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Hou Q, Gao T, Liu R, Ma C, Zhang W. S-nitrosoproteomics profiling elucidates the regulatory mechanism of S-nitrosylation on beef quality. Meat Sci 2024; 216:109580. [PMID: 38941777 DOI: 10.1016/j.meatsci.2024.109580] [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: 04/16/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024]
Abstract
This study aimed to quantitively profile the S-nitrosylation in beef semimembranosus (SM) with different treatments (nitric oxide donor or nitric oxide synthase inhibitor) by applying iodoTMT-based nitrosoproteomics. Results showed that 2096 S-nitrosylated cysteine sites in 368 proteins were detected in beef SM. Besides, differential SNO-modified proteins were screened, some of which were involved in crucial biochemical pathways, including calcium-releasing-related proteins, energy metabolic enzymes, myofibrils, and cytoskeletal proteins. GO analysis indicated that differential proteins were localized in a wide range of cellular compartments, such as cytoplasm, organelle, and mitochondrion, providing a prerequisite for S-nitrosylation exerting broad roles in post-mortem muscles. Furthermore, KEGG analysis validated that these proteins participated in the regulation of diverse post-mortem metabolic processes, especially glycolysis. To conclude, changes of S-nitrosylation levels in post-mortem muscles could impact the structure and function of crucial muscle proteins, which lead to different levels of muscle metabolism and ultimately affect beef quality.
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Affiliation(s)
- Qin Hou
- School of Tourism and Cuisine, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, Jiangsu 225127, China; Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tianyi Gao
- School of Tourism and Cuisine, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, Jiangsu 225127, China
| | - Rui Liu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Chao Ma
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wangang Zhang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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2
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Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [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: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
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Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
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3
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Adams C, Boonen K, Laukens K, Bittremieux W. Open Modification Searching of SARS-CoV-2-Human Protein Interaction Data Reveals Novel Viral Modification Sites. Mol Cell Proteomics 2022; 21:100425. [PMID: 36241021 PMCID: PMC9554009 DOI: 10.1016/j.mcpro.2022.100425] [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: 03/16/2022] [Revised: 09/18/2022] [Accepted: 10/09/2022] [Indexed: 01/18/2023] Open
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus 2019 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications. We have reanalyzed public affinity purification-mass spectrometry data using open modification searching to investigate the presence of post-translational modifications in the context of the SARS-CoV-2 virus-host protein-protein interaction network. Based on an over twofold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. In addition, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium,Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium,Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,For correspondence: Wout Bittremieux
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4
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Ye H, Wu J, Liang Z, Zhang Y, Huang Z. Protein S-Nitrosation: Biochemistry, Identification, Molecular Mechanisms, and Therapeutic Applications. J Med Chem 2022; 65:5902-5925. [PMID: 35412827 DOI: 10.1021/acs.jmedchem.1c02194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein S-nitrosation (SNO), a posttranslational modification (PTM) of cysteine (Cys) residues elicited by nitric oxide (NO), regulates a wide range of protein functions. As a crucial form of redox-based signaling by NO, SNO contributes significantly to the modulation of physiological functions, and SNO imbalance is closely linked to pathophysiological processes. Site-specific identification of the SNO protein is critical for understanding the underlying molecular mechanisms of protein function regulation. Although careful verification is needed, SNO modification data containing numerous functional proteins are a potential research direction for druggable target identification and drug discovery. Undoubtedly, SNO-related research is meaningful not only for the development of NO donor drugs but also for classic target-based drug design. Herein, we provide a comprehensive summary of SNO, including its origin and transport, identification, function, and potential contribution to drug discovery. Importantly, we propose new views to develop novel therapies based on potential protein SNO-sourced targets.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Zhuangzhuang Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Zhangjian Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
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5
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Abstract
Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.
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6
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Sharma V, Fernando V, Letson J, Walia Y, Zheng X, Fackelman D, Furuta S. S-Nitrosylation in Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms22094600. [PMID: 33925645 PMCID: PMC8124305 DOI: 10.3390/ijms22094600] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
S-nitrosylation is a selective and reversible post-translational modification of protein thiols by nitric oxide (NO), which is a bioactive signaling molecule, to exert a variety of effects. These effects include the modulation of protein conformation, activity, stability, and protein-protein interactions. S-nitrosylation plays a central role in propagating NO signals within a cell, tissue, and tissue microenvironment, as the nitrosyl moiety can rapidly be transferred from one protein to another upon contact. This modification has also been reported to confer either tumor-suppressing or tumor-promoting effects and is portrayed as a process involved in every stage of cancer progression. In particular, S-nitrosylation has recently been found as an essential regulator of the tumor microenvironment (TME), the environment around a tumor governing the disease pathogenesis. This review aims to outline the effects of S-nitrosylation on different resident cells in the TME and the diverse outcomes in a context-dependent manner. Furthermore, we will discuss the therapeutic potentials of modulating S-nitrosylation levels in tumors.
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Recent Advances in Predicting Protein S-Nitrosylation Sites. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5542224. [PMID: 33628788 PMCID: PMC7892234 DOI: 10.1155/2021/5542224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023]
Abstract
Protein S-nitrosylation (SNO) is a process of covalent modification of nitric oxide (NO) and its derivatives and cysteine residues. SNO plays an essential role in reversible posttranslational modifications of proteins. The accurate prediction of SNO sites is crucial in revealing a certain biological mechanism of NO regulation and related drug development. Identification of the sites of SNO in proteins is currently a very hot topic. In this review, we briefly summarize recent advances in computationally identifying SNO sites. The challenges and future perspectives for identifying SNO sites are also discussed. We anticipate that this review will provide insights into research on SNO site prediction.
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Wang Y, Liu R, Hou Q, Tian X, Fan X, Zhang W, Zhou G. Comparison of activity, expression and S-nitrosylation of glycolytic enzymes between pale, soft and exudative and red, firm and non-exudative pork during post-mortem aging. Food Chem 2020; 314:126203. [PMID: 31978718 DOI: 10.1016/j.foodchem.2020.126203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/09/2019] [Accepted: 01/11/2020] [Indexed: 11/18/2022]
Abstract
The activity, expression and S-nitrosylation of glycogen phosphorylase (GP), phosphofructokinase (PFK) and pyruvate kinase (PK) was compared between pale, soft and exudative (PSE) and red, firm and non-exudative (RFN) pork. The nitric oxide synthase (NOS) activity of RFN pork was higher than PSE pork (P < 0.05). Glycogen and lactic acid content were significantly different between PSE and RFN samples at 1 h postmortem (P < 0.05). Compared to PSE pork, RFN pork had lower activities and higher S-nitrosylation levels of GP, PFK and PK (P < 0.05). Moreover, GP expression in RFN pork was lower (P < 0.05) while no significant differences of PFK and PK expression were observed between these two groups. These data suggest that protein S-nitrosylation can presumably regulate glycolysis by modulating glycolytic enzymes activities and then regulate the development of PSE pork.
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Affiliation(s)
- Yingying Wang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Liu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Qin Hou
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaona Tian
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoquan Fan
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangang Zhang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, China
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9
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Xu Y, Andrade J, Ueberheide B, Neel BG. Activated Thiol Sepharose-based proteomic approach to quantify reversible protein oxidation. FASEB J 2019; 33:12336-12347. [PMID: 31451050 PMCID: PMC6902679 DOI: 10.1096/fj.201900693r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/23/2019] [Indexed: 01/19/2023]
Abstract
Reactive oxygen species (ROS) can act as second messengers in various signaling pathways, and abnormal oxidation contributes to multiple diseases, including cancer. Detecting and quantifying protein oxidation is crucial for a detailed understanding of reduction-oxidation reaction (redox) signaling. We developed an Activated Thiol Sepharose-based proteomic (ATSP) approach to quantify reversible protein oxidation. ATSP can enrich H2O2-sensitive thiol peptides, which are more likely to contain reactive cysteines involved in redox signaling. We applied our approach to analyze hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a type of kidney cancer that harbors fumarate hydratase (FH)-inactivating mutations and has elevated ROS levels. Multiple proteins were oxidized in FH-deficient cells, including many metabolic proteins such as the pyruvate kinase M2 isoform (PKM2). Treatment of HLRCC cells with dimethyl fumarate or PKM2 activators altered PKM2 oxidation levels. Finally, we found that ATSP could detect Src homology region 2 domain-containing phosphatase-2 and PKM2 oxidation in cells stimulated with platelet-derived growth factor. This newly developed redox proteomics workflow can detect reversible oxidation of reactive cysteines and can be employed to analyze multiple physiologic and pathologic conditions.-Xu, Y., Andrade, J., Ueberheide, B., Neel, B. G. Activated Thiol Sepharose-based proteomic approach to quantify reversible protein oxidation.
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Affiliation(s)
- Yang Xu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University (NYU) Langone Health, New York, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University (NYU) Langone Health, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Health, New York, New York, USA
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
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10
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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11
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Liu R, Zhang C, Xing L, Zhang L, Zhou G, Zhang W. A bioinformatics study on characteristics, metabolic pathways, and cellular functions of the identified S-nitrosylated proteins in postmortem pork muscle. Food Chem 2019; 274:407-414. [PMID: 30372958 DOI: 10.1016/j.foodchem.2018.09.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022]
Abstract
This study aimed to determine the characteristics, metabolic pathways and cellular functions of S-nitrosylated proteins from pork postmortem muscle using bioinformatics analysis. The results showed that S-nitrosylated proteins had a broad range of molecular weight and pI value and were mainly located in the functional region of secondary structure. The motif revealed the lysine (K) positioned at -5, -7, +1 and +5 through the S-nitrosocysteine while "C-X-X-C" was identified as the motif for non-S-nitrosylation-modified cysteine. The proteins were widely localized in cell compartments and mostly belonged to enzymes participating in the metabolic process. Glycolysis was the most significant pathways of S-nitrosylated proteins in postmortem muscle. The cell death of muscle cells was predicted to be inhibited by S-nitrosylation with the potential influence on the apoptosis. Those identified pathways and cellular functions of S-nitrosylation are proposed to have a profound influence on meat quality and should be highly regarded.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Chaoyang Zhang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lujuan Xing
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lili Zhang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangang Zhang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education China, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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12
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Xu X, Qiu H, Shi F, Wang Z, Wang X, Jin L, Chi L, Zhang Q. The protein S-nitrosylation of splicing and translational machinery in vascular endothelial cells is susceptible to oxidative stress induced by oxidized low-density lipoprotein. J Proteomics 2019; 195:11-22. [PMID: 30630120 DOI: 10.1016/j.jprot.2019.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/18/2018] [Accepted: 01/05/2019] [Indexed: 12/24/2022]
Abstract
Oxidized low-density lipoprotein (ox-LDL) can impair endothelial function and lead to the atherosclerosis development. Protein S-nitrosylation is sensitive to cellular redox state and acts as a crucial regulator and executor of nitric oxide (NO) signaling pathways. Aberrant S-nitrosylation contributes to the pathogenesis of cardiovascular and cerebrovascular diseases. However, the effect of ox-LDL on S-nitrosylation and its significance for endothelial dysfunction have not been studied at proteome level. Herein, the combined quantitative analysis of proteome and S-nitrosoproteome was performed using an integrated biotin switch and iTRAQ labeling approach in EA.hy926 cell line derived from human umbilical vein endothelial cell (HUVEC) treated with ox-LDL. A total of 2204 S-nitrosylated (SNO) peptides of 1318 SNO-proteins were quantified. Notably, 352 SNO-peptides of 262 SNO-proteins were significantly regulated after excluding S-nitrosylation changes caused by protein expression alterations. Many of them belonged to mRNA splicing, ribosomal structure and translational regulatory proteins, covering the entire translation process. The results indicated that S-nitrosylation of the splicing and translational machinery in vascular endothelial cells was susceptible to ox-LDL. Abnormal protein S-nitrosylation may be one pivotal mechanism underlying endothelial dysfunction induced by ox-LDL. This study potentially enriches the present understanding of pro-atherogenic effect of ox-LDL from the perspective of S-nitrosylation. SIGNIFICANCE: The role of ox-LDL in endothelial dysfunction and atherosclerosis development has been recognized from the aspect of impaired NO production. However, its effect on S-nitrosylation, which is directly related to NO signaling pathway, still remains largely unexplored. Our work initially provided a systematic characterization of S-nitrosoproteome in ox-LDL-treated endothelial cells after ruling out the changes of S-nitrosylation modification caused by protein expression alone. MS-based approach coupled with iTRAQ technique indicated 262 SNO-proteins were significantly regulated. Functional enrichment and interaction network analysis revealed that proteins involved in mRNA splicing and translational machinery were susceptible to abnormal S-nitrosylation under ox-LDL treatment. This achievement suggested one potential mechanism underlying endothelial dysfunction induced by ox-LDL from the perspective of S-nitrosoproteome.
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Affiliation(s)
- Xiaohui Xu
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Hongyan Qiu
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Feng Shi
- Scientific Research Division, Shandong Institute for Food and Drug Control, Jinan, Shandong 250101, China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Provincial Hospital affiliated with Shandong University, Jinan, Shandong 250021, China
| | - Xiaowei Wang
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Lan Jin
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Lianli Chi
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China.
| | - Qunye Zhang
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China.
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13
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Identification of S-nitrosylated proteins in postmortem pork muscle using modified biotin switch method coupled with isobaric tags. Meat Sci 2018; 145:431-439. [DOI: 10.1016/j.meatsci.2018.07.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/15/2018] [Accepted: 07/19/2018] [Indexed: 11/18/2022]
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14
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Contribution of nitric oxide and protein S-nitrosylation to variation in fresh meat quality. Meat Sci 2018; 144:135-148. [DOI: 10.1016/j.meatsci.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/12/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
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15
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Alcock LJ, Perkins MV, Chalker JM. Chemical methods for mapping cysteine oxidation. Chem Soc Rev 2018; 47:231-268. [DOI: 10.1039/c7cs00607a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.
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Affiliation(s)
- Lisa J. Alcock
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Michael V. Perkins
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Justin M. Chalker
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
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16
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Peroxisomes and Cellular Oxidant/Antioxidant Balance: Protein Redox Modifications and Impact on Inter-organelle Communication. Subcell Biochem 2018; 89:435-461. [PMID: 30378035 DOI: 10.1007/978-981-13-2233-4_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disturbances in cellular redox balance have been associated with pro-aging mechanisms and increased risk for various chronic disease states. Multiple lines of evidence indicate that peroxisomes are central players in cellular redox metabolism. Nevertheless, the potential role of this organelle as intracellular redox signaling platform has been largely overlooked for a long time. Fortunately, this situation is now changing. This review provides a snapshot of the current progress in the field, with an emphasis on the situation in mammals. We first briefly introduce the basics of redox biology and how reactive oxygen and nitrogen species can drive cellular signaling events. Next, we discuss current evidence linking peroxisome (dys)function to redox signaling, both in health and disease. We also highlight what is currently known about the downstream targets of peroxisome-derived oxidants. In addition, we present an extensive list of proteins that are involved in peroxisome functioning and have been identified as being responsive to oxidative stress in large scale redox proteomics studies. Finally, we address how changes in peroxisomal redox state may impact on functional mechanisms underlying inter-organelle communication. Gaining more insight into these mechanisms is key to our understanding of how peroxisomes are embedded in cellular signaling networks implicated in aging and diseases such as cancer, diabetes, and neurodegenerative disorders.
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17
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Liu JZ, Duan J, Ni M, Liu Z, Qiu WL, Whitham SA, Qian WJ. S-Nitrosylation inhibits the kinase activity of tomato phosphoinositide-dependent kinase 1 (PDK1). J Biol Chem 2017; 292:19743-19751. [PMID: 28972151 DOI: 10.1074/jbc.m117.803882] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/13/2017] [Indexed: 01/01/2023] Open
Abstract
It is well known that the reactive oxygen species NO can trigger cell death in plants and other organisms, but the underlying molecular mechanisms are not well understood. Here we provide evidence that NO may trigger cell death in tomato (Solanum lycopersicum) by inhibiting the activity of phosphoinositide-dependent kinase 1 (SlPDK1), a conserved negative regulator of cell death in yeasts, mammals, and plants, via S-nitrosylation. Biotin-switch assays indicated that SlPDK1 is a target of S-nitrosylation. Moreover, the kinase activity of SlPDK1 was inhibited by S-nitrosoglutathione in a concentration-dependent manner, indicating that SlPDK1 activity is abrogated by S-nitrosylation. The S-nitrosoglutathione-induced inhibition was reversible in the presence of a reducing agent but additively enhanced by hydrogen peroxide (H2O2). Our LC-MS/MS analyses further indicated that SlPDK1 is primarily S-nitrosylated on a cysteine residue at position 128 (Cys128), and substitution of Cys128 with serine completely abolished SlPDK1 kinase activity, suggesting that S-nitrosylation of Cys128 is responsible for SlPDK1 inhibition. In summary, our results establish a potential link between NO-triggered cell death and inhibition of the kinase activity of tomato PDK1.
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Affiliation(s)
- Jian-Zhong Liu
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China,
| | - Jicheng Duan
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and
| | - Min Ni
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China
| | - Zhen Liu
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China
| | - Wen-Li Qiu
- the Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Steven A Whitham
- the Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and
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18
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Zhou C, Liang J, Cheng S, Shi T, Houk KN, Wei DQ, Zhao YL. Ab initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1319059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chao Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Juan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shangli Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
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19
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Fancy NN, Bahlmann AK, Loake GJ. Nitric oxide function in plant abiotic stress. PLANT, CELL & ENVIRONMENT 2017; 40:462-472. [PMID: 26754426 DOI: 10.1111/pce.12707] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/09/2015] [Accepted: 12/26/2015] [Indexed: 05/17/2023]
Abstract
Abiotic stress is one of the main threats affecting crop growth and production. An understanding of the molecular mechanisms that underpin plant responses against environmental insults will be crucial to help guide the rational design of crop plants to counter these challenges. A key feature during abiotic stress is the production of nitric oxide (NO), an important concentration dependent, redox-related signalling molecule. NO can directly or indirectly interact with a wide range of targets leading to the modulation of protein function and the reprogramming of gene expression. The transfer of NO bioactivity can occur through a variety of potential mechanisms but chief among these is S-nitrosylation, a prototypic, redox-based, post-translational modification. However, little is known about this pivotal molecular amendment in the regulation of abiotic stress signalling. Here, we describe the emerging knowledge concerning the function of NO and S-nitrosylation during plant responses to abiotic stress.
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Affiliation(s)
- Nurun Nahar Fancy
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh, UK, EH9 3BF
| | - Ann-Kathrin Bahlmann
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh, UK, EH9 3BF
- Technische Universität Braunschweig, Braunschweig, D-38106, Germany
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh, UK, EH9 3BF
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20
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Price ME, Pavlik JA, Liu M, Ding SJ, Wyatt TA, Sisson JH. Alcohol drives S-nitrosylation and redox activation of protein phosphatase 1, causing bovine airway cilia dysfunction. Am J Physiol Lung Cell Mol Physiol 2017; 312:L432-L439. [PMID: 28062487 DOI: 10.1152/ajplung.00513.2016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 11/22/2022] Open
Abstract
Individuals with alcohol (ethanol)-use disorders are at increased risk for lung infections, in part, due to defective mucociliary clearance driven by motile cilia in the airways. We recently reported that isolated, demembranated bovine cilia (axonemes) are capable of producing nitric oxide (∙NO) when exposed to biologically relevant concentrations of alcohol. This increased presence of ∙NO can lead to protein S-nitrosylation, a posttranslational modification signaling mechanism involving reversible adduction of nitrosonium cations or ∙NO to thiolate or thiyl radicals, respectively, of proteins forming S-nitrosothiols (SNOs). We quantified and compared SNO content between isolated, demembranated axonemes extracted from bovine tracheae, with or without in situ alcohol exposure (100 mM × 24 h). We demonstrate that relevant concentrations of alcohol exposure shift the S-nitrosylation status of key cilia regulatory proteins, including 20-fold increases in S-nitrosylation of proteins that include protein phosphatase 1 (PP1). With the use of an ATP-reactivated axoneme motility system, we demonstrate that alcohol-driven S-nitrosylation of PP1 is associated with PP1 activation and dysfunction of axoneme motility. These new data demonstrate that alcohol can shift the S-nitrothiol balance at the level of the cilia organelle and highlight S-nitrosylation as a novel signaling mechanism to regulate PP1 and cilia motility.
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Affiliation(s)
- Michael E Price
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska.,Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Jacqueline A Pavlik
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Miao Liu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shi-Jian Ding
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Todd A Wyatt
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska.,Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha, Nebraska; and.,Research Service, Nebraska-Western Iowa VA Healthcare System, Omaha, Nebraska
| | - Joseph H Sisson
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska;
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21
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Luebker SA, Wojtkiewicz M, Koepsell SA. Two methods for proteomic analysis of formalin-fixed, paraffin embedded tissue result in differential protein identification, data quality, and cost. Proteomics 2016; 15:3744-53. [PMID: 26306679 DOI: 10.1002/pmic.201500147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/06/2015] [Accepted: 08/19/2015] [Indexed: 12/18/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC-MS/MS exist, but standardization of procedures and critical analysis of data quality is limited. This study compared and characterized data obtained from FFPE tissue using two methods: a urea in-solution digestion method (UISD) versus a commercially available Qproteome FFPE Tissue Kit method (Qkit). Each method was performed independently three times on serial sections of homogenous FFPE tissue to minimize pre-analytical variations and analyzed with three technical replicates by LC-MS/MS. Data were evaluated for reproducibility and physiochemical distribution, which highlighted differences in the ability of each method to identify proteins of different molecular weights and isoelectric points. Each method replicate resulted in a significant number of new protein identifications, and both methods identified significantly more proteins using three technical replicates as compared to only two. UISD was cheaper, required less time, and introduced significant protein modifications as compared to the Qkit method, which provided more precise and higher protein yields. These data highlight significant variability among method replicates and type of method used, despite minimizing pre-analytical variability. Utilization of only one method or too few replicates (both method and technical) may limit the subset of proteomic information obtained.
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Affiliation(s)
- Stephen A Luebker
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, NE, USA
| | - Melinda Wojtkiewicz
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, NE, USA
| | - Scott A Koepsell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, NE, USA
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22
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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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23
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Kramer PA, Duan J, Qian WJ, Marcinek DJ. The Measurement of Reversible Redox Dependent Post-translational Modifications and Their Regulation of Mitochondrial and Skeletal Muscle Function. Front Physiol 2015; 6:347. [PMID: 26635632 PMCID: PMC4658434 DOI: 10.3389/fphys.2015.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/09/2015] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial oxidative stress is a common feature of skeletal myopathies across multiple conditions; however, the mechanism by which it contributes to skeletal muscle dysfunction remains controversial. Oxidative damage to proteins, lipids, and DNA has received the most attention, yet an important role for reversible redox post-translational modifications (PTMs) in pathophysiology is emerging. The possibility that these PTMs can exert dynamic control of muscle function implicates them as a mechanism contributing to skeletal muscle dysfunction in chronic disease. Herein, we discuss the significance of thiol-based redox dependent modifications to mitochondrial, myofibrillar, and excitation-contraction (EC) coupling proteins with an emphasis on how these changes could alter skeletal muscle performance under chronically stressed conditions. A major barrier to a better mechanistic understanding of the role of reversible redox PTMs in muscle function is the technical challenges associated with accurately measuring the changes of site-specific redox PTMs. Here we will critically review current approaches with an emphasis on sample preparation artifacts, quantitation, and specificity. Despite these challenges, the ability to accurately quantify reversible redox PTMs is critical to understanding the mechanisms by which mitochondrial oxidative stress contributes to skeletal muscle dysfunction in chronic diseases.
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Affiliation(s)
- Philip A Kramer
- Department of Radiology, University of Washington Seattle, WA, USA
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - David J Marcinek
- Department of Radiology, University of Washington Seattle, WA, USA ; Department of Bioengineering, University of Washington Seattle, WA, USA
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24
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Shi YF, Wang DL, Wang C, Culler AH, Kreiser MA, Suresh J, Cohen JD, Pan J, Baker B, Liu JZ. Loss of GSNOR1 Function Leads to Compromised Auxin Signaling and Polar Auxin Transport. MOLECULAR PLANT 2015; 8:1350-65. [PMID: 25917173 DOI: 10.1016/j.molp.2015.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/30/2015] [Accepted: 04/16/2015] [Indexed: 05/21/2023]
Abstract
Cross talk between phytohormones, nitric oxide (NO), and auxin has been implicated in the control of plant growth and development. Two recent reports indicate that NO promoted auxin signaling but inhibited auxin transport probably through S-nitrosylation. However, genetic evidence for the effect of S-nitrosylation on auxin physiology has been lacking. In this study, we used a genetic approach to understand the broader role of S-nitrosylation in auxin physiology in Arabidopsis. We compared auxin signaling and transport in Col-0 and gsnor1-3, a loss-of-function GSNOR1 mutant defective in protein de-nitrosylation. Our results showed that auxin signaling was impaired in the gsnor1-3 mutant as revealed by significantly reduced DR5-GUS/DR5-GFP accumulation and compromised degradation of AXR3NT-GUS, a useful reporter in interrogating auxin-mediated degradation of Aux/IAA by auxin receptors. In addition, polar auxin transport was compromised in gsnor1-3, which was correlated with universally reduced levels of PIN or GFP-PIN proteins in the roots of the mutant in a manner independent of transcription and 26S proteasome degradation. Our results suggest that S-nitrosylation and GSNOR1-mediated de-nitrosylation contribute to auxin physiology, and impaired auxin signaling and compromised auxin transport are responsible for the auxin-related morphological phenotypes displayed by the gsnor1-3 mutant.
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Affiliation(s)
- Ya-Fei Shi
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Da-Li Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Chao Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Angela Hendrickson Culler
- Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Molly A Kreiser
- Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jayanti Suresh
- Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jerry D Cohen
- Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jianwei Pan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Barbara Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jian-Zhong Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.
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25
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:615-630. [PMID: 25588721 DOI: 10.1007/s13361-014-1059-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/22/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Cysteine-selective proteomics approaches simplify complex protein mixtures and improve the chance of detecting low abundant proteins. It is possible that cysteinyl-peptide/protein enrichment methods could be coupled to isotopic labeling and isobaric tagging methods for quantitative proteomics analyses in as few as two or up to 10 samples, respectively. Here we present two novel cysteine-selective proteomics approaches: cysteine-selective dimethyl labeling (cysDML) and cysteine-selective combined precursor isotopic labeling and isobaric tagging (cPILOT). CysDML is a duplex precursor quantification technique that couples cysteinyl-peptide enrichment with on-resin stable-isotope dimethyl labeling. Cysteine-selective cPILOT is a novel 12-plex workflow based on cysteinyl-peptide enrichment, on-resin stable-isotope dimethyl labeling, and iodoTMT tagging on cysteine residues. To demonstrate the broad applicability of the approaches, we applied cysDML and cPILOT methods to liver tissues from an Alzheimer's disease (AD) mouse model and wild-type (WT) controls. From the cysDML experiments, an average of 850 proteins were identified and 594 were quantified, whereas from the cPILOT experiment, 330 and 151 proteins were identified and quantified, respectively. Overall, 2259 unique total proteins were detected from both cysDML and cPILOT experiments. There is tremendous overlap in the proteins identified and quantified between both experiments, and many proteins have AD/WT fold-change values that are within ~20% error. A total of 65 statistically significant proteins are differentially expressed in the liver proteome of AD mice relative to WT. The performance of cysDML and cPILOT are demonstrated and advantages and limitations of using multiple duplex experiments versus a single 12-plex experiment are highlighted.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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26
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Correani V, Francesco LD, Cera I, Mignogna G, Giorgi A, Mazzanti M, Fumagalli L, Fabrizi C, Maras B, Schininà ME. Reversible redox modifications in the microglial proteome challenged by beta amyloid. MOLECULAR BIOSYSTEMS 2015; 11:1584-93. [DOI: 10.1039/c4mb00703d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reversible redox modifications of the microglial proteome contribute to switching of these neuronal sentinel cells toward a neuroinflammatory phenotype.
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Affiliation(s)
- Virginia Correani
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Laura Di Francesco
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Isabella Cera
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Giuseppina Mignogna
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Michele Mazzanti
- Dipartimento di Bioscienze
- Università degli Studi di Milano
- Milan
- Italy
| | - Lorenzo Fumagalli
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Cinzia Fabrizi
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Bruno Maras
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - M. Eugenia Schininà
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
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27
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Chaki M, Kovacs I, Spannagl M, Lindermayr C. Computational prediction of candidate proteins for S-nitrosylation in Arabidopsis thaliana. PLoS One 2014; 9:e110232. [PMID: 25333472 PMCID: PMC4204854 DOI: 10.1371/journal.pone.0110232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 09/17/2014] [Indexed: 02/04/2023] Open
Abstract
Nitric oxide (NO) is an important signaling molecule that regulates many physiological processes in plants. One of the most important regulatory mechanisms of NO is S-nitrosylation-the covalent attachment of NO to cysteine residues. Although the involvement of cysteine S-nitrosylation in the regulation of protein functions is well established, its substrate specificity remains unknown. Identification of candidates for S-nitrosylation and their target cysteine residues is fundamental for studying the molecular mechanisms and regulatory roles of S-nitrosylation in plants. Several experimental methods that are based on the biotin switch have been developed to identify target proteins for S-nitrosylation. However, these methods have their limits. Thus, computational methods are attracting considerable attention for the identification of modification sites in proteins. Using GPS-SNO version 1.0, a recently developed S-nitrosylation site-prediction program, a set of 16,610 candidate proteins for S-nitrosylation containing 31,900 S-nitrosylation sites was isolated from the entire Arabidopsis proteome using the medium threshold. In the compartments "chloroplast," "CUL4-RING ubiquitin ligase complex," and "membrane" more than 70% of the proteins were identified as candidates for S-nitrosylation. The high number of identified candidates in the proteome reflects the importance of redox signaling in these compartments. An analysis of the functional distribution of the predicted candidates showed that proteins involved in signaling processes exhibited the highest prediction rate. In a set of 46 proteins, where 53 putative S-nitrosylation sites were already experimentally determined, the GPS-SNO program predicted 60 S-nitrosylation sites, but only 11 overlap with the results of the experimental approach. In general, a computer-assisted method for the prediction of targets for S-nitrosylation is a very good tool; however, further development, such as including the three dimensional structure of proteins in such analyses, would improve the identification of S-nitrosylation sites.
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Affiliation(s)
- Mounira Chaki
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Izabella Kovacs
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
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28
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Prediction of S-nitrosylation modification sites based on kernel sparse representation classification and mRMR algorithm. BIOMED RESEARCH INTERNATIONAL 2014; 2014:438341. [PMID: 25184139 PMCID: PMC4145740 DOI: 10.1155/2014/438341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 07/23/2014] [Indexed: 12/02/2022]
Abstract
Protein S-nitrosylation plays a very important role in a wide variety of cellular biological activities. Hitherto, accurate prediction of S-nitrosylation sites is still of great challenge. In this paper, we presented a framework to computationally predict S-nitrosylation sites based on kernel sparse representation classification and minimum Redundancy Maximum Relevance algorithm. As much as 666 features derived from five categories of amino acid properties and one protein structure feature are used for numerical representation of proteins. A total of 529 protein sequences collected from the open-access databases and published literatures are used to train and test our predictor. Computational results show that our predictor achieves Matthews' correlation coefficients of 0.1634 and 0.2919 for the training set and the testing set, respectively, which are better than those of k-nearest neighbor algorithm, random forest algorithm, and sparse representation classification algorithm. The experimental results also indicate that 134 optimal features can better represent the peptides of protein S-nitrosylation than the original 666 redundant features. Furthermore, we constructed an independent testing set of 113 protein sequences to evaluate the robustness of our predictor. Experimental result showed that our predictor also yielded good performance on the independent testing set with Matthews' correlation coefficients of 0.2239.
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29
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Importance of NO and its related compounds in enteric nervous system regulation of gut homeostasis and disease susceptibility. Curr Opin Pharmacol 2014; 19:54-60. [PMID: 25108170 DOI: 10.1016/j.coph.2014.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022]
Abstract
Nitric oxide (NO) produced by the enteric nervous system represents an important regulatory mechanism in gut homeostasis. Aberrant NO signaling contributes significantly toward enteric disease by altering gut motility, vascular tone, blood supply, mucosal barrier function, secretions and immunity. Consequently, there is much interest in therapeutically targeting NO production and its bioactive intermediates. This article highlights recent advances in NO signaling and therapeutics as it relates to the gastrointestinal tract and its associated NO producing microbiota. Because of its limited scope, a particular emphasis is placed on S-nitrosylation as the emerging physiologic mechanism for NO signal transduction, and how such signals are modulated by other gaseous transmitters - notably hydrogen disulfide and carbon monoxide - that are produced by the enteric nervous system and share common molecular targets. Recent findings also indicate that druggable regulators of S-nitrosylation, for example S-nitrosoglutathione (GSNO) reductase, provide for a superior pharmacology and finer therapeutic control over classical NO donors, and may be better suited for oral delivery to the gastrointestinal tract.
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30
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Zaręba-Kozioł M, Szwajda A, Dadlez M, Wysłouch-Cieszyńska A, Lalowski M. Global analysis of S-nitrosylation sites in the wild type (APP) transgenic mouse brain-clues for synaptic pathology. Mol Cell Proteomics 2014; 13:2288-305. [PMID: 24895380 DOI: 10.1074/mcp.m113.036079] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by an early synaptic loss, which strongly correlates with the severity of dementia. The pathogenesis and causes of characteristic AD symptoms are not fully understood. Defects in various cellular cascades were suggested, including the imbalance in production of reactive oxygen and nitrogen species. Alterations in S-nitrosylation of several proteins were previously demonstrated in various AD animal models and patients. In this work, using combined biotin-switch affinity/nano-LC-MS/MS and bioinformatic approaches we profiled endogenous S-nitrosylation of brain synaptosomal proteins from wild type and transgenic mice overexpressing mutated human Amyloid Precursor Protein (hAPP). Our data suggest involvement of S-nitrosylation in the regulation of 138 synaptic proteins, including MAGUK, CamkII, or synaptotagmins. Thirty-eight proteins were differentially S-nitrosylated in hAPP mice only. Ninety-five S-nitrosylated peptides were identified for the first time (40% of total, including 33 peptides exclusively in hAPP synaptosomes). We verified differential S-nitrosylation of 10 (26% of all identified) synaptosomal proteins from hAPP mice, by Western blotting with specific antibodies. Functional enrichment analysis linked S-nitrosylated proteins to various cellular pathways, including: glycolysis, gluconeogenesis, calcium homeostasis, ion, and vesicle transport, suggesting a basic role of this post-translational modification in the regulation of synapses. The linkage of SNO-proteins to axonal guidance and other processes related to APP metabolism exclusively in the hAPP brain, implicates S-nitrosylation in the pathogenesis of Alzheimer's disease.
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Affiliation(s)
- Monika Zaręba-Kozioł
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Michał Dadlez
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Maciej Lalowski
- ¶Biomedicum Helsinki, Institute of Biomedicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Unit, University of Helsinki, Finland; ‖Folkhälsan Institute of Genetics, Helsinki, Finland
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31
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Su D, Gaffrey MJ, Guo J, Hatchell KE, Chu RK, Clauss TRW, Aldrich JT, Wu S, Purvine S, Camp DG, Smith RD, Thrall BD, Qian WJ. Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling. Free Radic Biol Med 2014; 67:460-70. [PMID: 24333276 PMCID: PMC3945121 DOI: 10.1016/j.freeradbiomed.2013.12.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/02/2013] [Accepted: 12/03/2013] [Indexed: 12/17/2022]
Abstract
S-Glutathionylation (SSG) is an important regulatory posttranslational modification on protein cysteine (Cys) thiols, yet the role of specific cysteine residues as targets of modification is poorly understood. We report a novel quantitative mass spectrometry (MS)-based proteomic method for site-specific identification and quantification of S-glutathionylation across different conditions. Briefly, this approach consists of initial blocking of free thiols by alkylation, selective reduction of glutathionylated thiols, and covalent capture of reduced thiols using thiol affinity resins, followed by on-resin tryptic digestion and isobaric labeling with iTRAQ (isobaric tags for relative and absolute quantitation) for MS-based identification and quantification. The overall approach was initially validated by application to RAW 264.7 mouse macrophages treated with different doses of diamide to induce glutathionylation. A total of 1071 Cys sites from 690 proteins were identified in response to diamide treatment, with ~90% of the sites displaying >2-fold increases in SSG modification compared to controls. This approach was extended to identify potential SSG-modified Cys sites in response to H2O2, an endogenous oxidant produced by activated macrophages and many pathophysiological stimuli. The results revealed 364 Cys sites from 265 proteins that were sensitive to S-glutathionylation in response to H2O2 treatment, thus providing a database of proteins and Cys sites susceptible to this modification under oxidative stress. Functional analysis revealed that the most significantly enriched molecular function categories for proteins sensitive to SSG modifications were free radical scavenging and cell death/survival. Overall the results demonstrate that our approach is effective for site-specific identification and quantification of SSG-modified proteins. The analytical strategy also provides a unique approach to determining the major pathways and cellular processes most susceptible to S-glutathionylation under stress conditions.
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Affiliation(s)
- Dian Su
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jia Guo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kayla E Hatchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Joshua T Aldrich
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sam Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David G Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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32
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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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33
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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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34
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Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications. Nat Protoc 2013; 9:64-75. [PMID: 24336471 DOI: 10.1038/nprot.2013.161] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reversible modifications of cysteine thiols have a key role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation (SNO) and S-glutathionylation (SSG), have been recognized for their significance in various physiological and pathological processes. Here we describe a procedure for the enrichment of peptides containing reversible cysteine modifications. Starting with tissue or cell lysate samples, all of the unmodified free thiols are blocked using N-ethylmaleimide (NEM). This is followed by the selective reduction of those cysteines bearing the reversible modification(s) of interest. The reduction is achieved by using different reducing reagents that react specifically with each type of cysteine modification (e.g., ascorbate for SNO). This protocol serves as a general approach for enrichment of thiol-containing proteins or peptides derived from reversibly modified proteins. The approach uses a commercially available thiol-affinity resin (thiopropyl Sepharose 6B) to directly capture free thiol-containing proteins through a disulfide exchange reaction, followed by on-resin protein digestion and multiplexed isobaric labeling to facilitate liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quantitative site-specific analysis of cysteine-based reversible modifications. The overall approach requires a simpler workflow with increased specificity compared with the commonly used biotinylation-based assays. The procedure for selective enrichment and analyses of SNO and the level of total reversible cysteine modifications (or total oxidation) is presented to demonstrate the utility of this general strategy. The entire protocol requires ∼3 d for sample processing with an additional day for LC-MS/MS and data analysis.
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35
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Lee YI, Giovinazzo D, Kang HC, Lee Y, Jeong JS, Doulias PT, Xie Z, Hu J, Ghasemi M, Ischiropoulos H, Qian J, Zhu H, Blackshaw S, Dawson VL, Dawson TM. Protein microarray characterization of the S-nitrosoproteome. Mol Cell Proteomics 2013; 13:63-72. [PMID: 24105792 PMCID: PMC3879630 DOI: 10.1074/mcp.m113.032235] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nitric oxide (NO) mediates a substantial part of its physiologic functions via S-nitrosylation, however the cellular substrates for NO-mediated S-nitrosylation are largely unknown. Here we describe the S-nitrosoproteome using a high-density protein microarray chip containing 16,368 unique human proteins. We identified 834 potentially S-nitrosylated human proteins. Using a unique and highly specific labeling and affinity capture of S-nitrosylated proteins, 138 cysteine residues on 131 peptides in 95 proteins were determined, defining critical sites of NO's actions. Of these cysteine residues 113 are novel sites of S-nitrosylation. A consensus sequence motif from these 834 proteins for S-nitrosylation was identified, suggesting that the residues flanking the S-nitrosylated cysteine are likely to be the critical determinant of whether the cysteine is S-nitrosylated. We identify eight ubiquitin E3 ligases, RNF10, RNF11, RNF41, RNF141, RNF181, RNF208, WWP2, and UBE3A, whose activities are modulated by S-nitrosylation, providing a unique regulatory mechanism of the ubiquitin proteasome system. These results define a new and extensive set of proteins that are susceptible to NO regulation via S-nitrosylation. Similar approaches could be used to identify other post-translational modification proteomes.
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Affiliation(s)
- Yun-Il Lee
- Neuroregeneration Program, Institute for Cell Engineering
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36
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Yang S, Zhang L, Liu M, Chong R, Ding SJ, Chen Y, Dong J. CDK1 phosphorylation of YAP promotes mitotic defects and cell motility and is essential for neoplastic transformation. Cancer Res 2013; 73:6722-33. [PMID: 24101154 DOI: 10.1158/0008-5472.can-13-2049] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Yes-associated protein, YAP, is a downstream effector of the Hippo pathway of cell-cycle control that plays important roles in tumorigenesis. Hippo-mediated phosphorylation YAP, mainly at S127, inactivates YAP function. In this study, we define a mechanism for positive regulation of YAP activity that is critical for its oncogenic function. Specifically, we found that YAP is phosphorylated in vitro and in vivo by the cell-cycle kinase CDK1 at T119, S289, and S367 during the G2-M phase of the cell cycle. We also found that ectopic expression of a phosphomimetic YAP mutant (YAP3D, harboring T119D/S289D/S367D) was sufficient to induce mitotic defects in immortalized epithelial cells, including centrosome amplification, multipolar spindles, and chromosome missegregation. Finally, we documented that mitotic phosphorylation of YAP was sufficient to promote cell migration and invasion in a manner essential for neoplastic cell transformation. In support of our findings, CDK1 inhibitors largely suppressed cell motility mediated by activated YAP-S127A but not the phosphomimetic mutant YAP3D. Collectively, our results reveal a previously unrecognized mechanism for controlling the activity of YAP that is crucial for its oncogenic function mediated by mitotic dysregulation.
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Affiliation(s)
- Shuping Yang
- Authors' Affiliations: Eppley Institute for Research in Cancer and Allied Diseases; Department of Pathology and Microbiology; and Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska
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37
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Paulsen C, Carroll KS. Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery. Chem Rev 2013; 113:4633-79. [PMID: 23514336 PMCID: PMC4303468 DOI: 10.1021/cr300163e] [Citation(s) in RCA: 801] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Candice
E. Paulsen
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
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38
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Kim JS, Dai Z, Aryal UK, Moore RJ, Camp DG, Baker SE, Smith RD, Qian WJ. Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Anal Chem 2013; 85:6826-32. [PMID: 23772796 DOI: 10.1021/ac401000q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A resin-assisted enrichment method has been developed for specific isolation of protein N-terminal peptides to facilitate LC-MS/MS characterization of proteolytic processing, a major form of posttranslational modifications. In this method, protein thiols are blocked by reduction and alkylation, and protein lysine residues are converted to homoarginines. Protein N-termini are selectively converted to reactive thiol groups, and the thiol-containing N-terminal peptides are then captured by a thiol-affinity resin with high specificity (>97%). The efficiencies of these sequential reactions were demonstrated to be nearly quantitative. The resin-assisted N-terminal peptide enrichment approach was initially applied to a cell lysate of the filamentous fungus Aspergillus niger. Subsequent C-MS/MS analyses resulted in the identification of 1672 unique protein N-termini or proteolytic cleavage sites from 690 unique proteins.
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Affiliation(s)
- Jong-Seo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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39
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Qiu H, Jiang JL, Liu M, Huang X, Ding SJ, Wang L. Quantitative phosphoproteomics analysis reveals broad regulatory role of heparan sulfate on endothelial signaling. Mol Cell Proteomics 2013; 12:2160-73. [PMID: 23649490 DOI: 10.1074/mcp.m112.026609] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heparan sulfate (HS) is a linear, abundant, highly sulfated polysaccharide that expresses in the vasculature. Recent genetic studies documented that HS critically modulates various endothelial cell functions. However, elucidation of the underlying molecular mechanism has been challenging because of the presence of a large number of HS-binding ligands found in the examined experimental conditions. In this report, we used quantitative phosphoproteomics to examine the global HS-dependent signaling by comparing wild type and HS-deficient endothelial cells that were cultured in a serum-containing medium. A total of 7222 phosphopeptides, corresponding to 1179 proteins, were identified. Functional correlation analysis identified 25 HS-dependent functional networks, and the top five are related to cell morphology, cellular assembly and organization, cellular function and maintenance, cell-to-cell communication, inflammatory response and disorder, cell growth and proliferation, cell movement, and cellular survival and death. This is consistent with cell function studies showing that HS deficiency altered endothelial cell growth and mobility. Mining for the underlying molecular mechanisms further revealed that HS modulates signaling pathways critically related to cell adhesion, migration, and coagulation, including ILK, integrin, actin cytoskeleton organization, tight junction and thrombin signaling. Intriguingly, this analysis unexpectedly determined that the top HS-dependent signaling is the IGF-1 signaling pathway, which has not been known to be modulated by HS. In-depth analysis of growth factor signaling identified 22 HS-dependent growth factor/cytokine/growth hormone signaling pathways, including those both previously known, such as HGF and VEGF, and those unknown, such as IGF-1, erythropoietin, angiopoietin/Tie, IL-17A and growth hormones. Twelve of the identified 22 growth factor/cytokine/growth hormone signaling pathways, including IGF-1 and angiopoietin/Tie signaling, were alternatively confirmed in phospho-receptor tyrosine kinase array analysis. In summary, our SILAC-based quantitative phosphoproteomic analysis confirmed previous findings and also uncovered novel HS-dependent functional networks and signaling, revealing a much broader regulatory role of HS on endothelial signaling.
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Affiliation(s)
- Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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40
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Su D, Shukla AK, Chen B, Kim JS, Nakayasu E, Qu Y, Aryal U, Weitz K, Clauss TR, Monroe ME, Camp DG, Bigelow DJ, Smith RD, Kulkarni RN, Qian WJ. Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry. Free Radic Biol Med 2013; 57:68-78. [PMID: 23277143 PMCID: PMC3771501 DOI: 10.1016/j.freeradbiomed.2012.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/12/2012] [Accepted: 12/13/2012] [Indexed: 12/18/2022]
Abstract
S-nitrosylation, the formation of S-nitrosothiol (SNO), is an important reversible thiol oxidation event that has been increasingly recognized for its role in cell signaling. Although many proteins susceptible to S-nitrosylation have been reported, site-specific identification of physiologically relevant SNO modifications remains an analytical challenge because of the low abundance and labile nature of this modification. Herein we present further improvement and optimization of the recently reported resin-assisted cysteinyl peptide enrichment protocol for SNO identification and its application to mouse skeletal muscle to identify specific cysteine sites sensitive to S-nitrosylation by a quantitative reactivity profiling strategy. Our results indicate that the protein- and peptide-level enrichment protocols provide comparable specificity and coverage of SNO-peptide identifications. S-nitrosylation reactivity profiling was performed by quantitatively comparing the site-specific SNO modification levels in samples treated with S-nitrosoglutathione, an NO donor, at two different concentrations (i.e., 10 and 100 μM). The reactivity profiling experiments led to the identification of 488 SNO-modified sites from 197 proteins with specificity of ∼95% at the unique peptide level, i.e., ∼95% of enriched peptides contain cysteine residues as the originally SNO-modified sites. Among these sites, 281 from 145 proteins were considered more sensitive to S-nitrosylation based on the ratios of observed SNO levels between the two treatments. These SNO-sensitive sites are more likely to be physiologically relevant. Many of the SNO-sensitive proteins are localized in mitochondria, contractile fiber, and actin cytoskeleton, suggesting the susceptibility of these subcellular compartments to redox regulation. Moreover, these observed SNO-sensitive proteins are primarily involved in metabolic pathways, including the tricarboxylic acid cycle, glycolysis/gluconeogenesis, glutathione metabolism, and fatty acid metabolism, suggesting the importance of redox regulation in muscle metabolism and insulin action.
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Affiliation(s)
- Dian Su
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Anil K. Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Baowei Chen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jong-Seo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yi Qu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Uma Aryal
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Karl Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Therese R.W. Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Diana J. Bigelow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rohit N. Kulkarni
- Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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41
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Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L. neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res 2012. [PMID: 23205526 DOI: 10.1021/pr300830v] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.
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Affiliation(s)
- Pascale Gaudet
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, Faculty of Medicine, University of Geneva, CMU-1, rue Michel Servet 1211 Geneva 4, Switzerland
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42
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Jones AW, Winn PJ, Cooper HJ. The radical ion chemistry of S-nitrosylated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2063-2074. [PMID: 23055078 DOI: 10.1007/s13361-012-0492-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/11/2012] [Accepted: 07/20/2012] [Indexed: 06/01/2023]
Abstract
The radical ion chemistry of a suite of S-nitrosopeptides has been investigated. Doubly and triply-protonated ions of peptides NYCGLPGEYWLGNDK, NYCGLPGEYWLGNDR, NYCGLPGERWLGNDR, NACGAPGEKWAGNDK, NYCGLPGEKYLGNDK, NYGLPGCEKWYGNDK and NYGLPGEKWYGCNDK were subjected to electron capture dissociation (ECD), and collision-induced dissociation (CID). The peptide sequences were selected such that the effect of the site of S-nitrosylation, the nature and position of the basic amino acid residues, and the nature of the other amino acid side chains, could be interrogated. The ECD mass spectra were dominated by a peak corresponding to loss of (•)NO from the charge-reduced precursor, which can be explained by a modified Utah-Washington mechanism. Some backbone fragmentation in which the nitrosyl modification was preserved was also observed in the ECD of some peptides. Molecular dynamics simulations of peptide ion structure suggest that the ECD behavior was dependent on the surface accessibility of the protonated residue. CID of the S-nitrosylated peptides resulted in homolysis of the S-N bond to form a long-lived radical with loss of (•)NO. The radical peptide ions were isolated and subjected to ECD and CID. ECD of the radical peptide ions provided an interesting comparison to ECD of the unmodified peptides. The dominant process was electron capture without further dissociation (ECnoD). CID of the radical peptide ions resulted in cysteine, leucine, and asparagine side chain losses, and radical-induced backbone fragmentation at tryptophan, tyrosine, and asparagine residues, in addition to charge-directed backbone fragmentation.
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Affiliation(s)
- Andrew W Jones
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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43
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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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44
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Protein S-nitrosylation and cancer. Cancer Lett 2012; 320:123-9. [PMID: 22425962 DOI: 10.1016/j.canlet.2012.03.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 11/23/2022]
Abstract
Protein S-nitrosylation is a covalent post-translational modification through coupling of a nitric oxide (NO) moiety with the reactive thiol group of a protein cysteine residue to form an S-nitrosothiol (SNO). S-nitrosylation is a key mechanism in the transmission of NO-based cellular signals in the vital cellular processes, including transcription regulation, DNA repair, and apoptosis. Contemporary research has implicated dysregulation of S-nitrosylation in severe pathological events, including cancer onset, progression, and treatment resistance. The S-nitrosylation status may be directly linked to many cancer therapy outcomes as well as therapeutic-resistance, emphasizing the need to develop S-nitrosylation-related anti-cancer therapeutics. The role of S-nitrosylated proteins in the development and progression of cancer are varied, generating a critical need for a thorough review of the current dynamic research in this area.
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45
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Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry. Top Curr Chem (Cham) 2012; 331:79-116. [DOI: 10.1007/128_2012_384] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Li BQ, Hu LL, Niu S, Cai YD, Chou KC. Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. J Proteomics 2011; 75:1654-65. [PMID: 22178444 DOI: 10.1016/j.jprot.2011.12.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/24/2011] [Accepted: 12/01/2011] [Indexed: 01/20/2023]
Abstract
S-nitrosylation (SNO) is one of the most important and universal post-translational modifications (PTMs) which regulates various cellular functions and signaling events. Identification of the exact S-nitrosylation sites in proteins may facilitate the understanding of the molecular mechanisms and biological function of S-nitrosylation. Unfortunately, traditional experimental approaches used for detecting S-nitrosylation sites are often laborious and time-consuming. However, computational methods could overcome this demerit. In this work, we developed a novel predictor based on nearest neighbor algorithm (NNA) with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). The features of physicochemical/biochemical properties, sequence conservation, residual disorder, amino acid occurrence frequency, second structure and the solvent accessibility were utilized to represent the peptides concerned. Feature analysis showed that the features except residual disorder affected identification of the S-nitrosylation sites. It was also shown via the site-specific feature analysis that the features of sites away from the central cysteine might contribute to the S-nitrosylation site determination through a subtle manner. It is anticipated that our prediction method may become a useful tool for identifying the protein S-nitrosylation sites and that the features analysis described in this paper may provide useful insights for in-depth investigation into the mechanism of S-nitrosylation.
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Affiliation(s)
- Bi-Qing Li
- Key Laboratory of Systems biology, Shanghai Institutes for Biological Science, Chinese Academy of Science, Shanghai 200031, PR China
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47
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Fares A, Rossignol M, Peltier JB. Proteomics investigation of endogenous S-nitrosylation in Arabidopsis. Biochem Biophys Res Commun 2011; 416:331-6. [PMID: 22115780 DOI: 10.1016/j.bbrc.2011.11.036] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 11/08/2011] [Indexed: 01/21/2023]
Abstract
S-Nitrosylation emerges as an important protein modification in many processes. However, most data were obtained at the protein level after addition of a NO donor, particularly in plants where information about the cysteines nitrosylated in these proteins is scarce. An adapted work-flow, combining the classical biotin switch method and labeling with isotope-coded affinity tags (ICAT), is proposed. Without addition of NO donor, a total of 53 endogenous nitrosocysteines was identified in Arabidopsis cells, in proteins belonging to all cell territories, including membranes, and covering a large panel of functions. This first repertoire of nitrosothiols in plants enabled also preliminary structural description. Three apolar motifs, not located in close vicinity of cysteines and accounting for half the dataset, were detected and are proposed to complement nitrosylation prediction algorithms, poorly trained with plant data to date. Analysis of changes induced by a brief salt stress showed that NaCl modified the nitrosylation level of a small proportion of endogenously nitrosylated proteins and did not concern all nitrosothiols in these proteins. The possible role of some NO targets in the response to salt stress was discussed.
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Affiliation(s)
- Abasse Fares
- INRA, UR1199, Laboratoire de Protéomique Fonctionnelle, 34060 Montpellier Cedex, France
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48
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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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49
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Savidge TC. S-nitrosothiol signals in the enteric nervous system: lessons learnt from big brother. Front Neurosci 2011; 5:31. [PMID: 21441985 PMCID: PMC3058138 DOI: 10.3389/fnins.2011.00031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/28/2011] [Indexed: 12/13/2022] Open
Abstract
Nitric oxide (NO) is a functionally important neurotransmitter signaling molecule generated by mammalian and bacterial nitric oxide synthases (NOS), and by chemical conversion of dietary nitrite in the gastrointestinal (GI) tract. Neuronal NOS (nNOS) is the most abundant isoenzyme in the enteric nervous system, and targeted deletion in transgenic mice has clearly demonstrated its importance in normal gut function. Enteric neuropathy is also often associated with abnormal NO production, for example in achalasia and diabetic gastroparesis. Not surprisingly therefore, aberrant nNOS activity is widely implicated in enteric disease, and represents a potential molecular target for therapeutic intervention. One physiological signaling mechanism of NO bioactivity is through chemical reaction with the heme center of guanylyl cyclase, resulting in the conversion of cGMP from GTP. This second messenger nucleotide signal activates cGMP-dependent protein kinases, phosphodiesterases, and ion channels, and is implicated in the neuronal control of GI function. However, few studies in the GI tract have fully related NO bioactivity with specific molecular targets of NO-derived signals. In the central nervous system (CNS), it is now increasingly appreciated that NO bioactivity is often actively transduced via S-nitrosothiol (SNO) signals rather than via activation of guanylyl cyclase. Moreover, aberrant S-nitrosylation of specific molecular targets is implicated in CNS pathology. S-nitrosylation refers to the post-translational modification of a protein cysteine thiol by NO, forming an endogenous SNO. Because cysteine residues are often key regulators of protein function, S-nitrosylation represents a physiologically important signaling mechanism analogous to other post-translational modifications, such as O-phosphorylation. This article provides an overview of how neurotransmitter NO is produced by nNOS as this represents the most prominent and well defined source of SNO production in the enteric nervous system. Further, it provides a perspective of how S-nitrosylation signals derived from multiple diverse sources may potentially transduce NO bioactivity in the GI tract. Possible lessons that might be learnt from the CNS, such as SNO mediated auto-inhibition of nNOS activity and modulation of neuronal cell death, are also explored as these may have pathophysiological relevance in enteric neuropathy. Thus, S-nitrosylation may mediate previously underappreciated NO-derived signals in the enteric nervous system that regulate homeostatic gut functions and disease susceptibility.
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Affiliation(s)
- Tor C Savidge
- Division of Gastroenterology and Hepatology, The University of Texas Medical Branch Galveston, TX, USA
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50
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The SNO-proteome: causation and classifications. Curr Opin Chem Biol 2010; 15:129-36. [PMID: 21087893 DOI: 10.1016/j.cbpa.2010.10.012] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 11/22/2022]
Abstract
Cell signaling is a complex and highly regulated process. Post-translational modifications of proteins serve to sense and transduce cellular signals in a precisely coordinated manner. It is increasingly recognized that protein S-nitrosylation, the addition of a nitric oxide group to cysteine thiols, serves an important role in a wide range of signaling pathways. In spite of the large number of SNO-proteins now identified (∼1000), the observed specificity of S-nitrosylation in terms of target proteins and specific cysteines within modified proteins is incompletely understood. Here we review the progress made in S-nitrosylation detection methods that have facilitated the study of the SNO-proteome under physiological and pathophysiological conditions, and some factors important in determining the SNO-proteome. Classification schemes for emergent denitrosylases and prospective 'protein S-nitrosylases' are provided.
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