in its environment.
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Affiliation(s)
- Brian McDonagh
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Agroalimentario CEIA3, Universidad de Córdoba, Spain
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Thiol redox proteomics seen with fluorescent eyes: The detection of cysteine oxidative modifications by fluorescence derivatization and 2-DE. J Proteomics 2011; 75:329-38. [DOI: 10.1016/j.jprot.2011.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022]
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39
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Zaffagnini M, Bedhomme M, Groni H, Marchand CH, Puppo C, Gontero B, Cassier-Chauvat C, Decottignies P, Lemaire SD. Glutathionylation in the photosynthetic model organism Chlamydomonas reinhardtii: a proteomic survey. Mol Cell Proteomics 2011; 11:M111.014142. [PMID: 22122882 DOI: 10.1074/mcp.m111.014142] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Protein glutathionylation is a redox post-translational modification occurring under oxidative stress conditions and playing a major role in cell regulation and signaling. This modification has been mainly studied in nonphotosynthetic organisms, whereas much less is known in photosynthetic organisms despite their important exposure to oxidative stress caused by changes in environmental conditions. We report a large scale proteomic analysis using biotinylated glutathione and streptavidin affinity chromatography that allowed identification of 225 glutathionylated proteins in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. Moreover, 56 sites of glutathionylation were also identified after peptide affinity purification and tandem mass spectrometry. The targets identified belong to a wide range of biological processes and pathways, among which the Calvin-Benson cycle appears to be a major target. The glutathionylation of four enzymes of this cycle, phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, ribose-5-phosphate isomerase, and phosphoglycerate kinase was confirmed by Western blot and activity measurements. The results suggest that glutathionylation could constitute a major mechanism of regulation of the Calvin-Benson cycle under oxidative stress conditions.
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Affiliation(s)
- Mirko Zaffagnini
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France
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40
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Sulfurous gases as biological messengers and toxins: comparative genetics of their metabolism in model organisms. J Toxicol 2011; 2011:394970. [PMID: 22131987 PMCID: PMC3216388 DOI: 10.1155/2011/394970] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/11/2011] [Indexed: 01/31/2023] Open
Abstract
Gasotransmitters are biologically produced gaseous signalling molecules. As gases with potent biological activities, they are toxic as air pollutants, and the sulfurous compounds are used as fumigants. Most investigations focus on medical aspects of gasotransmitter biology rather than toxicity toward invertebrate pests of agriculture. In fact, the pathways for the metabolism of sulfur containing gases in lower organisms have not yet been described. To address this deficit, we use protein sequences from Homo sapiens to query Genbank for homologous proteins in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. In C. elegans, we find genes for all mammalian pathways for synthesis and catabolism of the three sulfur containing gasotransmitters, H2S, SO2 and COS. The genes for H2S synthesis have actually increased in number in C. elegans. Interestingly, D. melanogaster and Arthropoda in general, lack a gene for 3-mercaptopyruvate sulfurtransferase, an enzym for H2S synthesis under reducing conditions.
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41
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Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang JK, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG, Cantley LC. Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses. Science 2011; 334:1278-83. [PMID: 22052977 DOI: 10.1126/science.1211485] [Citation(s) in RCA: 863] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Control of intracellular reactive oxygen species (ROS) concentrations is critical for cancer cell survival. We show that, in human lung cancer cells, acute increases in intracellular concentrations of ROS caused inhibition of the glycolytic enzyme pyruvate kinase M2 (PKM2) through oxidation of Cys(358). This inhibition of PKM2 is required to divert glucose flux into the pentose phosphate pathway and thereby generate sufficient reducing potential for detoxification of ROS. Lung cancer cells in which endogenous PKM2 was replaced with the Cys(358) to Ser(358) oxidation-resistant mutant exhibited increased sensitivity to oxidative stress and impaired tumor formation in a xenograft model. Besides promoting metabolic changes required for proliferation, the regulatory properties of PKM2 may confer an additional advantage to cancer cells by allowing them to withstand oxidative stress.
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Affiliation(s)
- Dimitrios Anastasiou
- Beth Israel Deaconess Medical Center, Department of Medicine-Division of Signal Transduction, Boston, MA 02115, USA
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Wu C, Parrott AM, Fu C, Liu T, Marino SM, Gladyshev VN, Jain MR, Baykal AT, Li Q, Oka S, Sadoshima J, Beuve A, Simmons WJ, Li H. Thioredoxin 1-mediated post-translational modifications: reduction, transnitrosylation, denitrosylation, and related proteomics methodologies. Antioxid Redox Signal 2011; 15:2565-604. [PMID: 21453190 PMCID: PMC3176348 DOI: 10.1089/ars.2010.3831] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite the significance of redox post-translational modifications (PTMs) in regulating diverse signal transduction pathways, the enzymatic systems that catalyze reversible and specific oxidative or reductive modifications have yet to be firmly established. Thioredoxin 1 (Trx1) is a conserved antioxidant protein that is well known for its disulfide reductase activity. Interestingly, Trx1 is also able to transnitrosylate or denitrosylate (defined as processes to transfer or remove a nitric oxide entity to/from substrates) specific proteins. An intricate redox regulatory mechanism has recently been uncovered that accounts for the ability of Trx1 to catalyze these different redox PTMs. In this review, we will summarize the available evidence in support of Trx1 as a specific disulfide reductase, and denitrosylation and transnitrosylation agent, as well as the biological significance of the diverse array of Trx1-regulated pathways and processes under different physiological contexts. The dramatic progress in redox proteomics techniques has enabled the identification of an increasing number of proteins, including peroxiredoxin 1, whose disulfide bond formation and nitrosylation status are regulated by Trx1. This review will also summarize the advancements of redox proteomics techniques for the identification of the protein targets of Trx1-mediated PTMs. Collectively, these studies have shed light on the mechanisms that regulate Trx1-mediated reduction, transnitrosylation, and denitrosylation of specific target proteins, solidifying the role of Trx1 as a master regulator of redox signal transduction.
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Affiliation(s)
- Changgong Wu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, Newark, 07103, USA
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Brandes N, Reichmann D, Tienson H, Leichert LI, Jakob U. Using quantitative redox proteomics to dissect the yeast redoxome. J Biol Chem 2011; 286:41893-41903. [PMID: 21976664 DOI: 10.1074/jbc.m111.296236] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To understand and eventually predict the effects of changing redox conditions and oxidant levels on the physiology of an organism, it is essential to gain knowledge about its redoxome: the proteins whose activities are controlled by the oxidation status of their cysteine thiols. Here, we applied the quantitative redox proteomic method OxICAT to Saccharomyces cerevisiae and determined the in vivo thiol oxidation status of almost 300 different yeast proteins distributed among various cellular compartments. We found that a substantial number of cytosolic and mitochondrial proteins are partially oxidized during exponential growth. Our results suggest that prevailing redox conditions constantly control central cellular pathways by fine-tuning oxidation status and hence activity of these proteins. Treatment with sublethal H(2)O(2) concentrations caused a subset of 41 proteins to undergo substantial thiol modifications, thereby affecting a variety of different cellular pathways, many of which are directly or indirectly involved in increasing oxidative stress resistance. Classification of the identified protein thiols according to their steady-state oxidation levels and sensitivity to peroxide treatment revealed that redox sensitivity of protein thiols does not predict peroxide sensitivity. Our studies provide experimental evidence that the ability of protein thiols to react to changing peroxide levels is likely governed by both thermodynamic and kinetic parameters, making predicting thiol modifications challenging and de novo identification of peroxide sensitive protein thiols indispensable.
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Affiliation(s)
- Nicolas Brandes
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Dana Reichmann
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Heather Tienson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Lars I Leichert
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109.
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McDonagh B, Requejo R, Fuentes-Almagro C, Ogueta S, Bárcena J, Padilla C. Thiol redox proteomics identifies differential targets of cytosolic and mitochondrial glutaredoxin-2 isoforms in Saccharomyces cerevisiae. Reversible S-glutathionylation of DHBP synthase (RIB3). J Proteomics 2011; 74:2487-97. [DOI: 10.1016/j.jprot.2011.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/08/2011] [Accepted: 04/18/2011] [Indexed: 12/24/2022]
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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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Giron P, Dayon L, Sanchez JC. Cysteine tagging for MS-based proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:366-395. [PMID: 21500242 DOI: 10.1002/mas.20285] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 05/30/2023]
Abstract
Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.
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Affiliation(s)
- Priscille Giron
- Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, University of Geneva, Geneva, Switzerland
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Murray DB, Haynes K, Tomita M. Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta Gen Subj 2011; 1810:945-58. [PMID: 21549177 DOI: 10.1016/j.bbagen.2011.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 03/16/2011] [Accepted: 04/17/2011] [Indexed: 11/30/2022]
Abstract
BACKGROUND In biological systems, redox reactions are central to most cellular processes and the redox potential of the intracellular compartment dictates whether a particular reaction can or cannot occur. Indeed the widespread use of redox reactions in biological systems makes their detailed description outside the scope of one review. SCOPE OF THE REVIEW Here we will focus on how system-wide redox changes can alter the reaction and transcriptional landscape of Saccharomyces cerevisiae. To understand this we explore the major determinants of cellular redox potential, how these are sensed by the cell and the dynamic responses elicited. MAJOR CONCLUSIONS Redox regulation is a large and complex system that has the potential to rapidly and globally alter both the reaction and transcription landscapes. Although we have a basic understanding of many of the sub-systems and a partial understanding of the transcriptional control, we are far from understanding how these systems integrate to produce coherent responses. We argue that this non-linear system self-organises, and that the output in many cases is temperature-compensated oscillations that may temporally partition incompatible reactions in vivo. GENERAL SIGNIFICANCE Redox biochemistry impinges on most of cellular processes and has been shown to underpin ageing and many human diseases. Integrating the complexity of redox signalling and regulation is perhaps one of the most challenging areas of biology. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
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Affiliation(s)
- Douglas B Murray
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
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McDonagh B, Padilla CA, Pedrajas JR, Bárcena JA. Biosynthetic and iron metabolism is regulated by thiol proteome changes dependent on glutaredoxin-2 and mitochondrial peroxiredoxin-1 in Saccharomyces cerevisiae. J Biol Chem 2011; 286:15565-76. [PMID: 21385868 DOI: 10.1074/jbc.m110.193102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Redoxins are involved in maintenance of thiol redox homeostasis, but their exact sites of action are only partly known. We have applied a combined redox proteomics and transcriptomics experimental strategy to discover specific functions of two interacting redoxins: dually localized glutaredoxin 2 (Grx2p) and mitochondrial peroxiredoxin 1 (Prx1p). We have identified 139 proteins showing differential postranslational thiol redox modifications when the cells do not express Grx2p, Prx1p, or both and have mapped the precise cysteines involved in each case. Some of these modifications constitute functional switches that affect metabolic and signaling pathways as the primary effect, leading to gene transcription remodeling as the secondary adaptive effect as demonstrated by a parallel high throughput gene expression analysis. The results suggest that in the absence of Grx2p, the metabolic flow toward nucleotide and aromatic amino acid biosynthesis is slowed down by redox modification of the key enzymes Rpe1p (D-ribulose-5-phosphate 3-epimerase), Tkl1p (transketolase) and Aro4p (3-deoxy-D-arabino-heptulosonate-7-phosphate synthase). The glycolytic mainstream is then diverted toward carbohydrate storage by induction of trehalose and glycogen biosynthesis genes. Porphyrin biosynthesis may also be compromised by inactivation of the redox-sensitive cytosolic enzymes Hem12p (uroporphyrinogen decarboxylase) and Sam1p (S-adenosyl methionine synthetase) and a battery of respiratory genes sensitive to low heme levels are induced. Genes of the Aft1p-dependent iron regulon were induced specifically in the absence of Prx1p despite optimal mitochondrial Fe-S biogenesis, suggesting dysfunction of the mitochondria to the cytosol signaling pathway. Strikingly, requirement of Grx2p for these events places dithiolic Grx2 in the framework of iron metabolism.
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Affiliation(s)
- Brian McDonagh
- Department of Biochemistry and Molecular Biology and Córdoba Maimónides Institute for Biomedical Research (IMIBIC), University of Córdoba, 14071 Córdoba, Spain
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Cyrne L, Antunes F, Sousa-Lopes A, Diaz-Bérrio J, Marinho HS. Glyceraldehyde-3-phosphate dehydrogenase is largely unresponsive to low regulatory levels of hydrogen peroxide in Saccharomyces cerevisiae. BMC BIOCHEMISTRY 2010; 11:49. [PMID: 21189144 PMCID: PMC3019127 DOI: 10.1186/1471-2091-11-49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/28/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND The reversible oxidation of protein SH groups has been considered to be the basis of redox regulation by which changes in hydrogen peroxide (H2O2) concentrations may control protein function. Several proteins become S-glutathionylated following exposure to H2O2 in a variety of cellular systems. In yeast, when using a high initial H2O2 dose, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the major target of S-glutathionylation which leads to reversible inactivation of the enzyme. GAPDH inactivation by H2O2 functions to reroute carbohydrate flux to produce NADPH. Here we report the effect of low regulatory H2O2 doses on GAPDH activity and expression in Saccharomyces cerevisiae. RESULTS A calibrated and controlled method of H2O2 delivery - the steady-state titration - in which cells are exposed to constant, low, and known H2O2 concentrations, was used in this study. This technique, contrary to the common bolus addition, allows determining which H2O2 concentrations trigger specific biological responses. This work shows that both in exponential- and stationary-phase cells, low regulatory H2O2 concentrations induce a large upregulation of catalase, a fingerprint of the cellular oxidative stress response, but GAPDH oxidation and the ensuing activity decrease are only observed at death-inducing high H2O2 doses. GAPDH activity is constant upon incubation with sub-lethal H2O2 doses, but in stationary-phase cells there is a differential response in the expression of the three GAPDH isoenzymes: Tdh1p is strongly upregulated while Tdh2p/Tdh3p are slightly downregulated. CONCLUSIONS In yeast GAPDH activity is largely unresponsive to low to moderate H2O2 doses. This points to a scenario where (a) cellular redoxins efficiently cope with levels of GAPDH oxidation induced by a vast range of sub-lethal H2O2 concentrations, (b) inactivation of GAPDH cannot be considered a sensitive biomarker of H2O2-induced oxidation in vivo. Since GAPDH inactivation only occurs at cell death-inducing high H2O2 doses, GAPDH-dependent rerouting of carbohydrate flux is probably important merely in pathophysiological situations. This work highlights the importance of studying H2O2-induced oxidative stress using concentrations closer to the physiological for determining the importance of protein oxidation phenomena in the regulation of cellular metabolism.
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Affiliation(s)
- Luísa Cyrne
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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50
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Szopinska A, Morsomme P. Quantitative Proteomic Approaches and Their Application in the Study of Yeast Stress Responses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:639-49. [DOI: 10.1089/omi.2010.0045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Aleksandra Szopinska
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
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