1
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Karami Y, Bignon E. Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad. Comput Struct Biotechnol J 2024; 23:1387-1396. [PMID: 38596314 PMCID: PMC11001638 DOI: 10.1016/j.csbj.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Gene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing to μs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome core particle dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangements of the communication networks and destabilizes the dyad, and that one modification is enough to induce a maximal structural signature. Our results suggest that cysteine hyperoxidation in the nucleosome core particle might favor its disassembly.
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Affiliation(s)
- Yasaman Karami
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France
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2
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Auverlot J, Dard A, Sáez-Vásquez J, Reichheld JP. Redox regulation of epigenetic and epitranscriptomic gene regulatory pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4459-4475. [PMID: 38642408 DOI: 10.1093/jxb/erae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
Developmental and environmental constraints influence genome expression through complex networks of regulatory mechanisms. Epigenetic modifications and remodelling of chromatin are some of the major actors regulating the dynamic of gene expression. Unravelling the factors relaying environmental signals that induce gene expression reprogramming under stress conditions is an important and fundamental question. Indeed, many enzymes involved in epigenetic and chromatin modifications are regulated by redox pathways, through post-translational modifications of proteins or by modifications of the flux of metabolic intermediates. Such modifications are potential hubs to relay developmental and environmental changes for gene expression reprogramming. In this review, we provide an update on the interaction between major redox mediators, such as reactive oxygen and nitrogen species and antioxidants, and epigenetic changes in plants. We detail how redox status alters post-translational modifications of proteins, intracellular epigenetic and epitranscriptional modifications, and how redox regulation interplays with DNA methylation, histone acetylation and methylation, miRNA biogenesis, and chromatin structure and remodelling to reprogram genome expression under environmental constraints.
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Affiliation(s)
- Juline Auverlot
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
| | - Avilien Dard
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
- Centre for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
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3
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Noctor G, Cohen M, Trémulot L, Châtel-Innocenti G, Van Breusegem F, Mhamdi A. Glutathione: a key modulator of plant defence and metabolism through multiple mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4549-4572. [PMID: 38676714 DOI: 10.1093/jxb/erae194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
Redox reactions are fundamental to energy conversion in living cells, and also determine and tune responses to the environment. Within this context, the tripeptide glutathione plays numerous roles. As an important antioxidant, glutathione confers redox stability on the cell and also acts as an interface between signalling pathways and metabolic reactions that fuel growth and development. It also contributes to the assembly of cell components, biosynthesis of sulfur-containing metabolites, inactivation of potentially deleterious compounds, and control of hormonal signalling intensity. The multiplicity of these roles probably explains why glutathione status has been implicated in influencing plant responses to many different conditions. In particular, there is now a considerable body of evidence showing that glutathione is a crucial player in governing the outcome of biotic stresses. This review provides an overview of glutathione synthesis, transport, degradation, and redox turnover in plants. It examines the expression of genes associated with these processes during pathogen challenge and related conditions, and considers the diversity of mechanisms by which glutathione can influence protein function and gene expression.
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Affiliation(s)
- Graham Noctor
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France
- Institut Universitaire de France (IUF), France
| | - Mathias Cohen
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lug Trémulot
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France
| | - Gilles Châtel-Innocenti
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France
| | - Frank Van Breusegem
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Amna Mhamdi
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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4
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Plskova Z, Van Breusegem F, Kerchev P. Redox regulation of chromatin remodelling in plants. PLANT, CELL & ENVIRONMENT 2024; 47:2780-2792. [PMID: 38311877 DOI: 10.1111/pce.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
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Affiliation(s)
- Zuzana Plskova
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Ghent, Belgium
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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5
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Glorieux C, Liu S, Trachootham D, Huang P. Targeting ROS in cancer: rationale and strategies. Nat Rev Drug Discov 2024; 23:583-606. [PMID: 38982305 DOI: 10.1038/s41573-024-00979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 07/11/2024]
Abstract
Reactive oxygen species (ROS) in biological systems are transient but essential molecules that are generated and eliminated by a complex set of delicately balanced molecular machineries. Disruption of redox homeostasis has been associated with various human diseases, especially cancer, in which increased ROS levels are thought to have a major role in tumour development and progression. As such, modulation of cellular redox status by targeting ROS and their regulatory machineries is considered a promising therapeutic strategy for cancer treatment. Recently, there has been major progress in this field, including the discovery of novel redox signalling pathways that affect the metabolism of tumour cells as well as immune cells in the tumour microenvironment, and the intriguing ROS regulation of biomolecular phase separation. Progress has also been made in exploring redox regulation in cancer stem cells, the role of ROS in determining cell fate and new anticancer agents that target ROS. This Review discusses these research developments and their implications for cancer therapy and drug discovery, as well as emerging concepts, paradoxes and future perspectives.
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Affiliation(s)
- Christophe Glorieux
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shihua Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | | | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
- Metabolic Innovation Center, Sun Yat-Sen University, Guangzhou, China.
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6
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Gantner BN, Palma FR, Kayzuka C, Lacchini R, Foltz DR, Backman V, Kelleher N, Shilatifard A, Bonini MG. Histone oxidation as a new mechanism of metabolic control over gene expression. Trends Genet 2024:S0168-9525(24)00134-3. [PMID: 38910033 DOI: 10.1016/j.tig.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The emergence of aerobic respiration created unprecedented bioenergetic advantages, while imposing the need to protect critical genetic information from reactive byproducts of oxidative metabolism (i.e., reactive oxygen species, ROS). The evolution of histone proteins fulfilled the need to shield DNA from these potentially damaging toxins, while providing the means to compact and structure massive eukaryotic genomes. To date, several metabolism-linked histone post-translational modifications (PTMs) have been shown to regulate chromatin structure and gene expression. However, whether and how PTMs enacted by metabolically produced ROS regulate adaptive chromatin remodeling remain relatively unexplored. Here, we review novel mechanistic insights into the interactions of ROS with histones and their consequences for the control of gene expression regulation, cellular plasticity, and behavior.
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Affiliation(s)
- Benjamin N Gantner
- Department of Medicine, Division of Endocrinology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Flavio R Palma
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cezar Kayzuka
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil; Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vadim Backman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Bioengineering, McCormick School of Engineering, Northwestern University, Chicago, IL, USA
| | - Neil Kelleher
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcelo G Bonini
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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7
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Palma FR, Coelho DR, Pulakanti K, Sakiyama MJ, Huang Y, Ogata FT, Danes JM, Meyer A, Furdui CM, Spitz DR, Gomes AP, Gantner BN, Rao S, Backman V, Bonini MG. Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance. Cell Rep 2024; 43:113897. [PMID: 38493478 PMCID: PMC11209755 DOI: 10.1016/j.celrep.2024.113897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Chromatin structure is regulated through posttranslational modifications of histone variants that modulate transcription. Although highly homologous, histone variants display unique amino acid sequences associated with specific functions. Abnormal incorporation of histone variants contributes to cancer initiation, therapy resistance, and metastasis. This study reports that, among its biologic functions, histone H3.1 serves as a chromatin redox sensor that is engaged by mitochondrial H2O2. In breast cancer cells, the oxidation of H3.1Cys96 promotes its eviction and replacement by H3.3 in specific promoters. We also report that this process facilitates the opening of silenced chromatin domains and transcriptional activation of epithelial-to-mesenchymal genes associated with cell plasticity. Scavenging nuclear H2O2 or amino acid substitution of H3.1(C96S) suppresses plasticity, restores sensitivity to chemotherapy, and induces remission of metastatic lesions. Hence, it appears that increased levels of H2O2 produced by mitochondria of breast cancer cells directly promote redox-regulated H3.1-dependent chromatin remodeling involved in chemoresistance and metastasis.
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Affiliation(s)
- Flavio R Palma
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Diego R Coelho
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Kirthi Pulakanti
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marcelo J Sakiyama
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Yunping Huang
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Fernando T Ogata
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Jeanne M Danes
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Alison Meyer
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52245, USA
| | - Ana P Gomes
- Molecular Oncology Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Benjamin N Gantner
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL 60208, USA
| | - Marcelo G Bonini
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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8
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Manoharan RR, Prasad A, Pospíšil P, Kzhyshkowska J. ROS signaling in innate immunity via oxidative protein modifications. Front Immunol 2024; 15:1359600. [PMID: 38515749 PMCID: PMC10954773 DOI: 10.3389/fimmu.2024.1359600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
The innate immune response represents the first-line of defense against invading pathogens. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) have been implicated in various aspects of innate immune function, which involves respiratory bursts and inflammasome activation. These reactive species widely distributed within the cellular environment are short-lived intermediates that play a vital role in cellular signaling and proliferation and are likely to depend on their subcellular site of formation. NADPH oxidase complex of phagocytes is known to generate superoxide anion radical (O2 •-) that functions as a precursor for antimicrobial hydrogen peroxide (H2O2) production, and H2O2 is utilized by myeloperoxidase (MPO) to generate hypochlorous acid (HOCl) that mediates pathogen killing. H2O2 modulates the expression of redox-responsive transcriptional factors, namely NF-kB, NRF2, and HIF-1, thereby mediating redox-based epigenetic modification. Survival and function of immune cells are under redox control and depend on intracellular and extracellular levels of ROS/RNS. The current review focuses on redox factors involved in the activation of immune response and the role of ROS in oxidative modification of proteins in macrophage polarization and neutrophil function.
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Affiliation(s)
| | - Ankush Prasad
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Pavel Pospíšil
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
- Laboratory of Genetic Technologies, Siberian State Medical University, Tomsk, Russia
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9
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Elftmaoui Z, Bignon E. Robust AMBER Force Field Parameters for Glutathionylated Cysteines. Int J Mol Sci 2023; 24:15022. [PMID: 37834470 PMCID: PMC10573104 DOI: 10.3390/ijms241915022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
S-glutathionylation is an oxidative post-translational modification, which is involved in the regulation of many cell signaling pathways. Increasing amounts of studies show that it is crucial in cell homeostasis and deregulated in several pathologies. However, the effect of S-glutathionylation on proteins' structure and activity is poorly understood, and a drastic lack of structural information at the atomic scale remains. Studies based on the use of molecular dynamics simulations, which can provide important information about modification-induced modulation of proteins' structure and function, are also sparse, and there is no benchmarked force field parameters for this modified cysteine. In this contribution, we provide robust AMBER parameters for S-glutathionylation, which we tested extensively against experimental data through a total of 33 μs molecular dynamics simulations. We show that our parameter set efficiently describes the global and local structural properties of S-glutathionylated proteins. These data provide the community with an important tool to foster new investigations into the effect of S-glutathionylation on protein dynamics and function, in a common effort to unravel the structural mechanisms underlying its critical role in cellular processes.
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Affiliation(s)
| | - Emmanuelle Bignon
- UMR 7019 LPCT, Université de Lorraine and CNRS, F-54000 Nancy, France
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10
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Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
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11
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Oxidative Stress and Nuclear Reprogramming: A Pilot Study of the Effects of Reactive Oxygen Species on Architectural and Epigenetic Landscapes. Int J Mol Sci 2022; 24:ijms24010153. [PMID: 36613595 PMCID: PMC9820425 DOI: 10.3390/ijms24010153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Cell genome integrity is continuously threatened by various sources, both endogenous and exogenous. Oxidative stress causes a multitude of damages, severely affecting cell viability, fidelity of genetic information inheritance, and determining profound alterations in gene expression. Epigenetics represents a major form of gene expression modulation, influencing DNA accessibility to transcription factors and the overall nuclear architecture. When assessing the stress-induced epigenome reprogramming, widely diffused biochemical and molecular approaches commonly fail to incorporate analyses such as architectural chromatin alterations and target molecules precise spatial localization. Unveiling the significance of the nuclear response to the oxidative stress, as well as the functional effects over the chromatin organization, may reveal targets and strategies for approaches aiming at limiting the impact on cellular stability. For these reasons, we utilized potassium bromate treatment, a stressor able to induce DNA damages without altering the cellular microenvironment, hence purely modeling nuclear oxidative stress. By means of high-resolution techniques, we described profound alterations in DNA and histone epigenetic modifications and in chromatin organization in response to the reactive oxygen species.
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12
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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13
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Histone Modifications in Neurological Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:95-107. [DOI: 10.1007/978-3-031-05460-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Dubas E, Żur I, Moravčiková J, Fodor J, Krzewska M, Surówka E, Nowicka A, Gerši Z. Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.745865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.
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15
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Huang S, Wang Z, Zhao L. The Crucial Roles of Intermediate Metabolites in Cancer. Cancer Manag Res 2021; 13:6291-6307. [PMID: 34408491 PMCID: PMC8364365 DOI: 10.2147/cmar.s321433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
Metabolic alteration, one of the hallmarks of cancer cells, is important for cancer initiation and development. To support their rapid growth, cancer cells alter their metabolism so as to obtain the necessary energy and building blocks for biosynthetic pathways, as well as to adjust their redox balance. Once thought to be merely byproducts of metabolic pathways, intermediate metabolites are now known to mediate epigenetic modifications and protein post-transcriptional modifications (PTM), as well as connect cellular metabolism with signal transduction. Consequently, they can affect a myriad of processes, including proliferation, apoptosis, and immunity. In this review, we summarize multiple representative metabolites involved in glycolysis, the pentose phosphate pathway (PPP), the tricarboxylic acid (TCA) cycle, lipid synthesis, ketogenesis, methionine metabolism, glutamine metabolism, and tryptophan metabolism, focusing on their roles in chromatin and protein modifications and as signal-transducing messengers.
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Affiliation(s)
- Sisi Huang
- Hengyang School of Medicine, University of South China, Hengyang, Hunan, 421001, People's Republic of China
| | - Zhiqin Wang
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Liang Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
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16
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Chen K, Su C, Tang W, Zhou Y, Xu Z, Chen J, Li H, Chen M, Ma Y. Nuclear transport factor GmNTF2B-1 enhances soybean drought tolerance by interacting with oxidoreductase GmOXR17 to reduce reactive oxygen species content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:740-759. [PMID: 33978999 DOI: 10.1111/tpj.15319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/18/2021] [Accepted: 05/03/2021] [Indexed: 05/27/2023]
Abstract
Drought is a critical abiotic stressor that modulates soybean yield. Drought stress drastically enhances reactive oxygen species (ROS) formation, and maintaining ROS content above a cytostatic level but below a cytotoxic level is essential for normal biology processes in plants. At present, most of the known ROS-scavenging systems are in the cytoplasm, and the mechanism of ROS regulation in the nucleus remains unclear. GmNTF2B-1 is a member of the IV subgroup in the nucleus transporter family. Its expression is localized to the roots and is stimulated by drought stress. In this study, the overexpression of GmNTF2B-1 was found to improve the drought tolerance of transgenic soybean by influencing the ROS content in plants. An oxidoreductase, GmOXR17, was identified to interact with GmNTF2B-1 in the nucleus through the yeast two-hybrid, coimmunoprecipitation and bimolecular fluorescence complementation assays. The drought tolerance of GmOXR17 transgenic soybean was similar to that of GmNTF2B-1. GmNTF2B-1 was expressed in both cytoplasm and nucleus, and GmOXR17 transferred from the cytoplasm to the nucleus under drought stress. The overexpression of GmNTF2B-1 enhanced the nuclear entry of GmOXR17, and the overexpression of GmNTF2B-1 or GmOXR17 could decrease the H2 O2 content and oxidation level in the nucleus. In conclusion, the interaction between GmNTF2B-1 and GmOXR17 may enhance the nuclear entry of GmOXR17, thereby enhancing nuclear ROS scavenging to improve the drought resistance of soybean.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Chen Su
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
- Agricultural Technology Extension Center of Xi'an, Xi'an 710000, China
| | - Wensi Tang
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
| | - Zhaoshi Xu
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
| | - Jun Chen
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
| | - Haiyan Li
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Ming Chen
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
| | - Youzhi Ma
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, Beijing, 100081, China
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17
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Mechanisms of Ataxia Telangiectasia Mutated (ATM) Control in the DNA Damage Response to Oxidative Stress, Epigenetic Regulation, and Persistent Innate Immune Suppression Following Sepsis. Antioxidants (Basel) 2021; 10:antiox10071146. [PMID: 34356379 PMCID: PMC8301080 DOI: 10.3390/antiox10071146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Cells have evolved extensive signaling mechanisms to maintain redox homeostasis. While basal levels of oxidants are critical for normal signaling, a tipping point is reached when the level of oxidant species exceed cellular antioxidant capabilities. Myriad pathological conditions are characterized by elevated oxidative stress, which can cause alterations in cellular operations and damage to cellular components including nucleic acids. Maintenance of nuclear chromatin are critically important for host survival and eukaryotic organisms possess an elaborately orchestrated response to initiate repair of such DNA damage. Recent evidence indicates links between the cellular antioxidant response, the DNA damage response (DDR), and the epigenetic status of the cell under conditions of elevated oxidative stress. In this emerging model, the cellular response to excessive oxidants may include redox sensors that regulate both the DDR and an orchestrated change to the epigenome in a tightly controlled program that both protects and regulates the nuclear genome. Herein we use sepsis as a model of an inflammatory pathophysiological condition that results in elevated oxidative stress, upregulation of the DDR, and epigenetic reprogramming of hematopoietic stem cells (HSCs) to discuss new evidence for interplay between the antioxidant response, the DNA damage response, and epigenetic status.
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18
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García-Giménez JL, Garcés C, Romá-Mateo C, Pallardó FV. Oxidative stress-mediated alterations in histone post-translational modifications. Free Radic Biol Med 2021; 170:6-18. [PMID: 33689846 DOI: 10.1016/j.freeradbiomed.2021.02.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation of gene expression provides a finely tuned response capacity for cells when undergoing environmental changes. However, in the context of human physiology or disease, any cellular imbalance that modulates homeostasis has the potential to trigger molecular changes that result either in physiological adaptation to a new situation or pathological conditions. These effects are partly due to alterations in the functionality of epigenetic regulators, which cause long-term and often heritable changes in cell lineages. As such, free radicals resulting from unbalanced/extended oxidative stress have been proved to act as modulators of epigenetic agents, resulting in alterations of the epigenetic landscape. In the present review we will focus on the particular effect that oxidative stress and free radicals produce in histone post-translational modifications that contribute to altering the histone code and, consequently, gene expression. The pathological consequences of the changes in this epigenetic layer of regulation of gene expression are thoroughly evidenced by data gathered in many physiological adaptive processes and in human diseases that range from age-related neurodegenerative pathologies to cancer, and that include respiratory syndromes, infertility, and systemic inflammatory conditions like sepsis.
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Affiliation(s)
- José-Luis García-Giménez
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Concepción Garcés
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain
| | - Carlos Romá-Mateo
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Federico V Pallardó
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
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19
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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20
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Konno T, Melo EP, Chambers JE, Avezov E. Intracellular Sources of ROS/H 2O 2 in Health and Neurodegeneration: Spotlight on Endoplasmic Reticulum. Cells 2021; 10:233. [PMID: 33504070 PMCID: PMC7912550 DOI: 10.3390/cells10020233] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023] Open
Abstract
Reactive oxygen species (ROS) are produced continuously throughout the cell as products of various redox reactions. Yet these products function as important signal messengers, acting through oxidation of specific target factors. Whilst excess ROS production has the potential to induce oxidative stress, physiological roles of ROS are supported by a spatiotemporal equilibrium between ROS producers and scavengers such as antioxidative enzymes. In the endoplasmic reticulum (ER), hydrogen peroxide (H2O2), a non-radical ROS, is produced through the process of oxidative folding. Utilisation and dysregulation of H2O2, in particular that generated in the ER, affects not only cellular homeostasis but also the longevity of organisms. ROS dysregulation has been implicated in various pathologies including dementia and other neurodegenerative diseases, sanctioning a field of research that strives to better understand cell-intrinsic ROS production. Here we review the organelle-specific ROS-generating and consuming pathways, providing evidence that the ER is a major contributing source of potentially pathologic ROS.
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Affiliation(s)
- Tasuku Konno
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Eduardo Pinho Melo
- CCMAR—Centro de Ciências do Mar, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal;
| | - Joseph E. Chambers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK;
| | - Edward Avezov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
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21
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Babbar R, Karpinska B, Grover A, Foyer CH. Heat-Induced Oxidation of the Nuclei and Cytosol. FRONTIERS IN PLANT SCIENCE 2021; 11:617779. [PMID: 33510759 PMCID: PMC7835529 DOI: 10.3389/fpls.2020.617779] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/14/2020] [Indexed: 05/14/2023]
Abstract
The concept that heat stress (HS) causes a large accumulation of reactive oxygen species (ROS) is widely accepted. However, the intracellular compartmentation of ROS accumulation has been poorly characterized. We therefore used redox-sensitive green fluorescent protein (roGFP2) to provide compartment-specific information on heat-induced redox changes of the nuclei and cytosol of Arabidopsis leaf epidermal and stomatal guard cells. We show that HS causes a large increase in the degree of oxidation of both compartments, causing large shifts in the glutathione redox potentials of the cells. Heat-induced increases in the levels of the marker transcripts, heat shock protein (HSP)101, and ascorbate peroxidase (APX)2 were maximal after 15 min of the onset of the heat treatment. RNAseq analysis of the transcript profiles of the control and heat-treated seedlings revealed large changes in transcripts encoding HSPs, mitochondrial proteins, transcription factors, and other nuclear localized components. We conclude that HS causes extensive oxidation of the nucleus as well as the cytosol. We propose that the heat-induced changes in the nuclear redox state are central to both genetic and epigenetic control of plant responses to HS.
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Affiliation(s)
- Richa Babbar
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
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22
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Zhou M, Malhan N, Ahkami AH, Engbrecht K, Myers G, Dahlberg J, Hollingsworth J, Sievert JA, Hutmacher R, Madera M, Lemaux PG, Hixson KK, Jansson C, Paša-Tolić L. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. Methods 2020; 184:29-39. [DOI: 10.1016/j.ymeth.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
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23
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Oxidative, Reductive, and Nitrosative Stress Effects on Epigenetics and on Posttranslational Modification of Enzymes in Cardiometabolic Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8819719. [PMID: 33204398 PMCID: PMC7649698 DOI: 10.1155/2020/8819719] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
Oxidative (OS), reductive (RS), and nitrosative (NSS) stresses produce carbonylation, glycation, glutathionylation, sulfhydration, nitration, and nitrosylation reactions. OS, RS, and NSS are interrelated since RS results from an overactivation of antioxidant systems and NSS is the result of the overactivation of the oxidation of nitric oxide (NO). Here, we discuss the general characteristics of the three types of stress and the way by which the reactions they induce (a) damage the DNA structure causing strand breaks or inducing the formation of 8-oxo-d guanosine; (b) modify histones; (c) modify the activities of the enzymes that determine the establishment of epigenetic cues such as DNA methyl transferases, histone methyl transferases, acetyltransferases, and deacetylases; (d) alter DNA reparation enzymes by posttranslational mechanisms; and (e) regulate the activities of intracellular enzymes participating in metabolic reactions and in signaling pathways through posttranslational modifications. Furthermore, the three types of stress may establish new epigenetic marks through these reactions. The development of cardiometabolic disorders in adult life may be programed since early stages of development by epigenetic cues which may be established or modified by OS, RS, and NSS. Therefore, the three types of stress participate importantly in mediating the impact of the early life environment on later health and heritability. Here, we discuss their impact on cardiometabolic diseases. The epigenetic modifications induced by these stresses depend on union and release of chemical residues on a DNA sequence and/or on amino acid residues in proteins, and therefore, they are reversible and potentially treatable.
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24
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Chan JC, Maze I. Nothing Is Yet Set in (Hi)stone: Novel Post-Translational Modifications Regulating Chromatin Function. Trends Biochem Sci 2020; 45:829-844. [PMID: 32498971 PMCID: PMC7502514 DOI: 10.1016/j.tibs.2020.05.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/28/2020] [Accepted: 05/14/2020] [Indexed: 01/04/2023]
Abstract
Histone post-translational modifications (PTMs) have emerged as exciting mechanisms of biological regulation, impacting pathways related to cancer, immunity, brain function, and more. Over the past decade alone, several histone PTMs have been discovered, including acylation, lipidation, monoaminylation, and glycation, many of which appear to have crucial roles in nucleosome stability and transcriptional regulation. In this review, we discuss novel histone PTMs identified within the past 10 years, with an extended focus on enzymatic versus nonenzymatic mechanisms underlying modification and adduction. Furthermore, we consider how these novel histone PTMs might fit within the framework of a so-called 'histone code', emphasizing the physiological relevance of these PTMs in metabolism, development, and disease states.
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Affiliation(s)
- Jennifer C Chan
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ian Maze
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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25
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Zheng Q, Maksimovic I, Upad A, David Y. Non-enzymatic covalent modifications: a new link between metabolism and epigenetics. Protein Cell 2020; 11:401-416. [PMID: 32356279 PMCID: PMC7251012 DOI: 10.1007/s13238-020-00722-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenetic modifications, including those on DNA and histones, have been shown to regulate cellular metabolism by controlling expression of enzymes involved in the corresponding metabolic pathways. In turn, metabolic flux influences epigenetic regulation by affecting the biosynthetic balance of enzyme cofactors or donors for certain chromatin modifications. Recently, non-enzymatic covalent modifications (NECMs) by chemically reactive metabolites have been reported to manipulate chromatin architecture and gene transcription through multiple mechanisms. Here, we summarize these recent advances in the identification and characterization of NECMs on nucleic acids, histones, and transcription factors, providing an additional mechanistic link between metabolism and epigenetics.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Igor Maksimovic
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Akhil Upad
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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26
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Dimauro I, Paronetto MP, Caporossi D. Exercise, redox homeostasis and the epigenetic landscape. Redox Biol 2020; 35:101477. [PMID: 32127290 PMCID: PMC7284912 DOI: 10.1016/j.redox.2020.101477] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Physical exercise represents one of the strongest physiological stimuli capable to induce functional and structural modifications in all biological systems. Indeed, beside the traditional genetic mechanisms, physical exercise can modulate gene expression through epigenetic modifications, namely DNA methylation, post-translational histone modification and non-coding RNA transcripts. Initially considered as merely damaging molecules, it is now well recognized that both reactive oxygen (ROS) and nitrogen species (RNS) produced under voluntary exercise play an important role as regulatory mediators in signaling processes. While robust scientific evidences highlight the role of exercise-associated redox modifications in modulating gene expression through the genetic machinery, the understanding of their specific impact on epigenomic profile is still at an early stage. This review will provide an overview of the role of ROS and RNS in modulating the epigenetic landscape in the context of exercise-related adaptations. Physical exercise can modulate gene expression through epigenetic modifications. Epigenetic regulation of ROS/RNS generating, sensing and neutralizing enzymes can impact the cellular levels of ROS and RNS. ROS might act as modulators of epigenetic machinery, interfering with DNA methylation, hPTMs and ncRNAs expression. Redox homeostasis might hold a relevant role in the epigenetic landscape modulating exercise-related adaptations.
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Affiliation(s)
- Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Maria Paola Paronetto
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy; Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy.
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27
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Castelli MA, Whiteley SL, Georges A, Holleley CE. Cellular calcium and redox regulation: the mediator of vertebrate environmental sex determination? Biol Rev Camb Philos Soc 2020; 95:680-695. [DOI: 10.1111/brv.12582] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Meghan A. Castelli
- CSIROAustralian National Wildlife Collection, GPO Box 1700 Canberra 2601 Australia
- Institute for Applied EcologyUniversity of Canberra Canberra 2617 Australia
| | - Sarah L. Whiteley
- CSIROAustralian National Wildlife Collection, GPO Box 1700 Canberra 2601 Australia
- Institute for Applied EcologyUniversity of Canberra Canberra 2617 Australia
| | - Arthur Georges
- Institute for Applied EcologyUniversity of Canberra Canberra 2617 Australia
| | - Clare E. Holleley
- CSIROAustralian National Wildlife Collection, GPO Box 1700 Canberra 2601 Australia
- Institute for Applied EcologyUniversity of Canberra Canberra 2617 Australia
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28
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Chia SB, Elko EA, Aboushousha R, Manuel AM, van de Wetering C, Druso JE, van der Velden J, Seward DJ, Anathy V, Irvin CG, Lam YW, van der Vliet A, Janssen-Heininger YMW. Dysregulation of the glutaredoxin/ S-glutathionylation redox axis in lung diseases. Am J Physiol Cell Physiol 2019; 318:C304-C327. [PMID: 31693398 DOI: 10.1152/ajpcell.00410.2019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glutathione is a major redox buffer, reaching millimolar concentrations within cells and high micromolar concentrations in airways. While glutathione has been traditionally known as an antioxidant defense mechanism that protects the lung tissue from oxidative stress, glutathione more recently has become recognized for its ability to become covalently conjugated to reactive cysteines within proteins, a modification known as S-glutathionylation (or S-glutathiolation or protein mixed disulfide). S-glutathionylation has the potential to change the structure and function of the target protein, owing to its size (the addition of three amino acids) and charge (glutamic acid). S-glutathionylation also protects proteins from irreversible oxidation, allowing them to be enzymatically regenerated. Numerous enzymes have been identified to catalyze the glutathionylation/deglutathionylation reactions, including glutathione S-transferases and glutaredoxins. Although protein S-glutathionylation has been implicated in numerous biological processes, S-glutathionylated proteomes have largely remained unknown. In this paper, we focus on the pathways that regulate GSH homeostasis, S-glutathionylated proteins, and glutaredoxins, and we review methods required toward identification of glutathionylated proteomes. Finally, we present the latest findings on the role of glutathionylation/glutaredoxins in various lung diseases: idiopathic pulmonary fibrosis, asthma, and chronic obstructive pulmonary disease.
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Affiliation(s)
- Shi B Chia
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Evan A Elko
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Reem Aboushousha
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Allison M Manuel
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Cheryl van de Wetering
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Joseph E Druso
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Jos van der Velden
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - David J Seward
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Charles G Irvin
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Ying-Wai Lam
- Department of Biology, University of Vermont, Burlington, Vermont
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
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29
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Parsanathan R, Jain SK. Glutathione deficiency induces epigenetic alterations of vitamin D metabolism genes in the livers of high-fat diet-fed obese mice. Sci Rep 2019; 9:14784. [PMID: 31616013 PMCID: PMC6794254 DOI: 10.1038/s41598-019-51377-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/28/2019] [Indexed: 02/06/2023] Open
Abstract
Obesity has been correlating with low levels of glutathione (GSH) and 25-hydroxyvitamin D3 (25(OH)VD3). The liver is the principal site for the 25(OH)VD3 biosynthesis. This study investigated whether GSH deficiency induces epigenetic alterations that impair Vitamin D (VD) metabolism genes in the livers of HFD-fed mice. The expression of the VD metabolism genes CYP2R1 and CYP27A1 (25-hydroxylase), CYP27B1 (1-α-hydroxylase), and vitamin D receptor (VDR) were downregulated in the livers of mice fed an HFD (GSH- deficient) compared with control diet-fed group. The expression of CYP24A1 (24-hydroxylase) was significantly increased, which catabolizes both 25(OH)VD3 and 1α,25-hydroxyvitaminD3. Gene-specific hypermethylation of 25-hydroxylase, 1-α-hydroxylase, and VDR, and hypomethylation of CYP24A1 was observed in HFD-fed mice. GSH deficiency induced in cultured hepatocytes caused an increase in oxidative stress and alterations in VD regulatory genes. Similarly, elevated global DNA methylation, Dnmt activity, and 5-methylcytosine but decreased Tet activity and 5-hydroxymethylcytosine were observed in the GSH-deficient hepatocytes and the liver of HFD-fed mice. Replenishment of GSH by its prodrugs treatment beneficially altered epigenetic enzymes, and VD-metabolism genes in hepatocytes. HFD-induces GSH deficiency and epigenetically alters VD-biosynthesis pathway genes. This provides a biochemical mechanism for the VD-deficiency and potential benefits of GSH treatment in reducing 25(OH)VD3-deficiency.
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Affiliation(s)
- Rajesh Parsanathan
- Department of Pediatrics and Center for Cardiovascular Diseases and Sciences, Louisiana State University Health Sciences Center-Shreveport, 1501 Kings Highway, Shreveport, LA, 71130, USA
| | - Sushil K Jain
- Department of Pediatrics and Center for Cardiovascular Diseases and Sciences, Louisiana State University Health Sciences Center-Shreveport, 1501 Kings Highway, Shreveport, LA, 71130, USA.
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30
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DeVallance E, Li Y, Jurczak MJ, Cifuentes-Pagano E, Pagano PJ. The Role of NADPH Oxidases in the Etiology of Obesity and Metabolic Syndrome: Contribution of Individual Isoforms and Cell Biology. Antioxid Redox Signal 2019; 31:687-709. [PMID: 31250671 PMCID: PMC6909742 DOI: 10.1089/ars.2018.7674] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Significance: Highly prevalent in Western cultures, obesity, metabolic syndrome, and diabetes increase the risk of cardiovascular morbidity and mortality and cost health care systems billions of dollars annually. At the cellular level, obesity, metabolic syndrome, and diabetes are associated with increased production of reactive oxygen species (ROS). Increased levels of ROS production in key organ systems such as adipose tissue, skeletal muscle, and the vasculature cause disruption of tissue homeostasis, leading to increased morbidity and risk of mortality. More specifically, growing evidence implicates the nicotinamide adenine dinucleotide phosphate oxidase (NOX) enzymes in these pathologies through impairment of insulin signaling, inflammation, and vascular dysfunction. The NOX family of enzymes is a major driver of redox signaling through its production of superoxide anion, hydrogen peroxide, and attendant downstream metabolites acting on redox-sensitive signaling molecules. Recent Advances: The primary goal of this review is to highlight recent advances and survey our present understanding of cell-specific NOX enzyme contributions to metabolic diseases. Critical Issues: However, due to the short half-lives of individual ROS and/or cellular defense systems, radii of ROS diffusion are commonly short, often restricting redox signaling and oxidant stress to localized events. Thus, special emphasis should be placed on cell type and subcellular location of NOX enzymes to better understand their role in the pathophysiology of metabolic diseases. Future Directions: We discuss the targeting of NOX enzymes as potential therapy and bring to light potential emerging areas of NOX research, microparticles and epigenetics, in the context of metabolic disease.
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Affiliation(s)
- Evan DeVallance
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Pittsburgh Heart, Lung and Blood, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yao Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Pittsburgh Heart, Lung and Blood, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael J Jurczak
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eugenia Cifuentes-Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Pittsburgh Heart, Lung and Blood, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick J Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Pittsburgh Heart, Lung and Blood, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
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31
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Cianfruglia L, Minnelli C, Laudadio E, Scirè A, Armeni T. Side Effects of Curcumin: Epigenetic and Antiproliferative Implications for Normal Dermal Fibroblast and Breast Cancer Cells. Antioxidants (Basel) 2019; 8:antiox8090382. [PMID: 31505772 PMCID: PMC6770744 DOI: 10.3390/antiox8090382] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 01/15/2023] Open
Abstract
Background: Curcumin is a yellow-orange pigment obtained from the plant Curcuma longa, which is known to exert beneficial effects in several diseases, including cancer. However, at high doses, it may produce toxic and carcinogenic effects in normal cells. In this context, we studied the effects of curcumin on normal human dermal fibroblast (HDF) cells and breast cancer cells (MCF7). Methods: We used cellular viability and growth assays to evaluate the antiproliferative action of curcumin, analyzed the endogenous glutathione levels, conducted cell cycle, apoptosis, and necrosis analyses, and performed immunodetection of glutathionylated and acetylated H3 histones. Results: We found that HDFs are more sensitive to curcumin treatment than MCF7 cells, resulting in pronounced arrest of cell cycle progression and higher levels of cellular death. In both cell types, the homeostasis of the redox cellular environment did not change after curcumin treatment; however, significant differences were observed in glutathione (GSH) levels and in S-glutathionylation of H3 histones. Conclusion: Curcumin administration can potentially confer benefits, but high doses may be toxic. Thus, its use as a dietary supplement or in cancer therapies has a double edge.
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Affiliation(s)
- Laura Cianfruglia
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche-Sez. Biochimica, Biologia e Fisica, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Cristina Minnelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Emiliano Laudadio
- Dipartimento S.I.M.A.U., Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Andrea Scirè
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Tatiana Armeni
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche-Sez. Biochimica, Biologia e Fisica, Università Politecnica delle Marche, 60131 Ancona, Italy.
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32
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García-Giménez JL, Romá-Mateo C, Pallardó FV. Oxidative post-translational modifications in histones. Biofactors 2019; 45:641-650. [PMID: 31185139 DOI: 10.1002/biof.1532] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 01/12/2023]
Abstract
Epigenetic regulation is attracting much attention because it explains many of the effects that the external environment induces in organisms. Changes in the cellular redox status and even more specifically in its nuclear redox compartment is one of these examples. Redox changes can induce modulation of the epigenetic regulation in cells. Here we present a few cases where reactive oxygen or nitrogen species induces epigenetic marks in histones. Posttranslational modification of these proteins like histone nitrosylation, carbonylation, or glutathionylation together with other mechanisms not reviewed here are the cornerstones of redox-related epigenetic regulation. We currently face a new field of research with potential important consequences for the treatment of many pathologies.
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Affiliation(s)
- José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Carlos Romá-Mateo
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
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33
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Lermant A, Murdoch CE. Cysteine Glutathionylation Acts as a Redox Switch in Endothelial Cells. Antioxidants (Basel) 2019; 8:E315. [PMID: 31426416 PMCID: PMC6720164 DOI: 10.3390/antiox8080315] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Oxidative post-translational modifications (oxPTM) of receptors, enzymes, ion channels and transcription factors play an important role in cell signaling. oxPTMs are a key way in which oxidative stress can influence cell behavior during diverse pathological settings such as cardiovascular diseases (CVD), cancer, neurodegeneration and inflammatory response. In addition, changes in oxPTM are likely to be ways in which low level reactive oxygen and nitrogen species (RONS) may contribute to redox signaling, exerting changes in physiological responses including angiogenesis, cardiac remodeling and embryogenesis. Among oxPTM, S-glutathionylation of reactive cysteines emerges as an important regulator of vascular homeostasis by modulating endothelial cell (EC) responses to their local redox environment. This review summarizes the latest findings of S-glutathionylated proteins in major EC pathways, and the functional consequences on vascular pathophysiology. This review highlights the diversity of molecules affected by S-glutathionylation, and the complex consequences on EC function, thereby demonstrating an intricate dual role of RONS-induced S-glutathionylation in maintaining vascular homeostasis and participating in various pathological processes.
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Affiliation(s)
- Agathe Lermant
- Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland DD1 9SY, UK
| | - Colin E Murdoch
- Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland DD1 9SY, UK.
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34
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Abstract
Cells are continuously subjected to an array of reactive/toxic chemical species which are produced both endogenously through metabolic pathways and taken up exogenously by diet and exposure to drugs or toxins. As a result, proteins often undergo non-enzymatic covalent modifications (NECMs) by these species, which can alter protein structure, function, stability, and binding partner affinity. NECMs accumulate over time and are linked to various diseases such as Alzheimer's disease, cancer, and diabetes. In the cellular proteome, histones have some of the longest half-lives, making them prime targets for NECMs. In addition, histones have emerged as key regulators of transcription, a function that is primarily controlled by modification of their tails. These modifications are usually installed or removed enzymatically, but recent evidence suggests that some may also occur non-enzymatically. Despite the vast knowledge detailing the relationship between histone modifications and gene regulation, NECMs on histones remain poorly explored. A major reason for this difference stems from the fact that, unlike their enzymatically installed counterparts, NECMs are difficult to both control and test in vivo. Here, we review advances in our understanding of the effect non-enzymatic covalent modifications (NECMs) have on the epigenetic landscape, cellular fate, and their implications in disease. Cumulatively, this illustrates how the epigenetic code is directly toxified by chemicals and detoxified by corresponding eraser enzymes.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas A. Prescott
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Igor Maksimovic
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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35
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Shukla A, Bunkar N, Kumar R, Bhargava A, Tiwari R, Chaudhury K, Goryacheva IY, Mishra PK. Air pollution associated epigenetic modifications: Transgenerational inheritance and underlying molecular mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:760-777. [PMID: 30530146 DOI: 10.1016/j.scitotenv.2018.11.381] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 11/25/2018] [Indexed: 05/28/2023]
Abstract
Air pollution is one of the leading causes of deaths in Southeast Asian countries including India. Exposure to air pollutants affects vital cellular mechanisms and is intimately linked with the etiology of a number of chronic diseases. Earlier work from our laboratory has shown that airborne particulate matter disturbs the mitochondrial machinery and causes significant damage to the epigenome. Mitochondrial reactive oxygen species possess the ability to trigger redox-sensitive signaling mechanisms and induce irreversible epigenomic changes. The electrophilic nature of reactive metabolites can directly result in deprotonation of cytosine at C-5 position or interfere with the DNA methyltransferases activity to cause alterations in DNA methylation. In addition, it also perturbs level of cellular metabolites critically involved in different epigenetic processes like acetylation and methylation of histone code and DNA hypo or hypermethylation. Interestingly, these modifications may persist through downstream generations and result in the transgenerational epigenomic inheritance. This phenomenon of subsequent transfer of epigenetic modifications is mainly associated with the germ cells and relies on the germline stability of the epigenetic states. Overall, the recent literature supports, and arguably strengthens, the contention that air pollution might contribute to transmission of epimutations from gametes to zygotes by involving mitochondrial DNA, parental allele imprinting, histone withholding and non-coding RNAs. However, larger prospective studies using innovative, integrated epigenome-wide metabolomic strategy are highly warranted to assess the air pollution induced transgenerational epigenetic inheritance and associated human health effects.
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Affiliation(s)
- Anushi Shukla
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajat Kumar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Koel Chaudhury
- School of Medical Science & Technology, Indian Institute of Technology, Kharagpur, India
| | - Irina Y Goryacheva
- Department of General and Inorganic Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna K Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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36
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Sun W, Dai L, Yu H, Puspita B, Zhao T, Li F, Tan JL, Lim YT, Chen MW, Sobota RM, Tenen DG, Prabhu N, Nordlund P. Monitoring structural modulation of redox-sensitive proteins in cells with MS-CETSA. Redox Biol 2019; 24:101168. [PMID: 30925293 PMCID: PMC6439307 DOI: 10.1016/j.redox.2019.101168] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 12/31/2022] Open
Abstract
Reactive oxygen species (ROS) induce different cellular stress responses but can also mediate cellular signaling. Augmented levels of ROS are associated with aging, cancer as well as various metabolic and neurological disorders. ROS can also affect the efficacy and adverse effects of drugs. Although proteins are key mediators of most ROS effects, direct studies of ROS-modulated-protein function in the cellular context are very challenging. Therefore the understanding of specific roles of different proteins in cellular ROS responses is still relatively rudimentary. In the present work we show that Mass Spectrometry-Cellular Thermal Shift Assay (MS-CETSA) can directly monitor ROS and redox modulations of protein structure at the proteome level. By altering ROS levels in cultured human hepatocellular carcinoma cell lysates and intact cells, we detected CETSA responses in many proteins known to be redox sensitive, and also revealed novel candidate ROS sensitive proteins. Studies in intact cells treated with hydrogen peroxide and sulfasalazine, a ROS modulating drug, identified not only proteins that are directly modified, but also proteins reporting on downstream cellular effects. Comprehensive changes are seen on rate-limiting proteins regulating key cellular processes, including known redox control systems, protein degradation, epigenetic control and protein translational processes. Interestingly, concerted shifts on ATP-binding proteins revealed redox-induced modulation of ATP levels, which likely control many cellular processes. Collectively, these studies establish CETSA as a novel method for cellular studies of redox modulations of proteins, which implicated in a wide range of processes and for the discovery of CETSA-based biomarkers reporting on the efficacy as well as adverse effects of drugs.
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Affiliation(s)
- Wendi Sun
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Brenda Puspita
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Tianyun Zhao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Feng Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Justin L Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Genome Institute of Singapore, A*STAR, 138672, Singapore
| | - Yan Ting Lim
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Ming Wei Chen
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | | | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden.
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37
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Scirè A, Cianfruglia L, Minnelli C, Bartolini D, Torquato P, Principato G, Galli F, Armeni T. Glutathione compartmentalization and its role in glutathionylation and other regulatory processes of cellular pathways. Biofactors 2019; 45:152-168. [PMID: 30561781 DOI: 10.1002/biof.1476] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022]
Abstract
Glutathione is considered the major non-protein low molecular weight modulator of redox processes and the most important thiol reducing agent of the cell. The biosynthesis of glutathione occurs in the cytosol from its constituent amino acids, but this tripeptide is also present in the most important cellular districts, such as mitochondria, nucleus, and endoplasmic reticulum, thus playing a central role in several metabolic pathways and cytoprotection mechanisms. Indeed, glutathione is involved in the modulation of various cellular processes and, not by chance, it is a ubiquitous determinant for redox signaling, xenobiotic detoxification, and regulation of cell cycle and death programs. The balance between its concentration and redox state is due to a complex series of interactions between biosynthesis, utilization, degradation, and transport. All these factors are of great importance to understand the significance of cellular redox balance and its relationship with physiological responses and pathological conditions. The purpose of this review is to give an overview on glutathione cellular compartmentalization. Information on its subcellular distribution provides a deeper understanding of glutathione-dependent processes and reflects the importance of compartmentalization in the regulation of specific cellular pathways. © 2018 BioFactors, 45(2):152-168, 2019.
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Affiliation(s)
- Andrea Scirè
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Laura Cianfruglia
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Università Politecnica delle Marche, Ancona, Italy
| | - Cristina Minnelli
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Università Politecnica delle Marche, Ancona, Italy
| | - Desirée Bartolini
- Clinical Biochemistry and Human Nutrition Labs, Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Pierangelo Torquato
- Clinical Biochemistry and Human Nutrition Labs, Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Giovanni Principato
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Galli
- Clinical Biochemistry and Human Nutrition Labs, Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Tatiana Armeni
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Università Politecnica delle Marche, Ancona, Italy
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Womersley JS, Townsend DM, Kalivas PW, Uys JD. Targeting redox regulation to treat substance use disorder using N‐acetylcysteine. Eur J Neurosci 2018; 50:2538-2551. [PMID: 30144182 DOI: 10.1111/ejn.14130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/28/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022]
Abstract
Substance use disorder (SUD) is a chronic relapsing disorder characterized by transitioning from acute drug reward to compulsive drug use. Despite the heavy personal and societal burden of SUDs, current treatments are limited and unsatisfactory. For this reason, a deeper understanding of the mechanisms underlying addiction is required. Altered redox status, primarily due to drug-induced increases in dopamine metabolism, is a unifying feature of abused substances. In recent years, knowledge of the effects of oxidative stress in the nervous system has evolved from strictly neurotoxic to include a more nuanced role in redox-sensitive signaling. More specifically, S-glutathionylation, a redox-sensitive post-translational modification, has been suggested to influence the response to drugs of abuse. In this review we will examine the evidence for redox-mediating drugs as therapeutic tools focusing on N-acetylcysteine as a treatment for cocaine addiction. We will conclude by suggesting future research directions that may further advance this field.
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Affiliation(s)
- Jacqueline S Womersley
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 409 Drug Discovery Building, 70 President Street, Charleston, SC, 29425, USA
| | - Danyelle M Townsend
- Department of Drug Discover and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Peter W Kalivas
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Joachim D Uys
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 409 Drug Discovery Building, 70 President Street, Charleston, SC, 29425, USA
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39
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Locato V, Cimini S, De Gara L. ROS and redox balance as multifaceted players of cross-tolerance: epigenetic and retrograde control of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3373-3391. [PMID: 29722828 DOI: 10.1093/jxb/ery168] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/27/2018] [Indexed: 05/07/2023]
Abstract
Retrograde pathways occurring between chloroplasts, mitochondria, and the nucleus involve oxidative and antioxidative signals that, working in a synergistic or antagonistic mode, control the expression of specific patterns of genes following stress perception. Increasing evidence also underlines the relevance of mitochondrion-chloroplast-nucleus crosstalk in modulating the whole cellular redox metabolism by a controlled and integrated flux of information. Plants can maintain the acquired tolerance by a stress memory, also operating at the transgenerational level, via epigenetic and miRNA-based mechanisms controlling gene expression. Data discussed in this review strengthen the idea that ROS, redox signals, and shifts in cellular redox balance permeate the signalling network leading to cross-tolerance. The identification of specific ROS/antioxidative signatures leading a plant to different fates under stress is pivotal for identifying strategies to monitor and increase plant fitness in a changing environment. This review provides an update of the plant redox signalling network implicated in stress responses, in particular in cross-tolerance acquisition. The interplay between reactive oxygen species (ROS), ROS-derived signals, and antioxidative pathways is also discussed in terms of plant acclimation to stress in the short and long term.
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Affiliation(s)
- Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
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40
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Bird RP. The Emerging Role of Vitamin B6 in Inflammation and Carcinogenesis. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 83:151-194. [PMID: 29477221 DOI: 10.1016/bs.afnr.2017.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vitamin B6 serves as a coenzyme catalyzing more than 150 enzymes regulating metabolism and synthesis of proteins, carbohydrates, lipids, heme, and important bioactive metabolites. For several years vitamin B6 and its vitamers (B6) were recognized as antioxidant and antiinflammatory and in modulating immunity and gene expression. During the last 10 years, there were growing reports implicating B6 in inflammation and inflammation-related chronic illnesses including cancer. It is unclear if the deficiency of B6 or additional intake of B6, above the current requirement, should be the focus. Whether the current recommended daily intake for B6 is adequate should be revisited, since B6 is important to human health beyond its role as a coenzyme and its status is affected by many factors including but not limited to age, obesity, and inflammation associated with chronic illnesses. A link between inflammation B6 status and carcinogenesis is not yet completely understood. B6-mediated synthesis of H2S, a gasotransmitter, and taurine in health and disease, especially in maintaining mitochondrial integrity and biogenesis and inflammation, remains an important area to be explored. Recent developments in the molecular role of B6 and its direct interaction with inflammasomes, and nuclear receptor corepressor and coactivator, receptor-interacting protein 140, provide a strong impetus to further explore the multifaceted role of B6 in carcinogenesis and human health.
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Affiliation(s)
- Ranjana P Bird
- School of Health Sciences, University of Northern British Columbia, Prince George, BC, Canada.
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41
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Martins L, Trujillo-Hernandez JA, Reichheld JP. Thiol Based Redox Signaling in Plant Nucleus. FRONTIERS IN PLANT SCIENCE 2018; 9:705. [PMID: 29892308 PMCID: PMC5985474 DOI: 10.3389/fpls.2018.00705] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/09/2018] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are well-described by-products of cellular metabolic activities, acting as signaling molecules and regulating the redox state of proteins. Solvent exposed thiol residues like cysteines are particularly sensitive to oxidation and their redox state affects structural and biochemical capacities of many proteins. While thiol redox regulation has been largely studied in several cell compartments like in the plant chloroplast, little is known about redox sensitive proteins in the nucleus. Recent works have revealed that proteins with oxidizable thiols are important for the regulation of many nuclear functions, including gene expression, transcription, epigenetics, and chromatin remodeling. Moreover, thiol reducing molecules like glutathione and specific isoforms of thiols reductases, thioredoxins and glutaredoxins were found in different nuclear subcompartments, further supporting that thiol-dependent systems are active in the nucleus. This mini-review aims to discuss recent progress in plant thiol redox field, taking examples of redox regulated nuclear proteins and focusing on major thiol redox systems acting in the nucleus.
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Affiliation(s)
- Laura Martins
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - José Abraham Trujillo-Hernandez
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
- *Correspondence: Jean-Philippe Reichheld,
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42
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Charbonnel C, Niazi AK, Elvira-Matelot E, Nowak E, Zytnicki M, de Bures A, Jobet E, Opsomer A, Shamandi N, Nowotny M, Carapito C, Reichheld JP, Vaucheret H, Sáez-Vásquez J. The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain. Nucleic Acids Res 2017; 45:11891-11907. [PMID: 28981840 PMCID: PMC5714217 DOI: 10.1093/nar/gkx820] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 09/13/2017] [Indexed: 01/20/2023] Open
Abstract
RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage. Furthermore, we demonstrate that RNase III and dsRNA binding domains (dsRBD) are both required for dsRNA cleavage. Interestingly, the four DCL and the three RTL that carry dsRBD share a conserved cysteine (C230 in Arabidopsis RTL1) in their dsRBD. C230 is essential for RTL1 and DCL1 activities and is subjected to post-transcriptional modification. Indeed, under oxidizing conditions, glutathionylation of C230 inhibits RTL1 cleavage activity in a reversible manner involving glutaredoxins. We conclude that the redox state of the dsRBD ensures a fine-tune regulation of dsRNA processing by plant RNase III.
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Affiliation(s)
- Cyril Charbonnel
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Adnan K Niazi
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Emilie Elvira-Matelot
- Institut Jean-Pierre Bourgin, UMR1318 INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Elzbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Anne de Bures
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Edouard Jobet
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Alisson Opsomer
- Laboratoire de Spectrométrie de Masse BioOrganique,Université de Strasbourg, CNRS, IPHC UMR 7178, 67037 Strasbourg, France
| | - Nahid Shamandi
- Institut Jean-Pierre Bourgin, UMR1318 INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France.,Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique,Université de Strasbourg, CNRS, IPHC UMR 7178, 67037 Strasbourg, France
| | - Jean-Philippe Reichheld
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR1318 INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France.,University of Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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43
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García-Giménez JL, Romá-Mateo C, Pérez-Machado G, Peiró-Chova L, Pallardó FV. Role of glutathione in the regulation of epigenetic mechanisms in disease. Free Radic Biol Med 2017; 112:36-48. [PMID: 28705657 DOI: 10.1016/j.freeradbiomed.2017.07.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 12/14/2022]
Abstract
Epigenetics is a rapidly growing field that studies gene expression modifications not involving changes in the DNA sequence. Histone H3, one of the basic proteins in the nucleosomes that make up chromatin, is S-glutathionylated in mammalian cells and tissues, making Gamma-L-glutamyl-L-cysteinylglycine, glutathione (GSH), a physiological antioxidant and second messenger in cells, a new post-translational modifier of the histone code that alters the structure of the nucleosome. However, the role of GSH in the epigenetic mechanisms likely goes beyond a mere structural function. Evidence supports the hypothesis that there is a link between GSH metabolism and the control of epigenetic mechanisms at different levels (i.e., substrate availability, enzymatic activity for DNA methylation, changes in the expression of microRNAs, and participation in the histone code). However, little is known about the molecular pathways by which GSH can control epigenetic events. Studying mutations in enzymes involved in GSH metabolism and the alterations of the levels of cofactors affecting epigenetic mechanisms appears challenging. However, the number of diseases induced by aberrant epigenetic regulation is growing, so elucidating the intricate network between GSH metabolism, oxidative stress and epigenetics could shed light on how their deregulation contributes to the development of neurodegeneration, cancer, metabolic pathologies and many other types of diseases.
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Affiliation(s)
- José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain.
| | - Carlos Romá-Mateo
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain; Faculty of Biomedicine and Health Sciences, Universidad Europea de Valencia, Valencia, Spain
| | - Gisselle Pérez-Machado
- Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain
| | | | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain.
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44
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Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Transl Res 2017; 189:30-50. [PMID: 28919341 PMCID: PMC5659875 DOI: 10.1016/j.trsl.2017.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/14/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The mammalian gut microbiota has been linked to host developmental, immunologic, and metabolic outcomes. This collection of trillions of microbes inhabits the gut and produces a myriad of metabolites, which are measurable in host circulation and contribute to the pathogenesis of human diseases. The link between endogenous metabolite availability and chromatin regulation is a well-established and active area of investigation; however, whether microbial metabolites can elicit similar effects is less understood. In this review, we focus on seminal and recent research that establishes chromatin regulatory roles for both endogenous and microbial metabolites. We also highlight key physiologic and disease settings where microbial metabolite-host chromatin interactions have been established and/or may be pertinent.
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Affiliation(s)
- Kimberly A Krautkramer
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis.
| | - Rashpal S Dhillon
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis; Morgridge Institute for Research, Madison, Wis
| | - Hannah V Carey
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, Wis
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45
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Giustarini D, Colombo G, Garavaglia ML, Astori E, Portinaro NM, Reggiani F, Badalamenti S, Aloisi AM, Santucci A, Rossi R, Milzani A, Dalle-Donne I. Assessment of glutathione/glutathione disulphide ratio and S-glutathionylated proteins in human blood, solid tissues, and cultured cells. Free Radic Biol Med 2017; 112:360-375. [PMID: 28807817 DOI: 10.1016/j.freeradbiomed.2017.08.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/04/2017] [Accepted: 08/09/2017] [Indexed: 12/24/2022]
Abstract
Glutathione (GSH) is the major non-protein thiol in humans and other mammals, which is present in millimolar concentrations within cells, but at much lower concentrations in the blood plasma. GSH and GSH-related enzymes act both to prevent oxidative damage and to detoxify electrophiles. Under oxidative stress, two GSH molecules become linked by a disulphide bridge to form glutathione disulphide (GSSG). Therefore, assessment of the GSH/GSSG ratio may provide an estimation of cellular redox metabolism. Current evidence resulting from studies in human blood, solid tissues, and cultured cells suggests that GSH also plays a prominent role in protein redox regulation via S -glutathionylation, i.e., the conjugation of GSH to reactive protein cysteine residues. A number of methodologies that enable quantitative analysis of GSH/GSSG ratio and S-glutathionylated proteins (PSSG), as well as identification and visualization of PSSG in tissue sections or cultured cells are currently available. Here, we have considered the main methodologies applied for GSH, GSSG and PSSG detection in biological samples. This review paper provides an up-to-date critical overview of the application of the most relevant analytical, morphological, and proteomics approaches to detect and analyse GSH, GSSG and PSSG in mammalian samples as well as discusses their current limitations.
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Affiliation(s)
- Daniela Giustarini
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy
| | - Graziano Colombo
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Emanuela Astori
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Nicola Marcello Portinaro
- Clinica ortopedica e traumatologica, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Francesco Reggiani
- Nephrology and Dialysis Unit, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Salvatore Badalamenti
- Nephrology and Dialysis Unit, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Anna Maria Aloisi
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Ranieri Rossi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Aldo Milzani
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Isabella Dalle-Donne
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy.
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46
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Xu YM, Yu FY, Lau ATY. Discovering Epimodifications of the Genome, Transcriptome, Proteome, and Metabolome: the Quest for Conquering the Uncharted Epi(c) Territories. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40495-017-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Kietzmann T, Petry A, Shvetsova A, Gerhold JM, Görlach A. The epigenetic landscape related to reactive oxygen species formation in the cardiovascular system. Br J Pharmacol 2017; 174:1533-1554. [PMID: 28332701 PMCID: PMC5446579 DOI: 10.1111/bph.13792] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases are among the leading causes of death worldwide. Reactive oxygen species (ROS) can act as damaging molecules but also represent central hubs in cellular signalling networks. Increasing evidence indicates that ROS play an important role in the pathogenesis of cardiovascular diseases, although the underlying mechanisms and consequences of pathophysiologically elevated ROS in the cardiovascular system are still not completely resolved. More recently, alterations of the epigenetic landscape, which can affect DNA methylation, post-translational histone modifications, ATP-dependent alterations to chromatin and non-coding RNA transcripts, have been considered to be of increasing importance in the pathogenesis of cardiovascular diseases. While it has long been accepted that epigenetic changes are imprinted during development or even inherited and are not changed after reaching the lineage-specific expression profile, it becomes more and more clear that epigenetic modifications are highly dynamic. Thus, they might provide an important link between the actions of ROS and cardiovascular diseases. This review will provide an overview of the role of ROS in modulating the epigenetic landscape in the context of the cardiovascular system. LINKED ARTICLES This article is part of a themed section on Redox Biology and Oxidative Stress in Health and Disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.12/issuetoc.
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Affiliation(s)
- Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluOuluFinland
| | - Andreas Petry
- Experimental and Molecular Pediatric CardiologyGerman Heart Center Munich at the TU MunichMunichGermany
- DZHK (German Centre for Cardiovascular Research)Partner Site Munich Heart AllianceMunichGermany
| | - Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluOuluFinland
| | - Joachim M Gerhold
- Institute of Molecular and Cell BiologyUniversity of TartuTartuEstonia
| | - Agnes Görlach
- Experimental and Molecular Pediatric CardiologyGerman Heart Center Munich at the TU MunichMunichGermany
- DZHK (German Centre for Cardiovascular Research)Partner Site Munich Heart AllianceMunichGermany
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48
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Abstract
Reliance on glutamine has long been considered a hallmark of cancer cell metabolism. However, some recent studies have challenged this notion in vivo, prompting a need for further clarifications on the role of glutamine metabolism in cancer. We find that there is ample evidence of an essential role for glutamine in tumors and that a variety of factors, including tissue type, the underlying cancer genetics, the tumor microenvironment and other variables such as diet and host physiology collectively influence the role of glutamine in cancer. Thus the requirements for glutamine in cancer are overall highly heterogeneous. In this review, we discuss the implications both for basic science and for targeting glutamine metabolism in cancer therapy.
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Affiliation(s)
- Ahmad A Cluntun
- Graduate Field of Biochemistry, Molecular & Cell Biology, Cornell University, Ithaca, NY, USA; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Michael J Lukey
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Richard A Cerione
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Chemistry and Chemical Biology, Cornell University, Ithaca NY 14853, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
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49
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Zhao R, Najmi M, Aluri S, Goldman ID. Impact of posttranslational modifications of engineered cysteines on the substituted cysteine accessibility method: evidence for glutathionylation. Am J Physiol Cell Physiol 2017; 312:C517-C526. [PMID: 28122733 DOI: 10.1152/ajpcell.00350.2016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 01/10/2023]
Abstract
The substituted cysteine accessibility method (SCAM) is widely used to study the structure and function of channels, receptors and transporters. In its usual application, a cysteine residue is introduced into a protein which lacks native cysteines following which the accessibility of the residue to the aqueous compartment is assessed. Implicit, and generally assumed, is that if the cysteine-substituted residue is not available to react with sulfhydryl reagents it is not exposed to the extracellular compartment or within the aqueous translocation pathway. We demonstrate here, in a Hela-derived cell line, that some cysteine-substituted residues of the proton-coupled folate transporter (PCFT, SLC46A1) that are inaccessible to 2-((biotinoyl)amino)ethyl methanethiosulfonate are glutathionylated by biotinylated glutathione ethyl ester in the absence of an oxidizing agent. Intramolecular disulfide formation involving cysteine-substituted residues was also identified in some instances. These posttranslational modifications limit the accessibility of the cysteine residues to sulfhydryl-reactive reagents and can have a profound impact on the interpretation of SCAM but may not alter function. When a posttranslationally modified residue is used as a reference extracellular control, the high level of exposure required for detection on Western blot results in erroneous detection of otherwise inaccessible intracellular cysteine-substituted residues. The data indicate that in the application of SCAM, when a cysteine-substituted residue does not appear to be accessible to sulfhydryl-reactive reagents, the possibility of a posttranslational modification should be excluded. The data explain the discrepancies in the assessment, and confirm the localization, of the first intracellular loop of PCFT.
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Affiliation(s)
- Rongbao Zhao
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; and.,Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Mitra Najmi
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; and
| | - Srinivas Aluri
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; and
| | - I David Goldman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; and .,Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
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50
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Zhou M, Paša-Tolić L, Stenoien DL. Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry. J Proteome Res 2016; 16:599-608. [DOI: 10.1021/acs.jproteome.6b00694] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mowei Zhou
- Pacific Northwest National
Laboratory, Earth and Biological Sciences Directorate, P.O. Box 999, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Pacific Northwest National
Laboratory, Earth and Biological Sciences Directorate, P.O. Box 999, Richland, Washington 99352, United States
| | - David L. Stenoien
- Pacific Northwest National
Laboratory, Earth and Biological Sciences Directorate, P.O. Box 999, Richland, Washington 99352, United States
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