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Basak S, Kundu P. Plant metacaspases: Decoding their dynamics in development and disease. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 180:50-63. [PMID: 35390704 DOI: 10.1016/j.plaphy.2022.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/02/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Plant metacaspases were evolved in parallel to well-characterized animal counterpart caspases and retained the similar histidine-cysteine catalytic dyad, leading to functional congruity between these endopeptidases. Although phylogenetic relatedness of the catalytic domain and functional commonality placed these proteases in the caspase family, credible counterarguments predominantly about their distinct substrate specificity raised doubts about the classification. Metacaspases are involved in regulating the PCD during development as well as in senescence. Balancing acts of metacaspase activity also dictate cell fate during defense upon the perception of adverse environmental cues. Accordingly, their activity is tightly regulated, while suppressing spurious activation, by a combination of genetic and post-translational modifications. Structural insights from recent studies provided vital clues on the functionality. This comprehensive review aims to explore the origin of plant metacaspases, and their regulatory and functional diversity in different plants while discussing their analogy to mammalian caspases. Besides, we have presented various modern methodologies for analyzing the proteolytic activity of these indispensable molecules in the healthy or stressed life of a plant. The review would serve as a repository of all the available pieces of evidence indicating metacaspases as the key regulator of PCD across the plant kingdom and highlight the prospect of studying metacaspases for their inclusion in a crop improvement program.
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Affiliation(s)
- Shrabani Basak
- Division of Plant Biology, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata, 700091, West Bengal, India.
| | - Pallob Kundu
- Division of Plant Biology, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata, 700091, West Bengal, India.
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Dagnell M, Schmidt EE, Arnér ESJ. The A to Z of modulated cell patterning by mammalian thioredoxin reductases. Free Radic Biol Med 2018; 115:484-496. [PMID: 29278740 PMCID: PMC5771652 DOI: 10.1016/j.freeradbiomed.2017.12.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/16/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022]
Abstract
Mammalian thioredoxin reductases (TrxRs) are selenocysteine-containing proteins (selenoproteins) that propel a large number of functions through reduction of several substrates including the active site disulfide of thioredoxins (Trxs). Well-known enzymatic systems that in turn are supported by Trxs and TrxRs include deoxyribonucleotide synthesis through ribonucleotide reductase, antioxidant defense through peroxiredoxins and methionine sulfoxide reductases, and redox modulation of a number of transcription factors. Although these functions may be essential for cells due to crucial roles in maintenance of cell viability and proliferation, findings during the last decade reveal that mammals have major redundancy in their cellular reductive systems. The synthesis of glutathione (GSH) and reductive functions of GSH-dependent pathways typically act in parallel with Trx-dependent pathways, with only one of these systems often being sufficient to support viability. Importantly, this does not imply that a modulation of the Trx system will remain without consequences, even when GSH-dependent pathways remain functional. As suggested by several recent findings, the Trx system in general and the TrxRs in particular, function as key regulators of signaling pathways. In this review article we will discuss findings that collectively suggest that modulation in mammalian systems of cytosolic TrxR1 (TXNRD1) or mitochondrial TrxR2 (TXNRD2) influence cell patterning and cellular stress responses. Effects of lower activities include increased adipogenesis, insulin responsiveness, glycogen accumulation, hyperproliferation, and distorted embryonic development, while increased activities correlate with decreased proliferation and extended lifespan, as well as worse cancer prognosis. The molecular mechanisms that underlie these diverse effects, involving regulation of protein phosphorylation cascades and of key transcription factors that guide cellular differentiation pathways, will be discussed. We conclude that the selenium-dependent oxidoreductases TrxR1 and TrxR2 should be considered as key components of signaling pathways that control cell differentiation and cellular stress responses.
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Affiliation(s)
- Markus Dagnell
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Edward E Schmidt
- Microbiology & Immunology, Montana State University, Bozeman, MT 59718, USA
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
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Zaffagnini M, De Mia M, Morisse S, Di Giacinto N, Marchand CH, Maes A, Lemaire SD, Trost P. Protein S-nitrosylation in photosynthetic organisms: A comprehensive overview with future perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:952-66. [PMID: 26861774 DOI: 10.1016/j.bbapap.2016.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/15/2016] [Accepted: 02/04/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND The free radical nitric oxide (NO) and derivative reactive nitrogen species (RNS) play essential roles in cellular redox regulation mainly through protein S-nitrosylation, a redox post-translational modification in which specific cysteines are converted to nitrosothiols. SCOPE OF VIEW This review aims to discuss the current state of knowledge, as well as future perspectives, regarding protein S-nitrosylation in photosynthetic organisms. MAJOR CONCLUSIONS NO, synthesized by plants from different sources (nitrite, arginine), provides directly or indirectly the nitroso moiety of nitrosothiols. Biosynthesis, reactivity and scavenging systems of NO/RNS, determine the NO-based signaling including the rate of protein nitrosylation. Denitrosylation reactions compete with nitrosylation in setting the levels of nitrosylated proteins in vivo. GENERAL SIGNIFICANCE Based on a combination of proteomic, biochemical and genetic approaches, protein nitrosylation is emerging as a pervasive player in cell signaling networks. Specificity of protein nitrosylation and integration among different post-translational modifications are among the major challenges for future experimental studies in the redox biology field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- M Zaffagnini
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - M De Mia
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - S Morisse
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - N Di Giacinto
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - C H Marchand
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - A Maes
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - S D Lemaire
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France.
| | - P Trost
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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Jia C, Lin X, Wang Z. Prediction of protein S-nitrosylation sites based on adapted normal distribution bi-profile Bayes and Chou's pseudo amino acid composition. Int J Mol Sci 2014; 15:10410-23. [PMID: 24918295 PMCID: PMC4100159 DOI: 10.3390/ijms150610410] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/12/2014] [Accepted: 05/20/2014] [Indexed: 11/16/2022] Open
Abstract
Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic conditions. Because of the inherent chemical instability of the S-NO bond and the low abundance of endogenous S-nitrosylated proteins, the unambiguous identification of S-nitrosylation sites by commonly used proteomic approaches remains challenging. Therefore, computational prediction of S-nitrosylation sites has been considered as a powerful auxiliary tool. In this work, we mainly adopted an adapted normal distribution bi-profile Bayes (ANBPB) feature extraction model to characterize the distinction of position-specific amino acids in 784 S-nitrosylated and 1568 non-S-nitrosylated peptide sequences. We developed a support vector machine prediction model, iSNO-ANBPB, by incorporating ANBPB with the Chou’s pseudo amino acid composition. In jackknife cross-validation experiments, iSNO-ANBPB yielded an accuracy of 65.39% and a Matthew’s correlation coefficient (MCC) of 0.3014. When tested on an independent dataset, iSNO-ANBPB achieved an accuracy of 63.41% and a MCC of 0.2984, which are much higher than the values achieved by the existing predictors SNOSite, iSNO-PseAAC, the Li et al. algorithm, and iSNO-AAPair. On another training dataset, iSNO-ANBPB also outperformed GPS-SNO and iSNO-PseAAC in the 10-fold crossvalidation test.
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Affiliation(s)
- Cangzhi Jia
- Department of Mathematics, Dalian Maritime University, Dalian 116026, China.
| | - Xin Lin
- Department of Mathematics, Dalian Maritime University, Dalian 116026, China.
| | - Zhiping Wang
- Department of Mathematics, Dalian Maritime University, Dalian 116026, China.
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Liu M, Talmadge JE, Ding SJ. Development and application of site-specific proteomic approach for study protein S-nitrosylation. Amino Acids 2012; 42:1541-51. [DOI: 10.1007/s00726-012-1279-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 03/17/2012] [Indexed: 12/19/2022]
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Astier J, Rasul S, Koen E, Manzoor H, Besson-Bard A, Lamotte O, Jeandroz S, Durner J, Lindermayr C, Wendehenne D. S-nitrosylation: an emerging post-translational protein modification in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:527-533. [PMID: 21893248 DOI: 10.1016/j.plantsci.2011.02.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/21/2011] [Accepted: 02/22/2011] [Indexed: 05/26/2023]
Abstract
Increasing evidences support the assumption that nitric oxide (NO) acts as a physiological mediator in plants. Understanding its pleiotropic effects requires a deep analysis of the molecular mechanisms underlying its mode of action. In the recent years, efforts have been made in the identification of plant proteins modified by NO at the post-translational level, notably by S-nitrosylation. This reversible process involves the formation of a covalent bond between NO and reactive cysteine residues. This research has now born fruits and numerous proteins regulated by S-nitrosylation have been identified and characterized. This review describes the basic principle of S-nitrosylation as well as the Biotin Switch Technique and its recent adaptations allowing the identification of S-nitrosylated proteins in physiological contexts. The impact of S-nitrosylation on the structure/function of selected proteins is further discussed.
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Affiliation(s)
- Jéremy Astier
- UMR INRA 1088/CNRS 5184/Université de Bourgogne, Plante-Microbe-Environnement, F-21065 Dijon cedex, France
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Regulation of mitochondrial processes by protein S-nitrosylation. Biochim Biophys Acta Gen Subj 2011; 1820:712-21. [PMID: 21397666 DOI: 10.1016/j.bbagen.2011.03.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/21/2011] [Accepted: 03/04/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Nitric oxide (NO) exerts powerful physiological effects through guanylate cyclase (GC), a non-mitochondrial enzyme, and through the generation of protein cysteinyl-NO (SNO) adducts-a post-translational modification relevant to mitochondrial biology. A small number of SNO proteins, generated by various mechanisms, are characteristically found in mammalian mitochondria and influence the regulation of oxidative phosphorylation and other aspects of mitochondrial function. SCOPE OF REVIEW The principles by which mitochondrial SNO proteins are formed and their actions, independently or collectively with NO binding to heme, iron-sulfur centers, or to glutathione (GSH) are reviewed on a molecular background of SNO-based signal transduction. MAJOR CONCLUSIONS Mitochondrial SNO-proteins have been demonstrated to inhibit Complex I of the electron transport chain, to modulate mitochondrial reactive oxygen species (ROS) production, influence calcium-dependent opening of the mitochondrial permeability transition pore (MPTP), promote selective importation of mitochondrial protein, and stimulate mitochondrial fission. The ease of reversibility and the affirmation of regulated S-nitros(yl)ating and denitros(yl)ating enzymatic reactions support hypotheses that SNO regulates the mitochondrion through redox mechanisms. SNO modification of mitochondrial proteins, whether homeostatic or adaptive (physiological), or pathogenic, is an area of active investigation. GENERAL SIGNIFICANCE Mitochondrial SNO proteins are associated with mainly protective, bur some pathological effects; the former mainly in inflammatory and ischemia/reperfusion syndromes and the latter in neurodegenerative diseases. Experimentally, mitochondrial SNO delivery is also emerging as a potential new area of therapeutics. This article is part of a Special Issue entitled: Regulation of cellular processes by S-nitrosylation.
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Naturally occurring free thiols within β2-glycoprotein I in vivo: nitrosylation, redox modification by endothelial cells, and regulation of oxidative stress–induced cell injury. Blood 2010; 116:1961-70. [DOI: 10.1182/blood-2009-04-215335] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstractβ2-Glycoprotein I (β2GPI) is an evolutionary conserved, abundant circulating protein. Although its function remains uncertain, accumulated evidence points toward interactions with endothelial cells and components of the coagulation system, suggesting a regulatory role in vascular biology. Our group has shown that thioredoxin 1 (TRX-1) generates free thiols in β2GPI, a process that may have a regulatory role in platelet adhesion. This report extends these studies and shows for the first time evidence of β2GPI with free thiols in vivo in both multiple human and murine serum samples. To explore how the vascular surface may modulate the redox status of β2GPI, unstimulated human endothelial cells and EAhy926 cells are shown to be capable of amplifying the effect of free thiol generation within β2GPI. Multiple oxidoreductase enzymes, such as endoplasmic reticulum protein 46 (ERp 46) and TRX-1 reductase, in addition to protein disulfide isomerase are secreted on the surface of endothelial cells. Furthermore, one or more of these generated free thiols within β2GPI are also shown to be nitrosylated. Finally, the functional significance of these findings is explored, by showing that free thiol–containing β2GPI has a powerful effect in protecting endothelial cells and EAhy926 cells from oxidative stress–induced cell death.
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LOSS OF CD40 ENDOGENOUS S-NITROSYLATION DURING INFLAMMATORY RESPONSE IN ENDOTOXEMIC MICE AND PATIENTS WITH SEPSIS. Shock 2010; 33:626-33. [DOI: 10.1097/shk.0b013e3181cb88e6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW. Targeted quantitation of site-specific cysteine oxidation in endogenous proteins using a differential alkylation and multiple reaction monitoring mass spectrometry approach. Mol Cell Proteomics 2010; 9:1400-10. [PMID: 20233844 DOI: 10.1074/mcp.m900643-mcp200] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reactive oxygen species (ROS) are both physiological intermediates in cellular signaling and mediators of oxidative stress. The cysteine-specific redox-sensitivity of proteins can shed light on how ROS are regulated and function, but low sensitivity has limited quantification of the redox state of many fundamental cellular regulators in a cellular context. Here we describe a highly sensitive and reproducible oxidation analysis approach (OxMRM) that combines protein purification, differential alkylation with stable isotopes, and multiple reaction monitoring mass spectrometry that can be applied in a targeted manner to virtually any cysteine or protein. Using this approach, we quantified the site-specific cysteine oxidation status of endogenous p53 for the first time and found that Cys182 at the dimerization interface of the DNA binding domain is particularly susceptible to diamide oxidation intracellularly. OxMRM enables analysis of sulfinic and sulfonic acid oxidation levels, which we validate by assessing the oxidation of the catalytic Cys215 of protein tyrosine phosphatase-1B under numerous oxidant conditions. OxMRM also complements unbiased redox proteomics discovery studies as a verification tool through its high sensitivity, accuracy, precision, and throughput.
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Affiliation(s)
- Jason M Held
- double daggerBuck Institute for Age Research, Novato, California 94945, USA
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Lam YW, Yuan Y, Isaac J, Babu CVS, Meller J, Ho SM. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithelial cells. PLoS One 2010; 5:e9075. [PMID: 20140087 PMCID: PMC2816712 DOI: 10.1371/journal.pone.0009075] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/17/2010] [Indexed: 12/20/2022] Open
Abstract
Background Although overexpression of nitric oxide synthases (NOSs) has been found associated with prostate diseases, the underlying mechanisms for NOS-related prostatic diseases remain unclear. One proposed mechanism is related to the S-nitrosylation of key regulatory proteins in cell-signaling pathways due to elevated levels of NO in the prostate. Thus, our primary objective was to identify S-nitrosylated targets in an immortalized normal prostate epithelial cell line, NPrEC. Methodology/Principal Findings We treated NPrEC with nitroso-cysteine and used the biotin switch technique followed by gel-based separation and mass spectrometry protein identification (using the LTQ-Orbitrap) to discover S-nitrosylated (SNO) proteins in the treated cells. In parallel, we adapted a peptide pull-down methodology to locate the site(s) of S-nitrosylation on the protein SNO targets identified by the first technique. This combined approach identified 116 SNO proteins and determined the sites of modification for 82 of them. Over 60% of these proteins belong to four functional groups: cell structure/cell motility/protein trafficking, protein folding/protein response/protein assembly, mRNA splicing/processing/transcriptional regulation, and metabolism. Western blot analysis validated a subset of targets related to disease development (proliferating cell nuclear antigen, maspin, integrin β4, α-catenin, karyopherin [importin] β1, and elongation factor 1A1). We analyzed the SNO sequences for their primary and secondary structures, solvent accessibility, and three-dimensional structural context. We found that about 80% of the SNO sites that can be mapped into resolved structures are buried, of which approximately half have charged amino acids in their three-dimensional neighborhood, and the other half residing within primarily hydrophobic pockets. Conclusions/Significance We here identified 116 potential SNO targets and mapped their putative SNO sites in NPrEC. Elucidation of how this post-translational modification alters the function of these proteins should shed light on the role of NO in prostate pathologies. To our knowledge, this is the first report identifying SNO targets in prostate epithelial cells.
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Affiliation(s)
- Ying Wai Lam
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Yong Yuan
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Jared Isaac
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - C. V. Suresh Babu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Jarek Meller
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Shuk-Mei Ho
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Cincinnati Cancer Consortium, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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Huang B, Liao CL, Lin YP, Chen SC, Wang DL. S-nitrosoproteome in endothelial cells revealed by a modified biotin switch approach coupled with Western blot-based two-dimensional gel electrophoresis. J Proteome Res 2010; 8:4835-43. [PMID: 19673540 DOI: 10.1021/pr9005662] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NO-mediated S-nitrosation of cysteine residues has been recognized as a fundamental post-translational modification. S-Nitrosation of endothelial cell (EC) proteins can alter function and affect vascular homeostasis. Trace amounts of S-nitrosoproteins in endothelial cells (ECs) in vivo coupled with lability of the S-nitroso bond have hindered a comprehensive characterization. We demonstrate a convenient and reliable method, requiring minimal sample, for the screening and identification of S-nitrosoproteins. ECs treated with the NO donor S-nitroso-N-acetylpenicillamine (SNAP) were subjected to the biotin switch method of labeling, then detected by analytical Western blot-based two-dimensional gel electrophoresis (2-DE). More than 89 SNAP-increased S-nitrosoproteins were detected and 28 of these were successfully excised from preparative 2-DE gel and identified by LC-MS/MS. Moreover, the nitrosocysteine residue for each protein (HSPA9/368, beta-actin/16, TMP3/170, vimentin/328) was also determined, and the relative ratio of S-nitrosation/non-S-nitrosation for Cys328 of vimentin was estimated using MASIC software. By the combination of the biotin switch method with 2-DE and Western blot analysis, S-nitrosoproteins can be screened and characterized by MS, providing a basis for further study of the physiological significance of each S-nitrosoproteins.
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Affiliation(s)
- Bin Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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Calabrese V, Cornelius C, Rizzarelli E, Owen JB, Dinkova-Kostova AT, Butterfield DA. Nitric oxide in cell survival: a janus molecule. Antioxid Redox Signal 2009; 11:2717-39. [PMID: 19558211 DOI: 10.1089/ars.2009.2721] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nitric oxide (NO), plays multiple roles in the nervous system. In addition to regulating proliferation, survival and differentiation of neurons, NO is involved in synaptic activity, neural plasticity, and memory function. Nitric oxide promotes survival and differentiation of neural cells and exerts long-lasting effects through regulation of transcription factors and modulation of gene expression. Signaling by reactive nitrogen species is carried out mainly by targeted modifications of critical cysteine residues in proteins, including S-nitrosylation and S-oxidation, as well as by lipid nitration. NO and other reactive nitrogen species are also involved in neuroinflammation and neurodegeneration, such as in Alzheimer disease, amyotrophic lateral sclerosis, Parkinson disease, multiple sclerosis, Friedreich ataxia, and Huntington disease. Susceptibility to NO and peroxynitrite exposure may depend on factors such as the intracellular reduced glutathione and cellular stress resistance signaling pathways. Thus, neurons, in contrast to astrocytes, appear particularly vulnerable to the effects of nitrosative stress. This article reviews the current understanding of the cytotoxic versus cytoprotective effects of NO in the central nervous system, highlighting the Janus-faced properties of this small molecule. The significance of NO in redox signaling and modulation of the adaptive cellular stress responses and its exciting future perspectives also are discussed.
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Affiliation(s)
- Vittorio Calabrese
- Department of Chemistry, Biochemistry and Molecular Biology Section, Faculty of Medicine, University of Catania , Catania, Italy.
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Structural analysis of cysteine S-nitrosylation: a modified acid-based motif and the emerging role of trans-nitrosylation. J Mol Biol 2009; 395:844-59. [PMID: 19854201 DOI: 10.1016/j.jmb.2009.10.042] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Revised: 09/28/2009] [Accepted: 10/19/2009] [Indexed: 01/27/2023]
Abstract
S-Nitrosylation, the selective and reversible addition of nitric oxide (NO) moiety to cysteine (Cys) sulfur in proteins, regulates numerous cellular processes. In recent years, proteomic approaches that are capable of identifying nitrosylated Cys residues have been developed. However, the features underlying the specificity of Cys modification with NO remain poorly defined. Previous studies suggested that S-nitrosylated Cys may be flanked by an acid-base motif or hydrophobic areas and show high reactivity, low pK(a), and high sulfur atom exposure. In the current study, we prepared an extensive, manually curated data set of proteins with S-nitrosothiols, accounting for a variety of biochemical functions, organisms of origin, and physiological responses to NO. Analysis of this generic NO-Cys data set revealed that proximal acid-base motif, Cys pK(a), sulfur atom exposure, and Cys conservation or hydrophobicity in the vicinity of the modified Cys do not define the specificity of S-nitrosylation. Instead, this analysis revealed a revised acid-base motif, which is located more distantly to the Cys and has its charged groups exposed. We hypothesize that, rather than being strictly used for direct activation of Cys, the modified acid-base motif is engaged in protein-protein interactions thereby contributing to trans-nitrosylation as an important and widespread mechanism for reversible modification of Cys with NO moiety. For proteins lacking the revised motif, we discuss alternative mechanisms including a potential role of nitrosoglutathione as a trans-acting agent.
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López-Sánchez LM, Muntané J, de la Mata M, Rodríguez-Ariza A. Unraveling the S-nitrosoproteome: tools and strategies. Proteomics 2009; 9:808-18. [PMID: 19160395 DOI: 10.1002/pmic.200800546] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the major tasks to be accomplished in the postgenomic era is the characterization of PTMs in proteins. The S-nitrosation of protein thiols is a redox-based PTM that modulating enzymatic activity, subcellular localization, complex formation, and degradation of proteins, largely contributes to the complexity of cellular proteomes. Although the detection of S-nitrosated proteins is problematical due to the lability of S-nitrosothiols, with the improvement of molecular tools an increasing range of proteins has been shown to undergo S-nitrosation. We here review recent proteomic approaches for the systematic assessment of potential targets for protein S-nitrosation. The development of new analytical methods and strategies over the past several years now allows us to investigate the nitrosoproteome on a global scale.
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Hawkins CL, Morgan PE, Davies MJ. Quantification of protein modification by oxidants. Free Radic Biol Med 2009; 46:965-88. [PMID: 19439229 DOI: 10.1016/j.freeradbiomed.2009.01.007] [Citation(s) in RCA: 338] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/12/2009] [Accepted: 01/12/2009] [Indexed: 12/19/2022]
Abstract
Proteins are major targets for oxidative damage due to their abundance and rapid rates of reaction with a wide range of radicals and excited state species, such as singlet oxygen. Exposure of proteins to these oxidants results in loss of the parent amino acid residue, formation of unstable intermediates, and the generation of stable products. Each of these events can be used, to a greater or lesser extent, to quantify damage to proteins. In this review the advantages and disadvantages of a number of these approaches are discussed, with an emphasis on methods that yield absolute quantitative data on the extent of protein modification. Detailed methods sheets are provided for many of these techniques.
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Arnér ESJ. Focus on mammalian thioredoxin reductases--important selenoproteins with versatile functions. Biochim Biophys Acta Gen Subj 2009; 1790:495-526. [PMID: 19364476 DOI: 10.1016/j.bbagen.2009.01.014] [Citation(s) in RCA: 498] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 01/30/2009] [Indexed: 02/07/2023]
Abstract
Thioredoxin systems, involving redox active thioredoxins and thioredoxin reductases, sustain a number of important thioredoxin-dependent pathways. These redox active proteins support several processes crucial for cell function, cell proliferation, antioxidant defense and redox-regulated signaling cascades. Mammalian thioredoxin reductases are selenium-containing flavoprotein oxidoreductases, dependent upon a selenocysteine residue for reduction of the active site disulfide in thioredoxins. Their activity is required for normal thioredoxin function. The mammalian thioredoxin reductases also display surprisingly multifaceted properties and functions beyond thioredoxin reduction. Expressed from three separate genes (in human named TXNRD1, TXNRD2 and TXNRD3), the thioredoxin reductases can each reduce a number of different types of substrates in different cellular compartments. Their expression patterns involve intriguingly complex transcriptional mechanisms resulting in several splice variants, encoding a number of protein variants likely to have specialized functions in a cell- and tissue-type restricted manner. The thioredoxin reductases are also targeted by a number of drugs and compounds having an impact on cell function and promoting oxidative stress, some of which are used in treatment of rheumatoid arthritis, cancer or other diseases. However, potential specific or essential roles for different forms of human or mouse thioredoxin reductases in health or disease are still rather unclear, although it is known that at least the murine Txnrd1 and Txnrd2 genes are essential for normal development during embryogenesis. This review is a survey of current knowledge of mammalian thioredoxin reductase function and expression, with a focus on human and mouse and a discussion of the striking complexity of these proteins. Several yet open questions regarding their regulation and roles in different cells or tissues are emphasized. It is concluded that the intriguingly complex regulation and function of mammalian thioredoxin reductases within the cellular context and in intact mammals strongly suggests that their functions are highly fi ne-tuned with the many pathways involving thioredoxins and thioredoxin-related proteins. These selenoproteins furthermore propagate many functions beyond a reduction of thioredoxins. Aberrant regulation of thioredoxin reductases, or a particular dependence upon these enzymes in diseased cells, may underlie their presumed therapeutic importance as enzymatic targets using electrophilic drugs. These reductases are also likely to mediate several of the effects on health and disease that are linked to different levels of nutritional selenium intake. The thioredoxin reductases and their splice variants may be pivotal components of diverse cellular signaling pathways, having importance in several redox-related aspects of health and disease. Clearly, a detailed understanding of mammalian thioredoxin reductases is necessary for a full comprehension of the thioredoxin system and of selenium dependent processes in mammals.
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Affiliation(s)
- Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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