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Seckler JM, Shen J, Lewis THJ, Abdulameer MA, Zaman K, Palmer LA, Bates JN, Jenkins MW, Lewis SJ. NADPH diaphorase detects S-nitrosylated proteins in aldehyde-treated biological tissues. Sci Rep 2020; 10:21088. [PMID: 33273578 PMCID: PMC7713249 DOI: 10.1038/s41598-020-78107-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
NADPH diaphorase is used as a histochemical marker of nitric oxide synthase (NOS) in aldehyde-treated tissues. It is thought that the catalytic activity of NOS promotes NADPH-dependent reduction of nitro-blue tetrazolium (NBT) to diformazan. However, it has been argued that a proteinaceous factor other than NOS is responsible for producing diformazan in aldehyde-treated tissues. We propose this is a NO-containing factor such as an S-nitrosothiol and/or a dinitrosyl-iron (II) cysteine complex or nitrosated proteins including NOS. We now report that (1) S-nitrosothiols covalently modify both NBT and TNBT, but only change the reduction potential of NBT after modification, (2) addition of S-nitrosothiols or β- or α-NADPH to solutions of NBT did not elicit diformazan, (3) addition of S-nitrosothiols to solutions of NBT plus β- or α-NADPH elicited rapid formation of diformazan in the absence or presence of paraformaldehyde, (4) addition of S-nitrosothiols to solutions of NBT plus β- or α-NADP did not produce diformazan, (5) S-nitrosothiols did not promote NADPH-dependent reduction of tetra-nitro-blue tetrazolium (TNBT) in which all four phenolic rings are nitrated, (6) cytoplasmic vesicles in vascular endothelial cells known to stain for NADPH diaphorase were rich in S-nitrosothiols, and (7) procedures that accelerate decomposition of S-nitrosothiols, markedly reduced NADPH diaphorase staining in tissue sections subsequently subjected to paraformaldehyde fixation. Our results suggest that NADPH diaphorase in aldehyde-fixed tissues is not enzymatic but is due to the presence of NO-containing factors (free SNOs or nitrosated proteins such as NOS), which promote NADPH-dependent reduction of NBT to diformazan.
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Affiliation(s)
- James M Seckler
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jinshan Shen
- Department of Pharmacology, University of Iowa, Iowa City, IA, 52242, USA
| | - Tristan H J Lewis
- Department of Pharmacology and Physiology, University of Georgia, Athens, GA, 30602, USA
| | - Mohammed A Abdulameer
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Khalequz Zaman
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lisa A Palmer
- Department of Pediatrics, University of Virginia, Charlottesville, VA, 801366, USA
| | - James N Bates
- Department of Anesthesia, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael W Jenkins
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Bioengineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Stephen J Lewis
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Mioto PT, Rodríguez-Ruiz M, Mot AC, Zuccarelli R, Corpas FJ, Freschi L, Mercier H. Alternative fluorimetric-based method to detect and compare total S-nitrosothiols in plants. Nitric Oxide 2017; 68:7-13. [PMID: 28274830 DOI: 10.1016/j.niox.2017.03.001] [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: 10/30/2016] [Revised: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 01/07/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule occurring in virtually all organisms, whose mechanism of action relies mainly on its interaction with proteins or peptides by nitrosylation, forming compounds such as S-nitrosothiols (SNO). The Saville reaction and the ozone-based chemiluminescence method are the main techniques used for nitrosylated protein quantification. While the Saville assay is not very sensitive, the ozone-based chemiluminescence is expensive and time-consuming. Here we propose a method in which the protein-bound NO groups are exposed to UV light, cleaving the bond and allowing the quantification of the derived NO molecules by diamino-rhodamine (DAR) dyes. The DAR-based method was shown to be specific in plant tissues by pre-treatment of the samples with reducing agents and parallel EPR analysis. Spike-and-recovery assays revealed 72% recovery after a GSNO spike. Moreover, the method was significantly more sensitive than the Saville reaction, and this increase in sensitivity was crucial for detecting the reduced levels of nitrosylated proteins in plant species other than Arabidopsis. The method presented here is a suitable alternative to compare plant samples, allowing simple and fast detection of nitrosylated proteins.
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Affiliation(s)
- Paulo Tamaso Mioto
- Department of Botany, Biological Sciences Center, Universidade Federal de Santa Catarina, Campus Reitor João David Ferreira Lima, s/n, 88040-900, Florianópolis, Brazil.
| | - Marta Rodríguez-Ruiz
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008, Granada, Spain
| | - Augustin Catalin Mot
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 1 Mihail Kogălniceanu, 400084, Cluj Napoca, Romania
| | - Rafael Zuccarelli
- Department of Botany, Institute of Biosciences, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Francisco J Corpas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008, Granada, Spain
| | - Luciano Freschi
- Department of Botany, Institute of Biosciences, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Helenice Mercier
- Department of Botany, Institute of Biosciences, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
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3
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López-Sánchez LM, López-Pedrera C, Rodríguez-Ariza A. Proteomics insights into deregulated proteinS-nitrosylation and disease. Expert Rev Proteomics 2014; 9:59-69. [DOI: 10.1586/epr.11.74] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Panis C. Unraveling Oxidation-Induced Modifications in Proteins by Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:19-38. [DOI: 10.1016/b978-0-12-800168-4.00002-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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5
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López-Sánchez LM, López-Pedrera C, Rodríguez-Ariza A. Proteomic approaches to evaluate protein S-nitrosylation in disease. MASS SPECTROMETRY REVIEWS 2014; 33:7-20. [PMID: 23775552 DOI: 10.1002/mas.21373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/29/2013] [Indexed: 06/02/2023]
Abstract
Many of nitric oxide (NO) actions are mediated through the coupling of a nitroso moiety to a reactive cysteine leading to the formation of a S-nitrosothiol (SNO), a process known as S-nitrosylation or S-nitrosation. In many cases this reversible post-translational modification is accompanied by altered protein function and aberrant S-nitrosylation of proteins, caused by altered production of NO and/or impaired SNO homeostasis, has been repeatedly reported in a variety of pathophysiological settings. A growing number of studies are directed to the identification and characterization of those proteins that undergo S-nitrosylation and the analysis of S-nitrosoproteomes under pathological conditions is beginning to be reported. The study of these S-nitrosoproteomes has been fueled by advances in proteomic technologies that are providing researchers with improved tools for exploring this post-translational modification. Here we review novel refinements and improvements to these methods, and some recent studies of the S-nitrosoproteome in disease.
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Affiliation(s)
- Laura M López-Sánchez
- Research Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofía, Universidad de Córdoba, Spain
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6
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Gould N, Doulias PT, Tenopoulou M, Raju K, Ischiropoulos H. Regulation of protein function and signaling by reversible cysteine S-nitrosylation. J Biol Chem 2013; 288:26473-9. [PMID: 23861393 DOI: 10.1074/jbc.r113.460261] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NO is a versatile free radical that mediates numerous biological functions within every major organ system. A molecular pathway by which NO accomplishes functional diversity is the selective modification of protein cysteine residues to form S-nitrosocysteine. This post-translational modification, S-nitrosylation, impacts protein function, stability, and location. Despite considerable advances with individual proteins, the in vivo biological chemistry, the structural elements that govern the selective S-nitrosylation of cysteine residues, and the potential overlap with other redox modifications are unknown. In this minireview, we explore the functional features of S-nitrosylation at the proteome level and the structural diversity of endogenously modified residues, and we discuss the potential overlap and complementation that may exist with other cysteine modifications.
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Affiliation(s)
- Neal Gould
- From the Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Pharmacology, Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Doulias PT, Tenopoulou M, Raju K, Spruce LA, Seeholzer SH, Ischiropoulos H. Site specific identification of endogenous S-nitrosocysteine proteomes. J Proteomics 2013; 92:195-203. [PMID: 23748021 DOI: 10.1016/j.jprot.2013.05.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/23/2013] [Accepted: 05/26/2013] [Indexed: 11/27/2022]
Abstract
UNLABELLED Cysteine S-nitrosylation is a post-translational modification regulating protein function and nitric oxide signaling. Herein the selectivity, reproducibility, and sensitivity of a mass spectrometry-based proteomic method for the identification of endogenous S-nitrosylated proteins are outlined. The method enriches for either S-nitrosylated proteins or peptides through covalent binding of the cysteine sulfur with phenylmercury at pH=6.0. Phenylmercury reacts selectively and efficiently with S-nitrosocysteine since no reactivity can be documented for disulfides, sulfinic or sulfonic acids, S-glutathionylated, S-alkylated or S-sulfhydrylated cysteine residues. A specificity of 97±1% for the identification of S-nitrosocysteine peptides in mouse liver tissue is achieved by the inclusion of negative controls. The method enables the detection of 36 S-nitrosocysteine peptides starting with 5pmolS-nitrosocysteine/mg of total tissue protein. Both the percentage of protein molecules modified as well as the occupancy by S-nitrosylation can be determined. Overall, selective, sensitive and reproducible enrichment of S-nitrosylated proteins and peptides is achieved by the use of phenylmercury. The inclusion of appropriate negative controls secures the precise identification of endogenous S-nitrosylated sites and proteins in biological samples. BIOLOGICAL SIGNIFICANCE The current study describes a selective, sensitive and reproducible method for the acquisition of endogenously S-nitrosylated proteins and peptides. The acquisition of endogenous S-nitrosoproteomes provides robust data that is necessary for investigating the mechanism(s) of S-nitrosylation in vivo, the factors that govern its selectivity, the dependency of the modification on different isoforms of nitric oxide synthases (NOS), as well as the physiological functions of this protein modification. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Maron BA, Tang SS, Loscalzo J. S-nitrosothiols and the S-nitrosoproteome of the cardiovascular system. Antioxid Redox Signal 2013; 18:270-87. [PMID: 22770551 PMCID: PMC3518544 DOI: 10.1089/ars.2012.4744] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/26/2012] [Accepted: 07/08/2012] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE Since their discovery in the early 1990's, S-nitrosylated proteins have been increasingly recognized as important determinants of many biochemical processes. Specifically, S-nitrosothiols in the cardiovascular system exert many actions, including promoting vasodilation, inhibiting platelet aggregation, and regulating Ca(2+) channel function that influences myocyte contractility and electrophysiologic stability. RECENT ADVANCES Contemporary developments in liquid chromatography-mass spectrometry methods, the development of biotin- and His-tag switch assays, and the availability of cyanide dye-labeling for S-nitrosothiol detection in vitro have increased significantly the identification of a number of cardiovascular protein targets of S-nitrosylation in vivo. CRITICAL ISSUES Recent analyses using modern S-nitrosothiol detection techniques have revealed the mechanistic significance of S-nitrosylation to the pathophysiology of numerous cardiovascular diseases, including essential hypertension, pulmonary hypertension, ischemic heart disease, stroke, and congestive heart failure, among others. FUTURE DIRECTIONS Despite enhanced insight into S-nitrosothiol biochemistry, translating these advances into beneficial pharmacotherapies for patients with cardiovascular diseases remains a primary as-yet unmet goal for investigators within the field.
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Affiliation(s)
- Bradley A Maron
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Wiesweg M, Berchner-Pfannschmidt U, Fandrey J, Petrat F, de Groot H, Kirsch M. Rocket fuel for the quantification of S-nitrosothiols. Highly specific reduction of S-nitrosothiols to thiols by methylhydrazine. Free Radic Res 2012. [PMID: 23181469 DOI: 10.3109/10715762.2012.744836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Reduction of S-nitrosothiols to the corresponding thiol function is the key step in analyzing S-nitrosocysteinyl residues in proteins. Though it has been shown to give low yields, ascorbate-dependent reduction is commonly performed in the frequently used biotin-switch technique. We demonstrate that the compound methylhydrazine can act as a specific and efficient reducing agent for S-nitrosothiols. The corresponding thiol function is exclusively generated from low molecular weight and proteinaceous S-nitrosothiols while methylhydrazine failed to reduce disulfides. It was possible to optimize the experimental conditions so that thiol autoxidation is excluded, and high reaction yields (>90%) are obtained for the thiol function. The biotin-switch technique performed with methylhydrazine-dependent reduction shows remarkably improved sensitivity compared to the ascorbate-dependent procedure.
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Affiliation(s)
- M Wiesweg
- Institut für Physiologische Chemie, Universitätsklinikum Essen, Hufelandstrasse 55, 45 122 Essen, Germany
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10
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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11
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Bechtold E, King SB. Chemical methods for the direct detection and labeling of S-nitrosothiols. Antioxid Redox Signal 2012; 17:981-91. [PMID: 22356122 PMCID: PMC3411347 DOI: 10.1089/ars.2012.4570] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SIGNIFICANCE Posttranslational modification of proteins through phosphorylation, glycosylation, and oxidation adds complexity to the proteome by reversibly altering the structure and function of target proteins in a highly controlled fashion. RECENT ADVANCES The study of reversible cysteine oxidation highlights a role for this oxidative modification in complex signal transduction pathways. Nitric oxide (NO), and its respective metabolites (including reactive nitrogen species), participates in a variety of these cellular redox processes, including the reversible oxidation of cysteine to S-nitrosothiols (RSNOs). RSNOs act as endogenous transporters of NO, but also possess beneficial effects independent of NO-related signaling, which suggests a complex and versatile biological role. In this review, we highlight the importance of RSNOs as a required posttranslational modification and summarize the current methods available for detecting S-nitrosation. CRITICAL ISSUES Given the limitations of these indirect detection methods, the review covers recent developments toward the direct detection of RSNOs by phosphine-based chemical probes. The intrinsic properties that dictate this phosphine/RSNO reactivity are summarized. In general, RSNOs (both small molecule and protein) react with phosphines to yield reactive S-substituted aza-ylides that undergo further reactions leading to stable RSNO-based adducts. FUTURE DIRECTIONS This newly explored chemical reactivity forms the basis of a number of exciting potential chemical methods for protein RSNO detection in biological systems.
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Affiliation(s)
- Erika Bechtold
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
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12
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Huang B, Li FA, Wu CH, Wang DL. The role of nitric oxide on rosuvastatin-mediated S-nitrosylation and translational proteomes in human umbilical vein endothelial cells. Proteome Sci 2012; 10:43. [PMID: 22799578 PMCID: PMC3533754 DOI: 10.1186/1477-5956-10-43] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 04/23/2012] [Indexed: 02/07/2023] Open
Abstract
Background The pleiotropic effects of 3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins), which are independent from their cholesterol-lowering action, have been widely recognized in various biological systems. Statins can affect endothelial homeostasis, which is partly modulated by the production of nitric oxide (NO). However, it is unclear how statin/NO-mediated posttranslational S-nitrosylation of endothelial proteins and changes in translational profiles may benefit endothelial integrity. Therefore, it is important to understand the statin/NO-mediated S-nitrosylation in endothelial cells. Results Rosuvastatin treatment of human umbilical vein endothelial cells (ECs) enhanced the enzymatic activity of endothelial nitric oxide synthase (eNOS) and the expression of 78 S-nitrosoproteins. Among these S-nitrosoproteins, we identified 17 proteins, including protein disulfide bond isomerase, phospholipase C, transaldolase and heat shock proteins. Furthermore, a hydrophobic Cys66 was determined as the S-nitrosylation site of the mitochondrial HSP70. In addition to the statin-modulated posttranslational S-nitrosylation, changes in the NO-mediated translational proteome were also observed. Seventeen major proteins were significantly upregulated after rosuvastatin treatment. However, 12 of these proteins were downregulated after pretreating ECs with an eNOS inhibitor (L-NAME), which indicated that their expression was modulated by NO. Conclusions ECs treated with rosuvastatin increase eNOS activation. The increased NO production is involved in modulating S-nitrosylation and translation of proteins. We provide further evidence of the pleiotropic effect of rosuvastatin on endothelial physiology.
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Affiliation(s)
- Bin Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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13
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Abstract
The process of lipid peroxidation is widespread in biology and is mediated through both enzymatic and non-enzymatic pathways. A significant proportion of the oxidized lipid products are electrophilic in nature, the RLS (reactive lipid species), and react with cellular nucleophiles such as the amino acids cysteine, lysine and histidine. Cell signalling by electrophiles appears to be limited to the modification of cysteine residues in proteins, whereas non-specific toxic effects involve modification of other nucleophiles. RLS have been found to participate in several physiological pathways including resolution of inflammation, cell death and induction of cellular antioxidants through the modification of specific signalling proteins. The covalent modification of proteins endows some unique features to this signalling mechanism which we have termed the ‘covalent advantage’. For example, covalent modification of signalling proteins allows for the accumulation of a signal over time. The activation of cell signalling pathways by electrophiles is hierarchical and depends on a complex interaction of factors such as the intrinsic chemical reactivity of the electrophile, the intracellular domain to which it is exposed and steric factors. This introduces the concept of electrophilic signalling domains in which the production of the lipid electrophile is in close proximity to the thiol-containing signalling protein. In addition, we propose that the role of glutathione and associated enzymes is to insulate the signalling domain from uncontrolled electrophilic stress. The persistence of the signal is in turn regulated by the proteasomal pathway which may itself be subject to redox regulation by RLS. Cell death mediated by RLS is associated with bioenergetic dysfunction, and the damaged proteins are probably removed by the lysosome-autophagy pathway.
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Kim YJ, Kim D, Illuzzi JL, Delaplane S, Su D, Bernier M, Gross ML, Georgiadis MM, Wilson DM. S-glutathionylation of cysteine 99 in the APE1 protein impairs abasic endonuclease activity. J Mol Biol 2011; 414:313-26. [PMID: 22024594 DOI: 10.1016/j.jmb.2011.10.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 10/03/2011] [Accepted: 10/12/2011] [Indexed: 12/24/2022]
Abstract
Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a central participant in the base excision repair pathway, exhibiting AP endonuclease activity that incises the DNA backbone 5' to an abasic site. Besides its prominent role as a DNA repair enzyme, APE1 was separately identified as a protein called redox effector factor 1, which is able to enhance the DNA binding activity of several transcription factors through a thiol-exchange-based reduction-oxidation mechanism. In the present study, we found that human APE1 is S-glutathionylated under conditions of oxidative stress both in the presence of glutathione in vitro and in cells. S-glutathionylated APE1 displayed significantly reduced AP endonuclease activity on abasic-site-containing oligonucleotide substrates, a result stemming from impaired DNA binding capacity. The combination of site-directed mutagenesis, biochemical assays, and mass spectrometric analysis identified Cys99 in human APE1 as the critical residue for the S-glutathionylation that leads to reduced AP endonuclease activity. This modification is reversible by reducing agents, which restore APE1 incision function. Our studies describe a novel posttranslational modification of APE1 that regulates the DNA repair function of the protein.
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Affiliation(s)
- Yun-Jeong Kim
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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15
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Martínez-Ruiz A, Cadenas S, Lamas S. Nitric oxide signaling: classical, less classical, and nonclassical mechanisms. Free Radic Biol Med 2011; 51:17-29. [PMID: 21549190 DOI: 10.1016/j.freeradbiomed.2011.04.010] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/10/2011] [Accepted: 04/04/2011] [Indexed: 12/20/2022]
Abstract
Although nitric oxide (NO) was identified more than 150 years ago and its effects were clinically tested in the form of nitroglycerine, it was not until the decades of 1970-1990 that it was described as a gaseous signal transducer. Since then, a canonical pathway linked to cyclic GMP (cGMP) as its quintessential effector has been established, but other modes of action have emerged and are now part of the common body of knowledge within the field. Classical (or canonical) signaling involves the selective activation of soluble guanylate cyclase, the generation of cGMP, and the activation of specific kinases (cGMP-dependent protein kinases) by this cyclic nucleotide. Nonclassical signaling alludes to the formation of NO-induced posttranslational modifications (PTMs), especially S-nitrosylation, S-glutathionylation, and tyrosine nitration. These PTMs are governed by specific biochemical mechanisms as well as by enzymatic systems. In addition, a less classical but equally important pathway is related to the interaction between NO and mitochondrial cytochrome c oxidase, which might have important implications for cell respiration and intermediary metabolism. Cross talk trespassing these necessarily artificial conceptual boundaries is progressively being identified and hence an integrated systems biology approach to the comprehension of NO function will probably emerge in the near future.
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Affiliation(s)
- Antonio Martínez-Ruiz
- Servicio de Inmunología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
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16
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Wiktorowicz JE, Stafford S, Rea H, Urvil P, Soman K, Kurosky A, Perez-Polo JR, Savidge TC. Quantification of cysteinyl S-nitrosylation by fluorescence in unbiased proteomic studies. Biochemistry 2011; 50:5601-14. [PMID: 21615140 PMCID: PMC3133729 DOI: 10.1021/bi200008b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cysteinyl S-nitrosylation has emerged as an important post-translational modification affecting protein function in health and disease. Great emphasis has been placed on global, unbiased quantification of S-nitrosylated proteins because of physiologic and oxidative stimuli. However, current strategies have been hampered by sample loss and altered protein electrophoretic mobility. Here, we describe a novel quantitative approach that uses accurate, sensitive fluorescence modification of cysteine S-nitrosylation that leaves electrophoretic mobility unaffected (SNOFlo) and introduce unique concepts for measuring changes in S-nitrosylation status relative to protein abundance. Its efficacy in defining the functional S-nitrosoproteome is demonstrated in two diverse biological applications: an in vivo rat hypoxia-ischemia/reperfusion model and antimicrobial S-nitrosoglutathione-driven transnitrosylation of an enteric microbial pathogen. The suitability of this approach for investigating endogenous S-nitrosylation is further demonstrated using Ingenuity Pathways analysis that identified nervous system and cellular development networks as the top two networks. Functional analysis of differentially S-nitrosylated proteins indicated their involvement in apoptosis, branching morphogenesis of axons, cortical neurons, and sympathetic neurites, neurogenesis, and calcium signaling. Major abundance changes were also observed for fibrillar proteins known to be stress-responsive in neurons and glia. Thus, both examples demonstrate the technique's power in confirming the widespread involvement of S-nitrosylation in hypoxia-ischemia/reperfusion injury and in antimicrobial host responses.
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Affiliation(s)
- John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch , Galveston, Texas 77555, USA.
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17
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Agnetti G, Husberg C, Van Eyk JE. Divide and conquer: the application of organelle proteomics to heart failure. Circ Res 2011; 108:512-26. [PMID: 21335433 PMCID: PMC3936251 DOI: 10.1161/circresaha.110.226910] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/19/2010] [Indexed: 01/16/2023]
Abstract
Chronic heart failure is a worldwide cause of mortality and morbidity and is the final outcome of a number of different etiologies. This reflects both the complexity of the disease and our incomplete understanding of its underlying molecular mechanisms. One experimental approach to address this is to study subcellular organelles and how their functions are activated and synchronized under physiological and pathological conditions. In this review, we discuss the application of proteomic technologies to organelles and how this has deepened our perception of the cellular proteome and its alterations with heart failure. The use of proteomics to monitor protein quantity and posttranslational modifications has revealed a highly intricate and sophisticated level of protein regulation. Posttranslational modifications have the potential to regulate organelle function and interplay most likely by targeting both structural and signaling proteins throughout the cell, ultimately coordinating their responses. The potentials and limitations of existing proteomic technologies are also discussed emphasizing that the development of novel methods will enhance our ability to further investigate organelles and decode intracellular communication.
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Affiliation(s)
- Giulio Agnetti
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- INRC, Dept. of Biochemistry, University of Bologna, Italy
| | - Cathrine Husberg
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- Institute for Experimental Medical Research, Oslo University Hospital - Ullevaal, Norway
| | - Jennifer E. Van Eyk
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
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18
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Chen YJ, Ku WC, Lin PY, Chou HC, Khoo KH, Chen YJ. S-alkylating labeling strategy for site-specific identification of the s-nitrosoproteome. J Proteome Res 2010; 9:6417-39. [PMID: 20925432 DOI: 10.1021/pr100680a] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
S-nitrosylation, a post-translational modification of cysteine residues induced by nitric oxide, mediates many physiological functions. Due to the labile nature of S-nitrosylation, detection by mass spectrometry (MS) is challenging. Here, we developed an S-alkylating labeling strategy using the irreversible biotinylation on S-nitrosocysteines for site-specific identification of the S-nitrosoproteome by LC-MS/MS. Using COS-7 cells without endogenous nitric oxide synthase, we demonstrated that the S-alkylating labeling strategy substantially improved the blocking efficiency of free cysteines, minimized the false-positive identification caused by disulfide interchange, and increased the digestion efficiency for improved peptide identification using MS analyses. Using this strategy, we identified total 586 unique S-nitrosylation sites corresponding to 384 proteins in S-nitroso-N-acetylpenicillamine (SNAP)/l-cysteine-treated mouse MS-1 endothelial cells, including 234 previously unreported S-nitrosylated proteins. When the topologies of 84 identified transmembrane proteins were further analyzed, their S-nitrosylation sites were found to mostly face the cytoplasmic side, implying that S-nitrosylation occurs in the cytoplasm. In addition to the previously known acid/basic motifs, the ten deduced consensus motifs suggested that combination of local hydrophobicity and acid/base motifs in the tertiary structure contribute to the specificity of S-nitrosylation. Moreover, the S-nitrosylated cysteines showed preference on beta-strand, having lower relative surface accessibility at the S-nitrosocysteines.
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Affiliation(s)
- Yi-Ju Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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19
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Lee YH, Tan HT, Chung MCM. Subcellular fractionation methods and strategies for proteomics. Proteomics 2010; 10:3935-56. [DOI: 10.1002/pmic.201000289] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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MacRae TH. Gene expression, metabolic regulation and stress tolerance during diapause. Cell Mol Life Sci 2010; 67:2405-24. [PMID: 20213274 PMCID: PMC11115916 DOI: 10.1007/s00018-010-0311-0] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 01/31/2010] [Accepted: 02/10/2010] [Indexed: 12/31/2022]
Abstract
Diapause entails molecular, physiological and morphological remodeling of living animals, culminating in a dormant state characterized by enhanced stress tolerance. Molecular mechanisms driving diapause resemble those responsible for biochemical processes in proliferating cells and include transcriptional, post-transcriptional and post-translational processes. The results are directed gene expression, differential mRNA and protein accumulation and protein modifications, including those that occur in response to changes in cellular redox potential. Biochemical pathways switch, metabolic products change and energy production is adjusted. Changes to biosynthetic activities result for example in the synthesis of molecular chaperones, late embryogenesis abundant (LEA) proteins and protective coverings, all contributing to stress tolerance. The purpose of this review is to consider regulatory and mechanistic strategies that are potentially key to metabolic control and stress tolerance during diapause, while remembering that organisms undergoing diapause are as diverse as the processes itself. Some of the parameters described have well-established roles in diapause, whereas the evidence for others is cursory.
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Affiliation(s)
- Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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21
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Waheed SM, Ghosh A, Chakravarti R, Biswas A, Haque MM, Panda K, Stuehr DJ. Nitric oxide blocks cellular heme insertion into a broad range of heme proteins. Free Radic Biol Med 2010; 48:1548-58. [PMID: 20211245 PMCID: PMC2866197 DOI: 10.1016/j.freeradbiomed.2010.02.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/26/2010] [Accepted: 02/27/2010] [Indexed: 11/18/2022]
Abstract
Although the insertion of heme into proteins enables their function in bioenergetics, metabolism, and signaling, the mechanisms and regulation of this process are not fully understood. We developed a means to study cellular heme insertion into apo-protein targets over a 3-h period and then investigated how nitric oxide (NO) released from a chemical donor (NOC-18) might influence heme (protoporphyrin IX) insertion into seven targets that present a range of protein structures, heme ligation states, and functions (three NO synthases, two cytochrome P450's, catalase, and hemoglobin). NO blocked cellular heme insertion into all seven apo-protein targets. The inhibition occurred at relatively low (nM/min) fluxes of NO, was reversible, and did not involve changes in intracellular heme levels, activation of guanylate cyclase, or inhibition of mitochondrial ATP production. These aspects and the range of protein targets suggest that NO can act as a global inhibitor of heme insertion, possibly by inhibiting a common step in the process.
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Affiliation(s)
- Syed Mohsin Waheed
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Arnab Ghosh
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Ritu Chakravarti
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Ashis Biswas
- Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Mohammad Mahfuzul Haque
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Koustubh Panda
- Center for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Dennis J. Stuehr
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
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22
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Haynes V, Traaseth NJ, Elfering S, Fujisawa Y, Giulivi C. Nitration of specific tyrosines in FoF1 ATP synthase and activity loss in aging. Am J Physiol Endocrinol Metab 2010; 298:E978-87. [PMID: 20159857 PMCID: PMC2867368 DOI: 10.1152/ajpendo.00739.2009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It has been reported that C-nitration of proteins occurs under nitrative/oxidative stress; however, its role in pathophysiological situations is not fully understood. In this study, we determined that nitration of Tyr(345) and Tyr(368) in the beta-subunit of the mitochondrial F(o)F(1)-ATPase is a major target for nitrative stress in rat liver under in vivo conditions. The chemical characteristics of these Tyr make them suitable for a facilitated nitration (solvent accessibility, consensus sequence, and pK(a)). Moreover, beta-subunit nitration increased significantly with the age of the rats (from 4 to 80 weeks old) and correlated with decreased ATP hydrolysis and synthesis rates. Although its affinity for ATP binding was unchanged, maximal ATPase activity decreased between young and old rats by a factor of two. These changes directly impacted the available ATP concentration in vivo, and it was expected that they would affect multiple cellular ATP-dependent processes. For instance, at least 50% of available [ATP] in the liver of older rats would have to be committed to sustain maximal Na(+)-K(+)-ATPase activity, whereas only 30% would be required for young rats. If this requirement was not fulfilled, the osmoregulation and Na(+)-nutrient cotransport in liver of older rats would be compromised. On the basis of our studies, we propose that targeted nitration of the beta-subunit is an early marker for nitrative stress and aging.
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Affiliation(s)
- Virginia Haynes
- University of California, Davis, Department of Molecular Biosciences, 1120 Haring Hall, One Shields Ave., Davis, CA 95616, USA
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23
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Hill BG, Dranka BP, Bailey SM, Lancaster JR, Darley-Usmar VM. What part of NO don't you understand? Some answers to the cardinal questions in nitric oxide biology. J Biol Chem 2010; 285:19699-704. [PMID: 20410298 PMCID: PMC2888379 DOI: 10.1074/jbc.r110.101618] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nitric oxide (NO) regulates biological processes through signaling mechanisms that exploit its unique biochemical properties as a free radical. For the last several decades, the key aspects of the chemical properties of NO relevant to biological systems have been defined, but it has been a challenge to assign these to specific cellular processes. Nevertheless, it is now clear that the high affinity of NO for transition metal centers, particularly iron, and the rapid reaction of NO with oxygen-derived free radicals can explain many of its biological and pathological properties. Emerging studies also highlight a growing importance of the secondary metabolites of NO-dependent reactions in the post-translational modification of key metabolic and signaling proteins. In this minireview, we emphasize the current understanding of the biochemistry of NO and place it in a biological context.
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Affiliation(s)
- Bradford G Hill
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294-2180, USA
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24
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Protein oxidation: role in signalling and detection by mass spectrometry. Amino Acids 2010; 42:5-21. [PMID: 20401673 DOI: 10.1007/s00726-010-0585-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 03/26/2010] [Indexed: 01/10/2023]
Abstract
Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while reversible modifications are thought to be relevant in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM, such as oxidation, chlorination or nitration. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to disulfide, glutathionylated or sulfenic acid forms that can be reversed by thiol reductants. Proline hydroxylation in HIF signalling is also quite well characterized, and there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. For some proteins regulated by cysteine oxidation, the residues and molecular mechanism involved have been extensively studied and are well understood, such as the protein tyrosine phosphatase PTP1B and MAP3 kinase ASK1, as well as transcription factor complex Keap1-Nrf2. The advances in understanding of the role oxPTMs in signalling have been facilitated by advances in analytical technology, in particular tandem mass spectrometry techniques. Combinations of peptide sequencing by collisionally induced dissociation and precursor ion scanning or neutral loss to select for specific oxPTMs have proved very useful for identifying oxidatively modified proteins and mapping the sites of oxidation. The development of specific labelling and enrichment procedures for S-nitrosylation or disulfide formation has proved invaluable, and there is ongoing work to establish analogous methods for detection of nitrotyrosine and other modifications.
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Abstract
A variety of post-translational protein modifications (PTMs) are known to be altered as a result of cancer development. Thus, these PTMs are potentially useful biomarkers for breast cancer. Mass spectrometry, antibody microarrays and immunohistochemistry techniques have shown promise for identifying changes in PTMs. In this review, we summarize the current literature on PTMs identified in the plasma and tumor tissue of breast-cancer patients or in breast cell lines. We also discuss some of the analytical techniques currently being used to evaluate PTMs.
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Affiliation(s)
- Hongjun Jin
- Cell Biology and Biochemistry Group, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, PO Box 999, 902 Battelle Blvd, Richland, WA 99352
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