1
|
Cadenas-Garrido P, Schonvandt-Alarcos A, Herrera-Quintana L, Vázquez-Lorente H, Santamaría-Quiles A, Ruiz de Francisco J, Moya-Escudero M, Martín-Oliva D, Martín-Guerrero SM, Rodríguez-Santana C, Aragón-Vela J, Plaza-Diaz J. Using Redox Proteomics to Gain New Insights into Neurodegenerative Disease and Protein Modification. Antioxidants (Basel) 2024; 13:127. [PMID: 38275652 PMCID: PMC10812581 DOI: 10.3390/antiox13010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Antioxidant defenses in biological systems ensure redox homeostasis, regulating baseline levels of reactive oxygen and nitrogen species (ROS and RNS). Oxidative stress (OS), characterized by a lack of antioxidant defenses or an elevation in ROS and RNS, may cause a modification of biomolecules, ROS being primarily absorbed by proteins. As a result of both genome and environment interactions, proteomics provides complete information about a cell's proteome, which changes continuously. Besides measuring protein expression levels, proteomics can also be used to identify protein modifications, localizations, the effects of added agents, and the interactions between proteins. Several oxidative processes are frequently used to modify proteins post-translationally, including carbonylation, oxidation of amino acid side chains, glycation, or lipid peroxidation, which produces highly reactive alkenals. Reactive alkenals, such as 4-hydroxy-2-nonenal, are added to cysteine (Cys), lysine (Lys), or histidine (His) residues by a Michael addition, and tyrosine (Tyr) residues are nitrated and Cys residues are nitrosylated by a Michael addition. Oxidative and nitrosative stress have been implicated in many neurodegenerative diseases as a result of oxidative damage to the brain, which may be especially vulnerable due to the large consumption of dioxygen. Therefore, the current methods applied for the detection, identification, and quantification in redox proteomics are of great interest. This review describes the main protein modifications classified as chemical reactions. Finally, we discuss the importance of redox proteomics to health and describe the analytical methods used in redox proteomics.
Collapse
Affiliation(s)
- Paula Cadenas-Garrido
- Research and Advances in Molecular and Cellular Immunology, Center of Biomedical Research, University of Granada, Avda, del Conocimiento s/n, 18016 Armilla, Spain; (P.C.-G.); (A.S.-A.); (A.S.-Q.); (J.R.d.F.); (M.M.-E.)
| | - Ailén Schonvandt-Alarcos
- Research and Advances in Molecular and Cellular Immunology, Center of Biomedical Research, University of Granada, Avda, del Conocimiento s/n, 18016 Armilla, Spain; (P.C.-G.); (A.S.-A.); (A.S.-Q.); (J.R.d.F.); (M.M.-E.)
| | - Lourdes Herrera-Quintana
- Department of Physiology, Schools of Pharmacy and Medicine, University of Granada, 18071 Granada, Spain; (L.H.-Q.); (H.V.-L.); (C.R.-S.)
- Biomedical Research Center, Health Sciences Technology Park, University of Granada, 18016 Granada, Spain
| | - Héctor Vázquez-Lorente
- Department of Physiology, Schools of Pharmacy and Medicine, University of Granada, 18071 Granada, Spain; (L.H.-Q.); (H.V.-L.); (C.R.-S.)
- Biomedical Research Center, Health Sciences Technology Park, University of Granada, 18016 Granada, Spain
| | - Alicia Santamaría-Quiles
- Research and Advances in Molecular and Cellular Immunology, Center of Biomedical Research, University of Granada, Avda, del Conocimiento s/n, 18016 Armilla, Spain; (P.C.-G.); (A.S.-A.); (A.S.-Q.); (J.R.d.F.); (M.M.-E.)
| | - Jon Ruiz de Francisco
- Research and Advances in Molecular and Cellular Immunology, Center of Biomedical Research, University of Granada, Avda, del Conocimiento s/n, 18016 Armilla, Spain; (P.C.-G.); (A.S.-A.); (A.S.-Q.); (J.R.d.F.); (M.M.-E.)
| | - Marina Moya-Escudero
- Research and Advances in Molecular and Cellular Immunology, Center of Biomedical Research, University of Granada, Avda, del Conocimiento s/n, 18016 Armilla, Spain; (P.C.-G.); (A.S.-A.); (A.S.-Q.); (J.R.d.F.); (M.M.-E.)
| | - David Martín-Oliva
- Department of Cell Biology, Faculty of Science, University of Granada, 18071 Granada, Spain;
| | - Sandra M. Martín-Guerrero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RT, UK
| | - César Rodríguez-Santana
- Department of Physiology, Schools of Pharmacy and Medicine, University of Granada, 18071 Granada, Spain; (L.H.-Q.); (H.V.-L.); (C.R.-S.)
- Biomedical Research Center, Health Sciences Technology Park, University of Granada, 18016 Granada, Spain
| | - Jerónimo Aragón-Vela
- Department of Health Sciences, Area of Physiology, Building B3, Campus s/n “Las Lagunillas”, University of Jaén, 23071 Jaén, Spain
| | - Julio Plaza-Diaz
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS, Complejo Hospitalario Universitario de Granada, 18071 Granada, Spain
| |
Collapse
|
2
|
Trevisan R, Mello DF. Redox control of antioxidants, metabolism, immunity, and development at the core of stress adaptation of the oyster Crassostrea gigas to the dynamic intertidal environment. Free Radic Biol Med 2024; 210:85-106. [PMID: 37952585 DOI: 10.1016/j.freeradbiomed.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
This review uses the marine bivalve Crassostrea gigas to highlight redox reactions and control systems in species living in dynamic intertidal environments. Intertidal species face daily and seasonal environmental variability, including temperature, oxygen, salinity, and nutritional changes. Increasing anthropogenic pressure can bring pollutants and pathogens as additional stressors. Surprisingly, C. gigas demonstrates impressive adaptability to most of these challenges. We explore how ROS production, antioxidant protection, redox signaling, and metabolic adjustments can shed light on how redox biology supports oyster survival in harsh conditions. The review provides (i) a brief summary of shared redox sensing processes in metazoan; (ii) an overview of unique characteristics of the C. gigas intertidal habitat and the suitability of this species as a model organism; (iii) insights into the redox biology of C. gigas, including ROS sources, signaling pathways, ROS-scavenging systems, and thiol-containing proteins; and examples of (iv) hot topics that are underdeveloped in bivalve research linking redox biology with immunometabolism, physioxia, and development. Given its plasticity to environmental changes, C. gigas is a valuable model for studying the role of redox biology in the adaptation to harsh habitats, potentially providing novel insights for basic and applied studies in marine and comparative biochemistry and physiology.
Collapse
Affiliation(s)
- Rafael Trevisan
- Univ Brest, Ifremer, CNRS, IRD, UMR 6539, LEMAR, Plouzané, 29280, France
| | - Danielle F Mello
- Univ Brest, Ifremer, CNRS, IRD, UMR 6539, LEMAR, Plouzané, 29280, France.
| |
Collapse
|
3
|
Borova S, Schlutt C, Nickel J, Luxenhofer R. A Transient Initiator for Polypeptoids Postpolymerization
α
‐Functionalization via Activation of a Thioester Group. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202100331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Solomiia Borova
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Institute for Functional Materials and Biofabrication, Department of Chemistry and Pharmacy Julius‐Maximilans‐University of Würzburg Röntgenring 11 Würzburg Bavaria 97070 Germany
| | - Christine Schlutt
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Institute for Functional Materials and Biofabrication, Department of Chemistry and Pharmacy Julius‐Maximilans‐University of Würzburg Röntgenring 11 Würzburg Bavaria 97070 Germany
| | - Joachim Nickel
- Department of Tissue Engineering and Regenerative Medicine University Hospital of Würzburg Röntgenring 11 Würzburg Bavaria 97070 Germany
| | - Robert Luxenhofer
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Institute for Functional Materials and Biofabrication, Department of Chemistry and Pharmacy Julius‐Maximilans‐University of Würzburg Röntgenring 11 Würzburg Bavaria 97070 Germany
- Soft Matter Chemistry, Department of Chemistry and Helsinki Institute of Sustainability Science, Faculty of Science University of Helsinki P.O. Box 55 Helsinki 00014 Finland
| |
Collapse
|
4
|
Zhao Z, Ozcan EE, VanArsdale E, Li J, Kim E, Sandler AD, Kelly DL, Bentley WE, Payne GF. Mediated Electrochemical Probing: A Systems-Level Tool for Redox Biology. ACS Chem Biol 2021; 16:1099-1110. [PMID: 34156828 DOI: 10.1021/acschembio.1c00267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biology uses well-known redox mechanisms for energy harvesting (e.g., respiration), biosynthesis, and immune defense (e.g., oxidative burst), and now we know biology uses redox for systems-level communication. Currently, we have limited abilities to "eavesdrop" on this redox modality, which can be contrasted with our abilities to observe and actuate biology through its more familiar ionic electrical modality. In this Perspective, we argue that the coupling of electrochemistry with diffusible mediators (electron shuttles) provides a unique opportunity to access the redox communication modality through its electrical features. We highlight previous studies showing that mediated electrochemical probing (MEP) can "communicate" with biology to acquire information and even to actuate specific biological responses (i.e., targeted gene expression). We suggest that MEP may reveal an extent of redox-based communication that has remained underappreciated in nature and that MEP could provide new technological approaches for redox biology, bioelectronics, clinical care, and environmental sciences.
Collapse
Affiliation(s)
- Zhiling Zhao
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Evrim E. Ozcan
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - Eric VanArsdale
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jinyang Li
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Anthony D. Sandler
- Department of General and Thoracic Surgery, Children’s National Hospital, Washington, D.C. 20010, United States
| | - Deanna L. Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland 21228, United States
| | - William E. Bentley
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
5
|
Bejaoui S, Michán C, Telahigue K, Nechi S, Cafsi ME, Soudani N, Blasco J, Costa PM, Alhama J. Metal body burden and tissue oxidative status in the bivalve Venerupis decussata from Tunisian coastal lagoons. MARINE ENVIRONMENTAL RESEARCH 2020; 159:105000. [PMID: 32662434 DOI: 10.1016/j.marenvres.2020.105000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Coastal transitional waters are exposed to many anthropogenic threats. This study aims to assess the trace metals' pollution status of transitional waters by evaluating its biological effects in the clam Venerupis decussata. Among the studied sites along the Tunisian littoral, South Tunis and Boughrara were the most impacted, since clams from these two lagoons presented significant differences in: (i) trace metal contents, (ii) in-cell hydrogen peroxide, (iii) enzymatic and non-enzymatic defenses, (iv) damage to lipids and proteins, and (v) protein post-translational modifications. These changes related to evident histopathological traits. PCA showed a clear separation between the digestive gland and gills tissues and illustrated an impact gradient in Tunisian coastal lagoons. Water temperature was revealed as an added natural stressor that, when concurring with high pollution, may jeopardize an ecosystem's health and contribute to the accumulation of hazardous metals in organisms.
Collapse
Affiliation(s)
- Safa Bejaoui
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain; Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Khaoula Telahigue
- Anatomy and Cytology Service, CHU Mohamed Taher Maamouri Hospital, University Tunis El Manar, Tunis, Tunisia
| | - Salwa Nechi
- Anatomy and Cytology Service, CHU Mohamed Taher Maamouri Hospital, University Tunis El Manar, Tunis, Tunisia
| | - Mhamed El Cafsi
- Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Nejla Soudani
- Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Julián Blasco
- Dpt. Ecology and Coastal Management, ICMAN-CSIC, Campus Rio San Pedro, E-11510, Puerto Real (Cadiz), Spain
| | - Pedro M Costa
- UCIBIO - Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
| |
Collapse
|
6
|
Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
Collapse
Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| |
Collapse
|
7
|
Greco V, Longone P, Spalloni A, Pieroni L, Urbani A. Crosstalk Between Oxidative Stress and Mitochondrial Damage: Focus on Amyotrophic Lateral Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:71-82. [PMID: 31452136 DOI: 10.1007/978-981-13-8367-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteins oxidation by reactive species is implicated in the aetiology or progression of a panoply of disorders and diseases such as neurodegenerative disorders. It is becoming increasingly evident that redox imbalance in the brain mediates neurodegeneration. Free radicals, as reactive species of oxygen (ROS) but also reactive nitrogen species (RNS) and reactive sulfur species (RSS), are generated in vivo from several sources. Within the cell the mitochondria represent the main source of ROS and mitochondrial dysfunction is both the major contributor to oxidative stress (OS) as well its major consequence.To date there are no doubts that a condition of OS added to other factors as mitochondrial damage in mtDNA or mitochondrial respiratory chain, may contribute to trigger or amplify mechanisms leading to neurodegenerative disorders.In this chapter, we aim at illustrate the molecular interplay occurring between mitochondria and OS focusing on Amyotrophic Lateral Sclerosis, describing a phenotypic reprogramming mechanism of mitochondria in complex neurological disorder.
Collapse
Affiliation(s)
- Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Patrizia Longone
- Molecular Neurobiology Unit, Fondazione Santa Lucia-IRCCS, Rome, Italy
| | - Alida Spalloni
- Molecular Neurobiology Unit, Fondazione Santa Lucia-IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, Fondazione Santa Lucia-IRCCS, Rome, Italy
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy. .,Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy.
| |
Collapse
|
8
|
Abstract
Infertility affects nearly 15 per cent of all couples within the reproductive age worldwide, with about 50 per cent being exhibited in the male, called male factor infertility. Successful reproduction is dependent on sperm chromatin integrity. Spermatozoa are highly specialized cells that aim to transmit the paternal genomic blueprint to the oocyte. The spermatozoon is regulated by redox mechanisms during its epididymal transit to acquire fertilizing ability. While, at physiological levels, the production of reactive oxygen species (ROS) supports the spermatozoon to acquire its fertilizing ability, at high concentrations, it affects sperm function leading to infertility. Emerging proteomic technologies provide an opportunity to address these key issues that may solve many fertility-associated problems resulting from oxidative stress (OS). This review highlights the need for an efficient therapeutic approach to male infertility with the application of high-throughput OS-mediated proteomic technology, and also addresses the question as to whether targeting these altered sperm-specific proteins may help in designing an efficient and reversible male contraceptive.
Collapse
Affiliation(s)
- Gayatri Mohanty
- Department of Zoology, Redox Biology Laboratory, Ravenshaw University, Cuttack, India
| | - Luna Samanta
- Department of Zoology, Redox Biology Laboratory, Ravenshaw University, Cuttack, India
| |
Collapse
|
9
|
Michán C, Chicano-Gálvez E, Fuentes-Almagro CA, Alhama J. Redox and global interconnected proteome changes in mice exposed to complex environmental hazards surrounding Doñana National Park. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:427-439. [PMID: 31158671 DOI: 10.1016/j.envpol.2019.05.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Natural environments are receiving an increasing number of contaminants. Therefore, the evaluation and identification of early responses to pollution in these complex habitats is an urgent and challenging task. Doñana National Park (DNP, SW Spain) has been widely used as a model area for environmental studies because, despite its strictly protected core, it is surrounded by numerous threat sources from agricultural, mining and industrial activities. Since many pollutants often induce oxidative stress, redox proteomics was used to detect redox-based variations within the proteome of Mus spretus mice captured in DNP and the surrounding areas. Functional analysis showed that most differentially oxidized proteins are involved in the maintenance of homeostasis, by eliciting mechanisms to respond to toxic substances and oxidative stress, such as antioxidant and biotransformation processes, immune and inflammatory responses, and blood coagulation. Furthermore, changes in the overall protein abundance were also analysed by label-free quantitative proteomics. The upregulation of phase I and II biotransformation enzymes in mice from Lucio del Palacio may be an alert for organic pollution in the area located at the heart of DNP. Metabolic processes involved in protein turnover (proteolysis, amino acid catabolism, new protein biosynthesis and folding) were activated in response to oxidative damage to these biomolecules. Consequently, aerobic respiratory metabolism increased to address the greater ATP demands. Alterations of cholesterol metabolism that could cause hepatic steatosis were also detected. The proteomic detection of globally altered metabolic and physiological processes offers a complete view of the main biological changes caused by environmental pollution in complex habitats.
Collapse
Affiliation(s)
- Carmen Michán
- Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | | | | | - José Alhama
- Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain.
| |
Collapse
|
10
|
Alhama J, Fuentes-Almagro CA, Abril N, Michán C. Alterations in oxidative responses and post-translational modification caused by p,p´-DDE in Mus spretus testes reveal Cys oxidation status in proteins related to cell-redox homeostasis and male fertility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 636:656-669. [PMID: 29723838 DOI: 10.1016/j.scitotenv.2018.04.305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
The major derivate of DDT, 1,1-dichloro-2,2-bis (p-chlorophenyl) ethylene (p,p´-DDE), is a persistent pollutant previously associated with oxidative stress. Additionally, p,p´-DDE has been linked to several metabolic alterations related to sexual function in rodents. In this study, we analysed the effects of a non-lethal p,p´-DDE dose to Mus spretus mice in testes, focusing on oxidative damage to biomolecules, defence mechanisms against oxidative stress and post-translational protein modifications. No increase in lipid or DNA oxidation was observed, although antioxidative enzymatic defences and redox status of glutathione were altered in several ways. Global protein carbonylation and phosphorylation were significantly reduced in testes from p,p´-DDE-exposed mice; however, the total redox state of Cys thiols did not exhibit a defined pattern. We analysed the reversible redox state of specific Cys residues in detail with differential isotopic labelling and a shotgun labelling-based MS/MS proteomic approach for identification and quantification of altered peptides. Our results show that Cys residues are significantly affected by p,p´-DDE in several proteins related to oxidative stress and/or male fertility, particularly those participating in fertilization, sperm capacitation and blood coagulation. These molecular changes could explain the sexual abnormalities previously described in p,p´-DDE exposed organisms.
Collapse
Affiliation(s)
- José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Carlos A Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, Edificio Ramón y Cajal, E-14071 Córdoba, Spain
| | - Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain.
| |
Collapse
|
11
|
Bouallegui Y, Ben Younes R, Oueslati R, Sheehan D. Role of endocytotic uptake routes in impacting the ROS-related toxicity of silver nanoparticles to Mytilus galloprovincialis: A redox proteomic investigation. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 200:21-27. [PMID: 29705565 DOI: 10.1016/j.aquatox.2018.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/18/2018] [Accepted: 04/21/2018] [Indexed: 06/08/2023]
Abstract
Oxidative stress is often implicated in nanoparticle toxicity. Several studies have highlighted the role of internalization routes in determining nanotoxicity. Here, we investigate how two endocytotic mechanisms (clathrin- and caveolae-mediated) impact on redox balance in gill and digestive gland of the mussel, Mytilus galloprovincialis. Animals were exposed (for 3, 6 and 12 h) to two sizes of silver nanoparticles (AgNP: <50 nm and <100 nm) prior to and after blockade of two endocytic pathways (amantadine blocks clathrin-mediated endocytosis while nystatin blocks caveolae-mediated endocytosis). Redox-proteomic tools were used to determine effects. Our results demonstrate the ability of both sizes of AgNP (<50 and <100 nm) to cause protein thiol oxidation and/or protein carbonylation. However, blockade of endocytotic routes mitigated AgNP toxicity. Differential ROS-related toxicity of AgNP to mussel tissues seemed to be linked to tissue-specific mode of action requirements. Cell uptake mechanism strongly influences toxicity of AgNPs in this filter-feeder.
Collapse
Affiliation(s)
- Younes Bouallegui
- Research Unit of Immuno-Microbiology Environmental and Carcinogenesis, Sciences Faculty of Bizerte, University of Carthage, Tunisia.
| | - Ridha Ben Younes
- Research Unit of Immuno-Microbiology Environmental and Carcinogenesis, Sciences Faculty of Bizerte, University of Carthage, Tunisia
| | - Ridha Oueslati
- Research Unit of Immuno-Microbiology Environmental and Carcinogenesis, Sciences Faculty of Bizerte, University of Carthage, Tunisia
| | - David Sheehan
- Proteomic Research Group, School of Biochemistry and Cell Biology, University College Cork, Ireland; Dept of Chemistry, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
12
|
Morales-Prieto N, Ruiz-Laguna J, Abril N. Dietary Se supplementation partially restores the REDOX proteomic map of M. spretus liver exposed to p,p ′-DDE. Food Chem Toxicol 2018; 114:292-301. [DOI: 10.1016/j.fct.2018.02.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/14/2018] [Accepted: 02/21/2018] [Indexed: 12/29/2022]
|
13
|
Morales-Prieto N, Abril N. REDOX proteomics reveals energy metabolism alterations in the liver of M. spretus mice exposed to p, p'-DDE. CHEMOSPHERE 2017; 186:848-863. [PMID: 28826133 DOI: 10.1016/j.chemosphere.2017.08.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/27/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
The toxicity induced by the pesticide 2,2-bis(p-chlorophenyl)-1,1,1,-trichloroethane (DDT) and its derivative 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (p,p'-DDE) has been associated with mitochondrial dysfunction, uncoupling of oxidative phosphorylation and respiratory chain electron transport, intracellular ion imbalance, generation of reactive oxygen species and impairment of the antioxidant defense system. A disruption in the cellular redox status causes protein Cys-based regulatory shifts that influence the activity of many proteins and trigger signal transduction alterations. Here, we analyzed the ability of p,p'-DDE to alter the activities of hepatic antioxidants and glycolytic enzymes to investigate the oxidative stress generation in the liver of p,p'-DDE-fed M. spretus mice. We also determined the consequences of the treatment on the redox status in the thiol Cys groups. The data indicate that the liver of p,p'-DDE exposed mice lacks certain protective enzymes, and p,p'-DDE caused a metabolic reprogramming that increased the glycolytic rate and disturbed the metabolism of lipids. Our results suggested that the overall metabolism of the liver was altered because important signaling pathways are controlled by p,p'-DDE-deregulated proteins. The histological data support the proposed metabolic consequences of the p,p'-DDE exposure.
Collapse
Affiliation(s)
- Noelia Morales-Prieto
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, España, Spain
| | - Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, España, Spain.
| |
Collapse
|
14
|
Fernández-Cisnal R, García-Sevillano MA, Gómez-Ariza JL, Pueyo C, López-Barea J, Abril N. 2D-DIGE as a proteomic biomarker discovery tool in environmental studies with Procambarus clarkii. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:813-827. [PMID: 28159302 DOI: 10.1016/j.scitotenv.2017.01.125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
UNLABELLED A 2D-DIGE/MS approach was used to assess protein abundance differences in the red swamp crayfish Procambarus clarkii from polluted aquatic ecosystems of Doñana National Park and surrounding areas with different pollution loads. Procambarus clarkii accumulated metals in the digestive glands and gills reflecting sediment concentrations. We first stated that, probably related to elements accumulation, pollution increased oxidative damage in P. clarkii tissues, as shown by the thiol oxidation status of proteins and MDA levels. In these animals, the altered redox status might be responsible for the deregulated abundance of proteins involved in cellular responses to oxidative stress including protein folding, mitochondrial imbalance and inflammatory processes. Interestingly, polluted P. clarkii crayfish also displayed a metabolic shift to enhanced aerobic glycolysis, most likely aimed at generating ATP and reduction equivalents in an oxidative stress situation that alters mitochondrial integrity. The deregulated proteins define the physiological processes affected by pollutants in DNP and its surrounding areas and may help us to unravel the molecular mechanisms underlying the toxicity of environmental pollutants. In addition, these proteins might be used as exposure biomarkers in environmental risk assessment. The results obtained might be extrapolated to many other locations all over the world and have the added value of providing information about the molecular responses of this environmentally and economically interesting animal. SIGNIFICANCE Metal content in digestive gland and gills of P. clarkii crayfish reflects their contents in sediments at sites of Doñana National Park and its surroundings. Accumulation of essential and toxic transition metals is paralleled by clear signs of oxidative stress to lipids and proteins and by significant deregulation of many proteins involved in protein folding, mitochondrial respiratory imbalance and inflammatory response. These results indicate that P. clarkii is an excellent bioindicator to be used in aquatic ecosystems quality monitoring. Additionally, results evidence that the anthropogenic activities carried out around Doñana National Park represent an extremely serious threat to this unique Biosphere Reserve and pose a risk to the environment and their inhabitants health. The identified deregulated proteins provide information about the metabolic pathways and/or physiological processes affected by pollutant-elicited oxidative stress, may also be useful as biomarkers of environmental pollution and have the added value of providing information about the molecular responses of this environmentally and economically interesting animal.
Collapse
Affiliation(s)
- Ricardo Fernández-Cisnal
- Department of Biochemistry and Molecular Biology and Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Miguel A García-Sevillano
- Department of Chemistry and Materials Science, Faculty of Experimental Science and Agrifood Campus of International Excellence (ceiA3), University of Huelva, El Carmen Campus, 21007 Huelva, Spain
| | - José L Gómez-Ariza
- Department of Chemistry and Materials Science, Faculty of Experimental Science and Agrifood Campus of International Excellence (ceiA3), University of Huelva, El Carmen Campus, 21007 Huelva, Spain
| | - Carmen Pueyo
- Department of Biochemistry and Molecular Biology and Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Juan López-Barea
- Department of Biochemistry and Molecular Biology and Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology and Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain..
| |
Collapse
|
15
|
The Emerging Role of Proteomics in Precision Medicine: Applications in Neurodegenerative Diseases and Neurotrauma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:59-70. [DOI: 10.1007/978-3-319-60733-7_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
16
|
Zhou L, Wen J, Huang Z, Nice EC, Huang C, Zhang H, Li Q. Redox proteomics screening cellular factors associated with oxidative stress in hepatocarcinogenesis. Proteomics Clin Appl 2016; 11. [PMID: 27763721 DOI: 10.1002/prca.201600089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
Liver cancer is a major global health problem being the sixth most common cancer and the third cause of cancer-related death, with hepatocellular carcinoma (HCC) representing more than 90% of primary liver cancers. Mounting evidence suggests that, compared with their normal counterparts, many types of cancer cell have increased levels of ROS. Therefore, cancer cells need to combat high levels of ROS, especially at early stages of tumor development. Recent studies have revealed that ROS-mediated regulation of redox-sensitive proteins (redox sensors) is involved in the pathogenesis and/or progression of many human diseases, including cancer. Unraveling the altered functions of redox sensors and the underlying mechanisms in hepatocarcinogenesis is critical for the development of novel cancer therapeutics. For this reason, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for the treatment of HCC. In this review, we will briefly introduce several novel redox proteomics techniques that are currently available to study various oxidative modifications in hepatocarcinogenesis and summarize the most important discoveries in the study of redox processes related to the development and progression of HCC.
Collapse
Affiliation(s)
- Li Zhou
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Ji Wen
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Visiting professor, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Haiyuan Zhang
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Qifu Li
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| |
Collapse
|
17
|
Ramallo Guevara C, Philipp O, Hamann A, Werner A, Osiewacz HD, Rexroth S, Rögner M, Poetsch A. Global Protein Oxidation Profiling Suggests Efficient Mitochondrial Proteome Homeostasis During Aging. Mol Cell Proteomics 2016; 15:1692-709. [PMID: 26884511 DOI: 10.1074/mcp.m115.055616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Indexed: 11/06/2022] Open
Abstract
The free radical theory of aging is based on the idea that reactive oxygen species (ROS) may lead to the accumulation of age-related protein oxidation. Because themajority of cellular ROS is generated at the respiratory electron transport chain, this study focuses on the mitochondrial proteome of the aging model Podospora anserina as target for ROS-induced damage. To ensure the detection of even low abundant modified peptides, separation by long gradient nLC-ESI-MS/MS and an appropriate statistical workflow for iTRAQ quantification was developed. Artificial protein oxidation was minimized by establishing gel-free sample preparation in the presence of reducing and iron-chelating agents. This first large scale, oxidative modification-centric study for P. anserina allowed the comprehensive quantification of 22 different oxidative amino acid modifications, and notably the quantitative comparison of oxidized and nonoxidized protein species. In total 2341 proteins were quantified. For 746 both protein species (unmodified and oxidatively modified) were detected and the modification sites determined. The data revealed that methionine residues are preferably oxidized. Further prominent identified modifications in decreasing order of occurrence were carbonylation as well as formation of N-formylkynurenine and pyrrolidinone. Interestingly, for the majority of proteins a positive correlation of changes in protein amount and oxidative damage were noticed, and a general decrease in protein amounts at late age. However, it was discovered that few proteins changed in oxidative damage in accordance with former reports. Our data suggest that P. anserina is efficiently capable to counteract ROS-induced protein damage during aging as long as protein de novo synthesis is functioning, ultimately leading to an overall constant relationship between damaged and undamaged protein species. These findings contradict a massive increase in protein oxidation during aging and rather suggest a protein damage homeostasis mechanism even at late age.
Collapse
Affiliation(s)
- Carina Ramallo Guevara
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Oliver Philipp
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany; ¶Molecular Bioinformatics, Faculty of Computer Science and Mathematics and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60325, Germany
| | - Andrea Hamann
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Alexandra Werner
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Heinz D Osiewacz
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Sascha Rexroth
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Matthias Rögner
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Ansgar Poetsch
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany;
| |
Collapse
|
18
|
Dattilo S, Mancuso C, Koverech G, Di Mauro P, Ontario ML, Petralia CC, Petralia A, Maiolino L, Serra A, Calabrese EJ, Calabrese V. Heat shock proteins and hormesis in the diagnosis and treatment of neurodegenerative diseases. Immun Ageing 2015; 12:20. [PMID: 26543490 PMCID: PMC4634585 DOI: 10.1186/s12979-015-0046-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022]
Abstract
Modulation of endogenous cellular defense mechanisms via the vitagene system represents an innovative approach to therapeutic intervention in diseases causing chronic tissue damage, such as in neurodegeneration. The possibility of high-throughoutput screening using proteomic techniques, particularly redox proteomics, provide more comprehensive overview of the interaction of proteins, as well as the interplay among processes involved in neuroprotection. Here by introducing the hormetic dose response concept, the mechanistic foundations and applications to the field of neuroprotection, we discuss the emerging role of heat shock protein as prominent member of vitagene network in neuroprotection and redox proteomics as a tool for investigating redox modulation of stress responsive vitagenes. Hormetic mechanisms are reviewed as possibility of targeted therapeutic manipulation in a cell-, tissue- and/or pathway-specific manner at appropriate points in the neurodegenerative disease process.
Collapse
Affiliation(s)
- Sandro Dattilo
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Cesare Mancuso
- />Institute of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - Guido Koverech
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Paola Di Mauro
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Maria Laura Ontario
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | | | - Antonino Petralia
- />Department of Clinical and Experimental Medicine, School of Medicine, University of Catania, Catania, Italy
| | - Luigi Maiolino
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Agostino Serra
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Edward J. Calabrese
- />Environmental Health Sciences Division, School of Public Health, University of Massachusetts, Amherst, MA USA
| | - Vittorio Calabrese
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| |
Collapse
|
19
|
Calabrese V, Dattilo S, Petralia A, Parenti R, Pennisi M, Koverech G, Calabrese V, Graziano A, Monte I, Maiolino L, Ferreri T, Calabrese EJ. Analytical approaches to the diagnosis and treatment of aging and aging-related disease: redox status and proteomics. Free Radic Res 2015; 49:511-24. [PMID: 25824967 DOI: 10.3109/10715762.2015.1020799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Basal levels of oxidants are indispensible for redox signaling to produce adaptive cellular responses such as vitagenes linked to cell survival; however, at higher levels, they are detrimental to cells, contributing to aging and to the pathogenesis of numerous age-related diseases. Aging is a complex systemic process and the major gap in aging research reminds the insufficient knowledge about pathways shifting from normal "healthy" aging to disease-associated pathological aging. The major complication of normal "healthy" aging is in fact the increasing risk of age-related diseases such as cardiovascular diseases, diabetes mellitus, and neurodegenerative pathologies that can adversely affect the quality of life in general, with enhanced incidences of comorbidities and mortality. In this context, global "omics" approaches may help to dissect and fully study the cellular and molecular mechanisms of aging and age-associated processes. The proteome, being more close to the phenotype than the transcriptome and more stable than the metabolome, represents the most promising "omics" field in aging research. In the present study, we exploit recent advances in the redox biology of aging and discuss the potential of proteomics approaches as innovative tools for monitoring at the proteome level the extent of protein oxidative insult and related modifications with the identification of targeted proteins.
Collapse
Affiliation(s)
- V Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania , Catania , Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Rainville LC, Coelho AV, Sheehan D. Application of a redox-proteomics toolbox to Daphnia magna challenged with model pro-oxidants copper and paraquat. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:84-91. [PMID: 25263122 DOI: 10.1002/etc.2761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/19/2014] [Accepted: 09/18/2014] [Indexed: 06/03/2023]
Abstract
The redox status of cells is involved in the regulation of several cellular stress-response pathways. It is frequently altered by xenobiotics, as well as by environmental stressors. As such, there is an increasing interest in understanding the redox status of proteins in different scenarios. Recent advances in proteomics enable researchers to measure oxidative lesions in a wide range of proteins. This opens the door to the sensitive detection of toxicity targets and helps decipher the molecular impact of pollutants and environmental stressors. The present study applies the measurement of protein carbonyls, the most common oxidative lesion of proteins, to gel-based proteomics in Daphnia magna. Daphnids were exposed to copper and paraquat, 2 well-known pro-oxidants. Catalase activity was decreased by paraquat, whereas global measurement of protein carbonyls and thiols indicated no change with treatment. Despite the absence of observed oxidative stress, 2-dimensional electrophoresis of the daphnid proteins and measurement of their carbonylation status revealed that 32 features were significantly affected by the treatments, showing higher sensitivity than single measurements. Identified proteins affected by copper indicated a decrease in the heat-shock response, whereas paraquat affected glycolysis. The present study demonstrates the applicability of redox-proteomics in daphnids, and indicates that the heat-shock response plays a counterintuitive role in metal resistance in daphnids.
Collapse
Affiliation(s)
- Louis-Charles Rainville
- Proteomics Research Group, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | | |
Collapse
|
21
|
Rainville LC, Carolan D, Varela AC, Doyle H, Sheehan D. Proteomic evaluation of citrate-coated silver nanoparticles toxicity in Daphnia magna. Analyst 2014; 139:1678-86. [PMID: 24482795 DOI: 10.1039/c3an02160b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent decades have seen a strong increase in the promise and uses of nanotechnology. This is correlated with their growing release in the environment and there is concern that nanomaterials may endanger ecosystems. Silver nanoparticles (AgNPs) have some of the most varied applications, making their release into the environment unavoidable. In order to assess their potential toxicity in aquatic environments, the acute toxicity of citrate-coated AgNPs to Daphnia magna was measured and compared to that of AgNO3. AgNPs were found to be ten times less toxic by mass than silver ions, and most of this toxicity was removed by ultracentrifuging. At the protein level, the two forms of silver had different impacts. Both increased protein thiol content, while only AgNP increased carbonyl levels. In 2DE of samples labelled for carbonyls, no feature was significantly affected by both compounds, indicating different modes of toxicity. Identified proteins showed functional overlap between the two compounds: vitellogenins (vtg) were present in most features identified, indicating their role as a general stress sensor. In addition to vtg, hemoglobin levels were increased by the AgNP exposure while 14-3-3 protein (a regulatory protein) carbonylation levels were reduced by AgNO3. Overall, this study confirms the previously observed lower acute toxicity of AgNPs, while demonstrating that the toxicity of both forms of silver follow somewhat different biologic pathways, potentially leading to different interactions with natural compounds or pollutants in the aquatic environment.
Collapse
Affiliation(s)
- Louis-Charles Rainville
- Proteomics Research Group, School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building 3.99, Western Road, Cork, Ireland.
| | | | | | | | | |
Collapse
|
22
|
Butterfield DA, Gu L, Di Domenico F, Robinson RAS. Mass spectrometry and redox proteomics: applications in disease. MASS SPECTROMETRY REVIEWS 2014; 33:277-301. [PMID: 24930952 DOI: 10.1002/mas.21374] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 06/03/2023]
Abstract
Proteomics techniques are continuously being developed to further understanding of biology and disease. Many of the pathways that are relevant to disease mechanisms rely on the identification of post-translational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation. Much attention has also been focused on oxidative PTMs which include protein carbonyls, protein nitration, and the incorporation of fatty acids and advanced glycation products to amino acid side chains, amongst others. The introduction of these PTMs in the cell can occur due to the attack of reactive oxygen and nitrogen species (ROS and RNS, respectively) on proteins. ROS and RNS can be present as a result of normal metabolic processes as well as external factors such as UV radiation, disease, and environmental toxins. The imbalance of ROS and RNS with antioxidant cellular defenses leads to a state of oxidative stress, which has been implicated in many diseases. Redox proteomics techniques have been used to characterize oxidative PTMs that result as a part of normal cell signaling processes as well as oxidative stress conditions. This review highlights many of the redox proteomics techniques which are currently available for several oxidative PTMs and brings to the reader's attention the application of redox proteomics for understanding disease pathogenesis in neurodegenerative disorders and others such as cancer, kidney, and heart diseases.
Collapse
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40506
| | | | | | | |
Collapse
|
23
|
Cole C, Coelho AV, James RH, Connelly D, Sheehan D. Proteomic responses to metal-induced oxidative stress in hydrothermal vent-living mussels, Bathymodiolus sp., on the Southwest Indian Ridge. MARINE ENVIRONMENTAL RESEARCH 2014; 96:29-37. [PMID: 24080408 DOI: 10.1016/j.marenvres.2013.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 06/02/2023]
Abstract
Bathymodiolin mussels are amongst the dominant fauna occupying hydrothermal vent ecosystems throughout the World's oceans. This subfamily inhabits a highly ephemeral and variable environment, where exceptionally high concentrations of reduced sulphur species and heavy metals necessitate adaptation of specialised detoxification mechanisms. Whilst cellular responses to common anthropogenic pollutants are well-studied in shallow-water species, they remain limited in deep-sea vent fauna. Bathymodiolus sp. were sampled from two newly-discovered vent sites on the Southwest Indian Ridge (Tiamat and Knuckers Gaff) by the remotely operated vehicle (ROV) Kiel 6000 during the RRS James Cook cruise, JC 067 in November 2011. Here, we use redox proteomics to investigate the effects of tissue metal accumulation on protein expression and thiol oxidation in gill. Following 2D PAGE, we demonstrate a significant difference in intensity in 30 protein spots in this organ between the two vent sites out of 205 matched spots. We also see significant variations in thiol oxidation in 15 spots, out of 143 matched. At Tiamat, 23 protein spots are up-regulated compared to Knuckers Gaff and we identify 5 of these with important roles in metabolism, cell structure, stress response, and redox homeostasis. We suggest that increased metal exposure triggers changes in the proteome, regulating tissue uptake. This is evident both between vent sites and across a chemical gradient within the Knuckers Gaff vent site. Our findings highlight the importance of proteomic plasticity in successful adaptation to the spatially and temporally fluctuating chemical environments that are characteristic of hydrothermal vent habitats.
Collapse
Affiliation(s)
- Catherine Cole
- Department of Ocean and Earth Science, University of Southampton, European Way, Waterfront Campus, Southampton SO14 3ZH, UK.
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rachael H James
- National Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Doug Connelly
- National Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - David Sheehan
- School of Biochemistry and Cell Biology, Environmental Research Institute, University College Cork, Ireland
| |
Collapse
|
24
|
Mermelekas G, Makridakis M, Koeck T, Vlahou A. Redox proteomics: from residue modifications to putative biomarker identification by gel- and LC-MS-based approaches. Expert Rev Proteomics 2014; 10:537-49. [DOI: 10.1586/14789450.2013.855611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
25
|
Butterfield DA, Dalle-Donne I. Redox proteomics: from protein modifications to cellular dysfunction and disease. MASS SPECTROMETRY REVIEWS 2014; 33:1-6. [PMID: 24285334 DOI: 10.1002/mas.21404] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, 40506
| | | |
Collapse
|
26
|
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
| |
Collapse
|
27
|
Pedriali A, Riva C, Parolini M, Cristoni S, Sheehan D, Binelli A. A redox proteomic investigation of oxidative stress caused by benzoylecgonine in the freshwater bivalveDreissena polymorpha. Drug Test Anal 2012; 5:646-56. [DOI: 10.1002/dta.1409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/04/2012] [Accepted: 08/13/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandra Pedriali
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Consuelo Riva
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Marco Parolini
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Simone Cristoni
- ISB Ion Source & Biotechnologies S.r.l.; via Lepetit 34; 21040; Gerenzano (VA); Italy
| | - David Sheehan
- Proteomics Research Group; Department of Biochemistry and Environmental Research Institute University College Cork; Lee Maltings, Prospect Row, Mardyke; Cork; Ireland
| | - Andrea Binelli
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| |
Collapse
|
28
|
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.
Collapse
|
29
|
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.
Collapse
Affiliation(s)
- Niels Gregersen
- Research Unit for Molecular Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
| | | | | |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Pablo Martínez-Acedo
- Centro de Biología Molecular Severo Ochoa, Nicolás Cabrera 1, 28049 Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Martyniuk CJ, Alvarez S, Denslow ND. DIGE and iTRAQ as biomarker discovery tools in aquatic toxicology. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 76:3-10. [PMID: 22056798 PMCID: PMC4238381 DOI: 10.1016/j.ecoenv.2011.09.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/27/2011] [Accepted: 09/28/2011] [Indexed: 05/31/2023]
Abstract
Molecular approaches in ecotoxicology have greatly enhanced mechanistic understanding of the impact of aquatic pollutants in organisms. These methods have included high throughput Omics technologies, including quantitative proteomics methods such as 2D differential in-gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ). These methods are becoming more widely used in ecotoxicology studies to identify and characterize protein bioindicators of adverse effect. In teleost fish, iTRAQ has been used successfully in different fish species (e.g. fathead minnow, goldfish, largemouth bass) and tissues (e.g. hypothalamus and liver) to quantify relative protein abundance. Of interest for ecotoxicology is that many proteins commonly utilized as bioindicators of toxicity or stress are quantifiable using iTRAQ on a larger scale, providing a global baseline of biological effect from which to assess changes in the proteome. This review highlights the successes to date for high throughput quantitative proteomics using DIGE and iTRAQ in aquatic toxicology. Current challenges for the iTRAQ method for biomarker discovery in fish are the high cost and the lack of complete annotated genomes for teleosts. However, the use of protein homology from teleost fishes in protein databases and the introduction of hybrid LTQ-FT (Linear ion trap-Fourier transform) mass spectrometers with high resolution, increased sensitivity, and high mass accuracy are able to improve significantly the protein identification rates. Despite these challenges, initial studies utilizing iTRAQ for ecotoxicoproteomics have exceeded expectations and it is anticipated that the use of non-gel based quantitative proteomics will increase for protein biomarker discovery and for characterization of chemical mode of action.
Collapse
Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada E2L 4L5.
| | | | | |
Collapse
|
32
|
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]
|
33
|
Redox proteomics and drug development. J Proteomics 2011; 74:2575-95. [DOI: 10.1016/j.jprot.2011.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/22/2010] [Accepted: 01/09/2011] [Indexed: 01/06/2023]
|
34
|
Braconi D, Bernardini G, Santucci A. Linking protein oxidation to environmental pollutants: redox proteomic approaches. J Proteomics 2011; 74:2324-37. [PMID: 21767673 DOI: 10.1016/j.jprot.2011.06.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/17/2011] [Accepted: 06/28/2011] [Indexed: 12/11/2022]
Abstract
Environmental pollutants, such as compounds used in agriculture or deriving from vehicles, industries and human activities, can represent major concern for human health since they are considered to contribute significantly to many diseased states with major public health significance. Besides considerable epidemiological evidence linking environmental pollutants with adverse health effects, little information is provided on the effects of these compounds at the cellular and molecular level. Though oxidative stress is generally acknowledged as one of the most important mechanisms of action for pollutant-induced toxicity, redox proteomics, the elective tool to identify post-translationally oxidized proteins, is still in its very infancy in this field of investigation. This review will provide the readers with an outline of the use of redox proteomics in evaluating pollutant-induced oxidative damage to proteins in various biological systems. Future potential applications of redox proteomic approaches from an environmental point of view will be discussed as well.
Collapse
Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Università degli Studi di Siena, SI, Italy
| | | | | |
Collapse
|
35
|
Bond AE, Row PE, Dudley E. Post-translation modification of proteins; methodologies and applications in plant sciences. PHYTOCHEMISTRY 2011; 72:975-96. [PMID: 21353264 DOI: 10.1016/j.phytochem.2011.01.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/21/2010] [Accepted: 01/21/2011] [Indexed: 05/03/2023]
Abstract
Proteins have the potential to undergo a variety of post-translational modifications and the different methods available to study these cellular processes has advanced rapidly with the continuing development of proteomic technologies. In this review we aim to detail five major post-translational modifications (phosphorylation, glycosylaion, lipid modification, ubiquitination and redox-related modifications), elaborate on the techniques that have been developed for their analysis and briefly discuss the study of these modifications in selected areas of plant science.
Collapse
Affiliation(s)
- A E Bond
- Biochemistry Group, College of Medicine, Swansea University, Swansea, UK
| | | | | |
Collapse
|
36
|
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.
Collapse
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
| | | | | |
Collapse
|
37
|
Sá-Correia I, Teixeira MC. 2D electrophoresis-based expression proteomics: a microbiologist's perspective. Expert Rev Proteomics 2011; 7:943-53. [PMID: 21142894 DOI: 10.1586/epr.10.76] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.
Collapse
Affiliation(s)
- Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering, Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Technical University of Lisbon, Av. Rovisco Pais, Lisbon, Portugal.
| | | |
Collapse
|