1
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Seth P, Hausladen A, Premont RT, Stamler JS. Protocol for preparing Thiopropyl Sepharose resin used for capturing S-nitrosylated proteins. STAR Protoc 2023; 4:102430. [PMID: 37925633 PMCID: PMC10652206 DOI: 10.1016/j.xpro.2023.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/26/2023] [Accepted: 06/12/2023] [Indexed: 11/07/2023] Open
Abstract
S-nitrosothiol (SNO)-Resin Assisted Capture (SNO-RAC) relies on a Thiopropyl Sepharose resin to identify S-nitrosylated proteins (SNO-proteins) and sites of S-nitrosylation. Here, we present a protocol for preparing Thiopropyl Sepharose resin with efficiency of SNO-protein capture comparable to the discontinued commercial version. We describe steps for amine coupling, disulfide reduction, and generation of thiol reactive resin. We then detail quality control procedures. This resin is also suitable for Acyl-RAC assays to capture palmitoylated proteins. For complete details on the use and execution of the SNO-RAC protocol, please refer to Forrester et al.,1 Fonseca et al.,2 and Seth et al.3.
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Affiliation(s)
- Puneet Seth
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard T Premont
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals, Cleveland, OH 44106, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals, Cleveland, OH 44106, USA.
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2
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Wang Z, Li J, Yang Q, Sun X. Global Proteome-Wide Analysis of Cysteine S-Nitrosylation in Toxoplasma gondii. Molecules 2023; 28:7329. [PMID: 37959749 PMCID: PMC10649196 DOI: 10.3390/molecules28217329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Toxoplasma gondii transmits through various routes, rapidly proliferates during acute infection and causes toxoplasmosis, which is an important zoonotic disease in human and veterinary medicine. T. gondii can produce nitric oxide and derivatives, and S-nitrosylation contributes to their signaling transduction and post-translation regulation. To date, the S-nitrosylation proteome of T. gondii remains mystery. In this study, we reported the first S-nitrosylated proteome of T. gondii using mass spectrometry in combination with resin-assisted enrichment. We found that 637 proteins were S-nitrosylated, more than half of which were localized in the nucleus or cytoplasm. Motif analysis identified seven motifs. Of these motifs, five and two contained lysine and isoleucine, respectively. Gene Ontology enrichment revealed that S-nitrosylated proteins were primarily located in the inner membrane of mitochondria and other organelles. These S-nitrosylated proteins participated in diverse biological and metabolic processes, including organic acid binding, carboxylic acid binding ribose and phosphate biosynthesis. T. gondii S-nitrosylated proteins significantly contributed to glycolysis/gluconeogenesis and aminoacyl-tRNA biosynthesis. Moreover, 27 ribosomal proteins and 11 microneme proteins were identified as S-nitrosylated proteins, suggesting that proteins in the ribosome and microneme were predominantly S-nitrosylated. Protein-protein interaction analysis identified three subnetworks with high-relevancy ribosome, RNA transport and chaperonin complex components. These results imply that S-nitrosylated proteins of T. gondii are associated with protein translation in the ribosome, gene transcription, invasion and proliferation of T. gondii. Our research is the first to identify the S-nitrosylated proteomic profile of T. gondii and will provide direction to the ongoing investigation of the functions of S-nitrosylated proteins in T. gondii.
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Affiliation(s)
- Zexiang Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (J.L.); (X.S.)
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3
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Li X, Gluth A, Zhang T, Qian WJ. Thiol redox proteomics: Characterization of thiol-based post-translational modifications. Proteomics 2023; 23:e2200194. [PMID: 37248656 PMCID: PMC10764013 DOI: 10.1002/pmic.202200194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.
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Affiliation(s)
- Xiaolu Li
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Austin Gluth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
- Department of Biological Systems Engineering, Washington State University, Richland, WA 99354
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
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4
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Liu R, Li K, Wu G, Qin M, Yu H, Wu M, Ge Q, Wu S, Bao W, Zhang W. A comparative study of S-nitrosylated myofibrillar proteins between red, firm and non-exudative (RFN) and pale, soft and exudative (PSE) pork by iodoTMT-based proteomics assay. Food Chem 2022; 395:133577. [DOI: 10.1016/j.foodchem.2022.133577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/19/2022]
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5
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Mosqueira M, Scheid LM, Kiemel D, Richardt T, Rheinberger M, Ollech D, Lutge A, Heißenberg T, Pfitzer L, Engelskircher L, Yildiz U, Porth I. nNOS-derived NO modulates force production and iNO-derived NO the excitability in C2C12-derived 3D tissue engineering skeletal muscle via different NO signaling pathways. Front Physiol 2022; 13:946682. [PMID: 36045747 PMCID: PMC9421439 DOI: 10.3389/fphys.2022.946682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022] Open
Abstract
Nitric oxide (NO) is a bioactive gas produced by one of the three NO synthases: neuronal NOS (nNOS), inducible (iNOS), and endothelial NOS (eNOS). NO has a relevant modulatory role in muscle contraction; this takes place through two major signaling pathways: (i) activation of soluble guanylate cyclase and, thus, protein kinase G or (ii) nitrosylation of sulfur groups of cysteine. Although it has been suggested that nNOS-derived NO is the responsible isoform in muscle contraction, the roles of eNOS and iNOS and their signaling pathways have not yet been clarified. To elucidate the action of each pathway, we optimized the generation of myooids, an engineered skeletal muscle tissue based on the C2C12 cell line. In comparison with diaphragm strips from wild-type mice, 180 myooids were analyzed, which expressed all relevant excitation–contraction coupling proteins and both nNOS and iNOS isoforms. Along with the biochemical results, myooids treated with NO donor (SNAP) and unspecific NOS blocker (L-NAME) revealed a comparable NO modulatory effect on force production as was observed in the diaphragm strips. Under the effects of pharmacological tools, we analyzed the myooids in response to electrical stimulation of two possible signaling pathways and NO sources. The nNOS-derived NO exerted its negative effect on force production via the sGG-PKG pathway, while iNOS-derived NO increased the excitability in response to sub-threshold electrical stimulation. These results strengthen the hypotheses of previous reports on the mechanism of action of NO during force production, showed a novel function of iNOS-derived NO, and establish the myooid as a novel and robust alternative model for pathophysiological skeletal muscle research.
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Affiliation(s)
- Matias Mosqueira
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- *Correspondence: Matias Mosqueira,
| | - Lisa-Mareike Scheid
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- PromoCell GmbH, Heidelberg, Germany
| | - Dominik Kiemel
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Talisa Richardt
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Mona Rheinberger
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Dirk Ollech
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Applied Physics Department, Science for Life Laboratory and KTH Royal Technical University, Solna, Sweden
| | - Almut Lutge
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Molecular Life Science at the University of Zürich, Zürich, Switzerland
| | - Tim Heißenberg
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Göttingen, Germany
| | - Lena Pfitzer
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- myNEO NV, Ghent, Belgium
| | - Lisa Engelskircher
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Immatics Biotechnology GmbH, Tübingen, Germany
| | - Umut Yildiz
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Isabel Porth
- Cardio-Ventilatory Muscle Physiology Laboratory, Institute of Physiology and Pathophysiology, Heidelberg University Hospital, Heidelberg, Germany
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, Mannheim, Germany
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6
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Liu R, Yang L, Yang T, Qin M, Li K, Bao W, Wu M, Yu H, Wu S, Ge Q. Effect of nitric oxide treatment on pork meat quality, microstructure, and total bacterial count during postmortem aging. Meat Sci 2022; 190:108806. [DOI: 10.1016/j.meatsci.2022.108806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/14/2022]
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7
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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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8
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Doulias PT, Tenopoulou M, Zakopoulos I, Ischiropoulos H. Organic mercury solid phase chemoselective capture for proteomic identification of S-nitrosated proteins and peptides. Nitric Oxide 2021; 117:1-6. [PMID: 34536587 DOI: 10.1016/j.niox.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/26/2022]
Abstract
Cysteine S-nitrosation mediates NO signaling and protein function under pathophysiological conditions. Herein, we provide a detailed protocol regarding the organic mercury chemoselective enrichment of S-nitrosated proteins and peptides. We discuss key aspects of the enrichment strategy and provide technical tips for the best performance of the experimental protocol.
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Affiliation(s)
- Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Research Institute, 3517 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA; Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, 45110, Greece.
| | - Margarita Tenopoulou
- Children's Hospital of Philadelphia Research Institute, 3517 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA; Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, 45110, Greece
| | - Iordanis Zakopoulos
- Children's Hospital of Philadelphia Research Institute, 3517 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute, 3517 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA.
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9
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Lau B, Fazelinia H, Mohanty I, Raimo S, Tenopoulou M, Doulias PT, Ischiropoulos H. Endogenous S-nitrosocysteine proteomic inventories identify a core of proteins in heart metabolic pathways. Redox Biol 2021; 47:102153. [PMID: 34610554 DOI: 10.1016/j.redox.2021.102153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022] Open
Abstract
Protein cysteine residues are essential for protein folding, participate in enzymatic catalysis, and coordinate the binding of metal ions to proteins. Enzymatically catalyzed and redox-dependent post-translational modifications of cysteine residues are also critical for signal transduction and regulation of protein function and localization. S-nitrosylation, the addition of a nitric oxide equivalent to a cysteine residue, is a redox-dependent modification. In this study, we curated and analyzed four different studies that employed various chemoselective platforms coupled to mass spectrometry to precisely identify S-nitrosocysteine residues in mouse heart proteins. Collectively 1974 S-nitrosocysteine residues in 761 proteins were identified and 33.4% were identified in two or more studies. A core of 75 S-nitrosocysteine residues in 44 proteins were identified in all four studies. Bioinformatic analysis of each study indicated a significant enrichment of mitochondrial proteins participating in metabolism. Regulatory proteins in glycolysis, TCA cycle, oxidative phosphorylation and ATP production, long chain fatty acid β-oxidation, and ketone and amino acid metabolism constitute the major functional pathways impacted by protein S-nitrosylation. In the cardiovascular system, nitric oxide signaling regulates vasodilation and cardiac muscle contractility. The meta-analysis of the proteomic data supports the hypothesis that nitric oxide signaling via protein S-nitrosylation is also a regulator of cardiomyocyte metabolism that coordinates fuel utilization to maximize ATP production. As such, protein cysteine S-nitrosylation represents a third functional dimension of nitric oxide signaling in the cardiovascular system to ensure optimal cardiac function.
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10
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Li X, Day NJ, Feng S, Gaffrey MJ, Lin TD, Paurus VL, Monroe ME, Moore RJ, Yang B, Xian M, Qian WJ. Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress. Redox Biol 2021; 46:102111. [PMID: 34425387 DOI: 10.1016/j.redox.2021.102111] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
Thiol-based post-translational modifications (PTMs) play a key role in redox-dependent regulation and signaling. Functional cysteine (Cys) sites serve as redox switches, regulated through multiple types of PTMs. Herein, we aim to characterize the complexity of thiol PTMs at the proteome level through the establishment of a direct detection workflow. The LC-MS/MS based workflow allows for simultaneous quantification of protein abundances and multiple types of thiol PTMs. To demonstrate its utility, the workflow was applied to mouse pancreatic β-cells (β-TC-6) treated with thapsigargin to induce endoplasmic reticulum (ER) stress. This resulted in the quantification of >9000 proteins and multiple types of thiol PTMs, including intra-peptide disulfide (S–S), S-glutathionylation (SSG), S-sulfinylation (SO2H), S-sulfonylation (SO3H), S-persulfidation (SSH), and S-trisulfidation (SSSH). Proteins with significant changes in abundance were observed to be involved in canonical pathways such as autophagy, unfolded protein response, protein ubiquitination pathway, and EIF2 signaling. Moreover, ~500 Cys sites were observed with one or multiple types of PTMs with SSH and S–S as the predominant types of modifications. In many cases, significant changes in the levels of different PTMs were observed on various enzymes and their active sites, while their protein abundance exhibited little change. These results provide evidence of independent translational and post-translational regulation of enzyme activity. The observed complexity of thiol modifications on the same Cys residues illustrates the challenge in the characterization and interpretation of protein thiol modifications and their functional regulation. Simultaneous quantification of protein abundances and multiple types of thiol PTMs. Multiple types PTMs observed on the same Cys sites for redox-regulated proteins. Data revealed complexity of thiol PTMs and their regulation. Distinctive translational and post-translational regulation under ER stress in β-cells.
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11
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Bago Á, Íñiguez MA, Serrador JM. Nitric Oxide and Electrophilic Cyclopentenone Prostaglandins in Redox signaling, Regulation of Cytoskeleton Dynamics and Intercellular Communication. Front Cell Dev Biol 2021; 9:673973. [PMID: 34026763 PMCID: PMC8137968 DOI: 10.3389/fcell.2021.673973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/01/2021] [Indexed: 12/16/2022] Open
Abstract
Nitric oxide (NO) and electrophilic cyclopentenone prostaglandins (CyPG) are local mediators that modulate cellular response to oxidative stress in different pathophysiological processes. In particular, there is increasing evidence about their functional role during inflammation and immune responses. Although the mechanistic details about their relationship and functional interactions are still far from resolved, NO and CyPG share the ability to promote redox-based post-translational modification (PTM) of proteins that play key roles in cellular homeostasis, signal transduction and transcription. NO-induced S-nitrosylation and S-glutathionylation as well as cyclopentenone-mediated adduct formation, are a few of the main PTMs by which intra- and inter-cellular signaling are regulated. There is a growing body of evidence indicating that actin and actin-binding proteins are susceptible to covalent PTM by these agents. It is well known that the actin cytoskeleton is key for the establishment of interactions among leukocytes, endothelial and muscle cells, enabling cellular activation and migration. In this review we analyze the current knowledge about the actions exerted by NO and CyPG electrophilic lipids on the regulation of actin dynamics and cytoskeleton organization, and discuss some open questions regarding their functional relevance in the regulation of intercellular communication.
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Affiliation(s)
- Ángel Bago
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
| | - Miguel A Íñiguez
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain.,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan M Serrador
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
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12
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Day NJ, Gaffrey MJ, Qian WJ. Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations. Antioxidants (Basel) 2021; 10:499. [PMID: 33807006 DOI: 10.3390/antiox10030499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications regulate the structure and function of proteins that can result in changes to the activity of different pathways. These include modifications altering the redox state of thiol groups on protein cysteine residues, which are sensitive to oxidative environments. While mass spectrometry has advanced the identification of protein thiol modifications and expanded our knowledge of redox-sensitive pathways, the quantitative aspect of this technique is critical for the field of redox proteomics. In this review, we describe how mass spectrometry-based redox proteomics has enabled researchers to accurately quantify the stoichiometry of reversible oxidative modifications on specific cysteine residues of proteins. We will describe advancements in the methodology that allow for the absolute quantitation of thiol modifications, as well as recent reports that have implemented this approach. We will also highlight the significance and application of such measurements and why they are informative for the field of redox biology.
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13
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Rookyard AW, Paulech J, Thyssen S, Liddy KA, Puckeridge M, Li DK, White MY, Cordwell SJ. A Global Profile of Reversible and Irreversible Cysteine Redox Post-Translational Modifications During Myocardial Ischemia/Reperfusion Injury and Antioxidant Intervention. Antioxid Redox Signal 2021; 34:11-31. [PMID: 32729339 DOI: 10.1089/ars.2019.7765] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aims: Cysteine (Cys) is a major target for redox post-translational modifications (PTMs) that occur in response to changes in the cellular redox environment. We describe multiplexed, peptide-based enrichment and quantitative mass spectrometry (MS) applied to globally profile reversible redox Cys PTM in rat hearts during ischemia/reperfusion (I/R) in the presence or absence of an aminothiol antioxidant, N-2-mercaptopropionylglycine (MPG). Parallel fractionation also allowed identification of irreversibly oxidized Cys peptides (Cys-SO2H/SO3H). Results: We identified 4505 reversibly oxidized Cys peptides of which 1372 were significantly regulated by ischemia and/or I/R. An additional 219 peptides (247 sites) contained Cys-SO2H/Cys-SO3H modifications, and these were predominantly identified from hearts subjected to I/R (n = 168 peptides). Parallel reaction monitoring MS (PRM-MS) enabled relative quantitation of 34 irreversibly oxidized Cys peptides. MPG attenuated a large cluster of I/R-associated reversibly oxidized Cys peptides and irreversible Cys oxidation to less than nonischemic controls (n = 24 and 34 peptides, respectively). PRM-MS showed that Cys sites oxidized during ischemia and/or I/R and "protected" by MPG were largely mitochondrial, and were associated with antioxidant functions (peroxiredoxins 5 and 6) and metabolic processes, including glycolysis. Metabolomics revealed I/R induced changes in glycolytic intermediates that were reversed in the presence of MPG, which were consistent with irreversible PTM of triose phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), altered GAPDH enzyme activity, and reduced I/R glycolytic payoff as evidenced by adenosine triphosphate and NADH levels. Innovation: Novel enrichment and PRM-MS approaches developed here enabled large-scale relative quantitation of Cys redox sites modified by reversible and irreversible PTM during I/R and antioxidant remediation. Conclusions: Cys sites identified here are targets of reactive oxygen species that can contribute to protein dysfunction and the pathogenesis of I/R.
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Affiliation(s)
- Alexander W Rookyard
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Jana Paulech
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Stine Thyssen
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Kiersten A Liddy
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Max Puckeridge
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Desmond K Li
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Melanie Y White
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
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14
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Abstract
The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.
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Affiliation(s)
- Tong Zhang
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew J Gaffrey
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Xiaolu Li
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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15
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Zhang T, Gaffrey MJ, Qian W, Thrall BD. Oxidative Stress and Redox Modifications in Nanomaterial–Cellular Interactions. In: Bonner JC, Brown JM, editors. Interaction of Nanomaterials with the Immune System. Cham: Springer International Publishing; 2020. pp. 127-48. [DOI: 10.1007/978-3-030-33962-3_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Ford MM, Smythers AL, McConnell EW, Lowery SC, Kolling DRJ, Hicks LM. Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes. Cells 2019; 8:cells8101171. [PMID: 31569396 PMCID: PMC6829209 DOI: 10.3390/cells8101171] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
The target of rapamycin (TOR) kinase is a master metabolic regulator with roles in nutritional sensing, protein translation, and autophagy. In Chlamydomonas reinhardtii, a unicellular green alga, TOR has been linked to the regulation of increased triacylglycerol (TAG) accumulation, suggesting that TOR or a downstream target(s) is responsible for the elusive “lipid switch” in control of increasing TAG accumulation under nutrient limitation. However, while TOR has been well characterized in mammalian systems, it is still poorly understood in photosynthetic systems, and little work has been done to show the role of oxidative signaling in TOR regulation. In this study, the TOR inhibitor AZD8055 was used to relate reversible thiol oxidation to the physiological changes seen under TOR inhibition, including increased TAG content. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 401 proteins were determined to have significant changes in oxidation following TOR inhibition. These oxidative changes mirrored characterized physiological modifications, supporting the role of reversible thiol oxidation in TOR regulation of TAG production, protein translation, carbohydrate catabolism, and photosynthesis through the use of reversible thiol oxidation. The delineation of redox-controlled proteins under TOR inhibition provides a framework for further characterization of the TOR pathway in photosynthetic eukaryotes.
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Affiliation(s)
- Megan M Ford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Amanda L Smythers
- Department of Chemistry, Marshall University, Huntington, WV 25755, USA.
| | - Evan W McConnell
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Sarah C Lowery
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Gong B, Shi Q. Identifying S-nitrosylated proteins and unraveling S-nitrosoglutathione reductase-modulated sodic alkaline stress tolerance in Solanum lycopersicum L. Plant Physiol Biochem 2019; 142:84-93. [PMID: 31277045 DOI: 10.1016/j.plaphy.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 05/13/2023]
Abstract
S-nitrosylation, regulated by S-nitrosoglutathione reductase (GSNOR), is considered as an important route for nitric oxide (NO)-modulated stress tolerance in plants. However, genetic evidence for the GSNOR-mediated integrated regulation of S-nitrosylation and plant stress response remains elusive until now. In the present study, we used a site-specific nitrosoproteomic approach to identify 334 endogenously S-nitrosylated proteins with 425 S-nitrosylated sites from the wild type (WT) and GSNOR-knockdown (G) tomato plants under both control (C) and sodic alkaline stress (S) conditions. In detail, the results revealed 68, 92, 54 and 56 up-regulated, as well as 10, 36, 14 and 10 down-regulated S-nitrosylated proteins in G-C/WT-C, G-S/WT-S, WT-S/WT-C, and G-S/G-C, which is the first dataset for S-nitrosylated proteins in Solanaceae. These S-nitrosylated proteins are involved in a wide range of various metabolic, cellular and catalytic processes. Based on this data, proteins involving in NO homeostasis control, signaling of Ca2+, ethylene and MAPK, reactive oxygen species (ROS) scavenging, osmotic regulation, as well as energy support pathway have been identified and selected as the key and sensitive targets that were regulated by GSNOR-modulated S-nitrosylation in response to sodic alkaline stress. Taken together, GSNOR is actively involved in the regulation of sodic alkaline stress tolerance by S-nitrosylation. And the present study provided valuable resources and new clues for the study of S-nitrosylation-regulated metabolism in tomato plants.
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Affiliation(s)
- Biao Gong
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, PR China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, PR China
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, PR China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, PR China.
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19
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Wang Y, Liu R, Tian X, Fan X, Shi Y, Zhang W, Hou Q, Zhou G. Comparison of Activity, Expression, and S-Nitrosylation of Calcium Transfer Proteins between Pale, Soft, and Exudative and Red, Firm, and Non-exudative Pork during Post-Mortem Aging. J Agric Food Chem 2019; 67:3242-3248. [PMID: 30807139 DOI: 10.1021/acs.jafc.8b06448] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The research was performed to investigate the difference of activity, expression, and S-nitrosylation of calcium transfer proteins between pale, soft, and exudative (PSE) and red, firm, and non-exudative (RFN) pork. Seven PSE and seven RFN pork longissimus thoracis (LT) muscles were chosen according to pH and L* at 1 h post-mortem and identified by drip loss at 24 h. The nitric oxide synthase (NOS) activity and neuronal nitric oxide synthase (nNOS) expression showed a significant difference between two groups ( p < 0.05). PSE meat had a considerably higher sarcoplasmic calcium concentration compared to RFN meat at 1 h post-mortem aging ( p < 0.05). In PSE meat, the expression of ryanodine receptor 1 (RyR1) and sarcoplasmic reticulum calcium ATPase 1 (SERCA1) was lower than that in RFN meat, while the relative S-nitrosylation level of RyR1 and SERCA1 was higher ( p < 0.05). In addition, a lower activity of SERCA was detected in PSE meat compared to RFN meat ( p < 0.05). Those results indicate that S-nitrosylation of RyR1 and SERCA1 can putatively play a crucial part in regulating calcium homeostasis. A high level of RyR1 and SERCA1 S-nitrosylation can induce the imbalance of calcium in cytoplasm, leading to accelerated pH decline and the development of PSE meat.
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Affiliation(s)
- Yingying Wang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Rui Liu
- College of Food Science and Engineering , Yangzhou University , Yangzhou , Jiangsu 225127 , People's Republic of China
| | - Xiaona Tian
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Xiaoquan Fan
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Yingwu Shi
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Wangang Zhang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Qin Hou
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture, and Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control , Nanjing Agricultural University ; Nanjing , Jiangsu 210095 , People's Republic of China
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20
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Liu R, Lonergan S, Steadham E, Zhou G, Zhang W, Huff-Lonergan E. Effect of nitric oxide on myofibrillar proteins and the susceptibility to calpain-1 proteolysis. Food Chem 2019; 276:63-70. [PMID: 30409642 DOI: 10.1016/j.foodchem.2018.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 12/23/2022]
Abstract
This study was designed to investigate the nature of modification of myofibrillar proteins by nitric oxide (NO) and the extent to which S-nitrosylation alters their susceptibility to calpain-1 proteolysis. Isolated myofibrils from porcine semimembranosus muscle were incubated with the NO donor S-nitrosoglutathione (GSNO) at 0, 20, 50, 250, 1000 µM for 30 min at 37 °C and then incubated with purified calpain-1. GSNO treatment decreased the thiol content of myofibrillar proteins and increased their intensity and amount of S-nitrosylation. GSNO caused the formation of proteins cross-linkage through intermolecular disulfide. More desmin and titin (T2, the degraded fragment of original titin) were degraded by calpain-1 when myofibrils were incubated with 1000 µM GSNO. Incubation with 250 and 1000 µM GSNO suppressed calpain-1-catalyzed cleavage of troponin-T. The data suggest that NO could change the redox state of myofibrillar proteins and subsequently affect the extent of proteolysis by calpain-1 in a protein-dependent manner.
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Affiliation(s)
- Rui Liu
- 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, PR China; College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Steven Lonergan
- Department of Animal Science, Iowa State University, Ames 50011, USA
| | - Edward Steadham
- Department of Animal Science, Iowa State University, Ames 50011, USA
| | - 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, PR 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, PR China.
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Zhang L, Liu R, Cheng Y, Xing L, Zhou G, Zhang W. Effects of protein S-nitrosylation on the glycogen metabolism in postmortem pork. Food Chem 2019; 272:613-618. [DOI: 10.1016/j.foodchem.2018.08.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 01/05/2023]
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24
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Liu R, Fu Q, Lonergan S, Huff-lonergan E, Xing L, Zhang L, Bai Y, Zhou G, Zhang W. Identification of S-nitrosylated proteins in postmortem pork muscle using modified biotin switch method coupled with isobaric tags. Meat Sci 2018; 145:431-9. [DOI: 10.1016/j.meatsci.2018.07.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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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25
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Liu R, Warner RD, Zhou G, Zhang W. Contribution of nitric oxide and protein S-nitrosylation to variation in fresh meat quality. Meat Sci 2018; 144:135-48. [DOI: 10.1016/j.meatsci.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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26
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Habich M, Salscheider SL, Riemer J. Cysteine residues in mitochondrial intermembrane space proteins: more than just import. Br J Pharmacol 2018; 176:514-531. [PMID: 30129023 DOI: 10.1111/bph.14480] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/20/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
The intermembrane space (IMS) is a very small mitochondrial sub-compartment with critical relevance for many cellular processes. IMS proteins fulfil important functions in transport of proteins, lipids, metabolites and metal ions, in signalling, in metabolism and in defining the mitochondrial ultrastructure. Our understanding of the IMS proteome has become increasingly refined although we still lack information on the identity and function of many of its proteins. One characteristic of many IMS proteins are conserved cysteines. Different post-translational modifications of these cysteine residues can have critical roles in protein function, localization and/or stability. The close localization to different ROS-producing enzyme systems, a dedicated machinery for oxidative protein folding, and a unique equipment with antioxidative systems, render the careful balancing of the redox and modification states of the cysteine residues, a major challenge in the IMS. In this review, we discuss different functions of human IMS proteins, the involvement of cysteine residues in these functions, the consequences of cysteine modifications and the consequences of cysteine mutations or defects in the machinery for disulfide bond formation in terms of human health. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
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Affiliation(s)
- Markus Habich
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Silja Lucia Salscheider
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
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27
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Zhang C, Liu R, Wang A, Kang D, Zhou G, Zhang W. Regulation of calpain-1 activity and protein proteolysis by protein nitrosylation in postmortem beef. Meat Sci 2018; 141:44-49. [DOI: 10.1016/j.meatsci.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 01/29/2023]
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28
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McConnell EW, Werth EG, Hicks LM. The phosphorylated redox proteome of Chlamydomonas reinhardtii: Revealing novel means for regulation of protein structure and function. Redox Biol 2018; 17:35-46. [PMID: 29673699 PMCID: PMC6006682 DOI: 10.1016/j.redox.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Post-translational modifications (PTMs) are covalent modifications to protein residues which may alter both conformation and activity, thereby modulating signaling and metabolic processes. While PTMs have been largely investigated independently, examination into how different modification interact, or crosstalk, will reveal a more complete understanding of the reciprocity of signaling cascades across numerous pathways. Combinatorial reversible thiol oxidation and phosphorylation in eukaryotes is largely recognized, but rigorous approaches for experimental discovery are underdeveloped. To begin meaningful interrogation of PTM crosstalk in systems biology research, knowledge of targeted proteins must be advanced. Herein, we demonstrate protein-level enrichment of reversibly oxidized proteoforms in Chlamydomonas reinhardtii with subsequent phosphopeptide analysis to determine the extent of phosphorylation in the redox thiol proteome. Label-free quantification was used to quantify 3353 oxidized Cys-sites on 1457 enriched proteins, where sequential phosphopeptide enrichment measured 1094 sites of phosphorylation on 720 proteins with 23% (172 proteins) also identified as reversibly oxidized. Proteins identified with both reversible oxidation and phosphorylation were involved in signaling transduction, ribosome and translation-related machinery, and metabolic pathways. Several redox-modified Calvin-Benson cycle proteins were found phosphorylated and many kinases/phosphatases involved in phosphorylation-dependent photosynthetic state transition and stress-response pathways had sites of reversible oxidation. Identification of redox proteins serves as a crucial element in understanding stress response in photosynthetic organisms and beyond, whereby knowing the ensemble of modifications co-occurring with oxidation highlights novel mechanisms for cellular control. Quantified reversible oxidation on protein cysteine residues. Sequential phosphopeptide enrichment to define the phosphorylated redox proteome. Found >3000 oxidized cysteines and >1000 phosphosites in Chlamydomonas reinhardtii. Co-modified proteins discovered across diverse metabolic and signaling pathways.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Wolhuter K, Eaton P. How widespread is stable protein S-nitrosylation as an end-effector of protein regulation? Free Radic Biol Med 2017; 109:156-166. [PMID: 28189849 DOI: 10.1016/j.freeradbiomed.2017.02.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/26/2017] [Accepted: 02/05/2017] [Indexed: 12/13/2022]
Abstract
Over the last 25 years protein S-nitrosylation, also known more correctly as S-nitrosation, has been progressively implicated in virtually every nitric oxide-regulated process within the cardiovascular system. The current, widely-held paradigm is that S-nitrosylation plays an equivalent role as phosphorylation, providing a stable and controllable post-translational modification that directly regulates end-effector target proteins to elicit biological responses. However, this concept largely ignores the intrinsic instability of the nitrosothiol bond, which rapidly reacts with typically abundant thiol-containing molecules to generate more stable disulfide bonds. These protein disulfides, formed via a nitrosothiol intermediate redox state, are rationally anticipated to be the predominant end-effector modification that mediates functional alterations when cells encounter nitrosative stimuli. In this review we present evidence and explain our reasoning for arriving at this conclusion that may be controversial to some researchers in the field.
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Affiliation(s)
- Kathryn Wolhuter
- King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital, London SE1 7EH, UK
| | - Philip Eaton
- King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital, London SE1 7EH, UK.
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30
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Xu Q, Huff LP, Fujii M, Griendling KK. Redox regulation of the actin cytoskeleton and its role in the vascular system. Free Radic Biol Med 2017; 109:84-107. [PMID: 28285002 PMCID: PMC5497502 DOI: 10.1016/j.freeradbiomed.2017.03.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/17/2017] [Accepted: 03/06/2017] [Indexed: 12/17/2022]
Abstract
The actin cytoskeleton is critical for form and function of vascular cells, serving mechanical, organizational and signaling roles. Because many cytoskeletal proteins are sensitive to reactive oxygen species, redox regulation has emerged as a pivotal modulator of the actin cytoskeleton and its associated proteins. Here, we summarize work implicating oxidants in altering actin cytoskeletal proteins and focus on how these alterations affect cell migration, proliferation and contraction of vascular cells. Finally, we discuss the role of oxidative modification of the actin cytoskeleton in vivo and highlight its importance for vascular diseases.
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Affiliation(s)
- Qian Xu
- Division of Cardiology, Department of Medicine, Emory University, 101 Woodruff Circle, 308a WMB, Atlanta, GA 30322, United States; Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Lauren P Huff
- Division of Cardiology, Department of Medicine, Emory University, 101 Woodruff Circle, 308a WMB, Atlanta, GA 30322, United States
| | - Masakazu Fujii
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Japan
| | - Kathy K Griendling
- Division of Cardiology, Department of Medicine, Emory University, 101 Woodruff Circle, 308a WMB, Atlanta, GA 30322, United States.
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31
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Duan J, Gaffrey MJ, Qian WJ. Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines. Mol Biosyst 2017; 13:816-829. [PMID: 28357434 PMCID: PMC5493446 DOI: 10.1039/c6mb00861e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein thiols play a crucial role in redox signaling, in the regulation of enzymatic activity and protein function, and in maintaining redox homeostasis in living systems. The unique chemical reactivity of the thiol group makes protein cysteines susceptible to reactions with reactive oxygen and nitrogen species that form various reversible and irreversible post-translational modifications (PTMs). The reversible PTMs in particular are major components of redox signaling and are involved in the regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in both healthy and disease states has been increasingly recognized. Herein, we review recent advances in quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including general considerations of sample processing, chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for specific biological applications. Although technical limitations remain, redox proteomics is paving the way to a better understanding of redox signaling and regulation in both healthy and disease states.
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Affiliation(s)
- Jicheng Duan
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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32
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Abstract
SIGNIFICANCE Reactive oxygen species are produced during normal metabolism in cells, and their excesses have been implicated in protein damage and toxicity, as well as in the activation of signaling events. In particular, hydrogen peroxide participates in the regulation of different physiological processes as well as in the induction of antioxidant cascades, and often the redox molecular events triggering these pathways are based on reversible cysteine (Cys) oxidation. Recent Advances: Increases in peroxides can cause the accumulation of reversible Cys oxidations in proteomes, which may be either protecting thiols from irreversible oxidations or may just be reporters of future toxicity. It is also becoming clear, however, that only a few proteins, such as the bacterial OxyR or peroxidases, can suffer direct oxidation of their Cys residues by hydrogen peroxide and, therefore, may be the only true sensors initiating signaling events. CRITICAL ISSUES We will in this study describe some of the methodologies used to characterize at the proteome level reversible thiol oxidations, specifically those combining gel-free approaches with mass spectrometry. In the second part of this review, we will summarize some of the electrophoretic and proteomic techniques used to monitor Cys oxidation at the protein level, needed to confirm that a protein contains redox Cys involved in signaling relays, using as examples some of the best characterized redox sensors such as bacterial OxyR or yeast Tpx1/Pap1. FUTURE DIRECTIONS While Cys oxidations are often detected in proteomes and in specific proteins, major efforts have to be made to establish that they are physiologically relevant. Antioxid. Redox Signal. 26, 329-344.
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Affiliation(s)
- Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona, Spain
| | - Alba Domènech
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona, Spain
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Dutka TL, Mollica JP, Lamboley CR, Weerakkody VC, Greening DW, Posterino GS, Murphy RM, Lamb GD. S-nitrosylation and S-glutathionylation of Cys134 on troponin I have opposing competitive actions on Ca2+ sensitivity in rat fast-twitch muscle fibers. Am J Physiol Cell Physiol 2017; 312:C316-C327. [DOI: 10.1152/ajpcell.00334.2016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 11/22/2022]
Abstract
Nitric oxide is generated in skeletal muscle with activity and decreases Ca2+ sensitivity of the contractile apparatus, putatively by S-nitrosylation of an unidentified protein. We investigated the mechanistic basis of this effect and its relationship to the oxidation-induced increase in Ca2+ sensitivity in mammalian fast-twitch (FT) fibers mediated by S-glutathionylation of Cys134 on fast troponin I (TnIf). Force-[Ca2+] characteristics of the contractile apparatus in mechanically skinned fibers were assessed by direct activation with heavily Ca2+-buffered solutions. Treatment with S-nitrosylating agents, S-nitrosoglutathione (GSNO) or S-nitroso- N-acetyl-penicillamine (SNAP), decreased pCa50 ( = −log10 [Ca2+] at half-maximal activation) by ~−0.07 pCa units in rat and human FT fibers without affecting maximum force, but had no effect on rat and human slow-twitch fibers or toad or chicken FT fibers, which all lack Cys134. The Ca2+ sensitivity decrease was 1) fully reversed with dithiothreitol or reduced glutathione, 2) at least partially reversed with ascorbate, indicative of involvement of S-nitrosylation, and 3) irreversibly blocked by low concentration of the alkylating agent, N-ethylmaleimide (NEM). The biotin-switch assay showed that both GSNO and SNAP treatments caused S-nitrosylation of TnIf. S-glutathionylation pretreatment blocked the effects of S-nitrosylation on Ca2+ sensitivity, and vice-versa. S-nitrosylation pretreatment prevented NEM from irreversibly blocking S-glutathionylation of TnIf and its effects on Ca2+ sensitivity, and likewise S-glutathionylation pretreatment prevented NEM block of S-nitrosylation. Following substitution of TnIf into rat slow-twitch fibers, S-nitrosylation treatment caused decreased Ca2+ sensitivity. These findings demonstrate that S-nitrosylation and S-glutathionylation exert opposing effects on Ca2+ sensitivity in mammalian FT muscle fibers, mediated by competitive actions on Cys134 of TnIf.
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Affiliation(s)
- T. L. Dutka
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - J. P. Mollica
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - C. R. Lamboley
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Institute of Sport, Exercise and Active Living (ISEAL), Victoria University, Melbourne, Victoria, Australia; and
| | - V. C. Weerakkody
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - D. W. Greening
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - G. S. Posterino
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - R. M. Murphy
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - G. D. Lamb
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
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35
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Abstract
S-nitrosylation is the covalent attachment of nitric oxide radical to the thiol side chain of cysteine. The death receptor Fas/CD95 can be S-nitrosylated in cancer cell lines by NO donors or iNOS activation. This posttranslational modification (PTM) induces Fas aggregation into lipid rafts and enhances FasL-mediated signaling and apoptosis. In this report, we describe the detection of Fas S-nitrosylation by the most commonly used method, the biotin switch assay (BSA) technique, that allows the detection of this very labile covalent modification in cells or tissues. Briefly, this technique relies on the ability of ascorbate to reduce the covalent bond between the NO radical and the protein, allowing the exchange of the NO radical with a thiol reactive biotin-HPDP. The biotinylated proteins are then easily purified by using NeutrAvidin resin, separated by SDS-PAGE resolution and analyzed by Western blotting.
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36
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Hasan MM, Guo D, Kurata H. Computational identification of protein S-sulfenylation sites by incorporating the multiple sequence features information. Mol BioSyst 2017; 13:2545-2550. [DOI: 10.1039/c7mb00491e] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cysteine S-sulfenylation is a major type of posttranslational modification that contributes to protein structure and function regulation in many cellular processes.
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Affiliation(s)
- Md. Mehedi Hasan
- Department of Bioscience and Bioinformatics
- Kyushu Institute of Technology
- Iizuka
- Japan
| | - Dianjing Guo
- School of Life Sciences and the State Key Lab of Agrobiotechnology
- The Chinese University of Hong Kong
- Shatin
- Hong Kong
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics
- Kyushu Institute of Technology
- Iizuka
- Japan
- Biomedical Informatics R&D Center
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37
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Fuseler JW, Valarmathi MT. Nitric Oxide Modulates Postnatal Bone Marrow-Derived Mesenchymal Stem Cell Migration. Front Cell Dev Biol 2016; 4:133. [PMID: 27933292 PMCID: PMC5122209 DOI: 10.3389/fcell.2016.00133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/01/2016] [Indexed: 01/06/2023] Open
Abstract
Nitric oxide (NO) is a small free-radical gas molecule, which is highly diffusible and can activate a wide range of downstream effectors, with rapid and widespread cellular effects. NO is a versatile signaling mediator with a plethora of cellular functions. For example, NO has been shown to regulate actin, the microfilament, dependent cellular functions, and also acts as a putative stem cell differentiation-inducing agent. In this study, using a wound-healing model of cellular migration, we have explored the effect of exogenous NO on the kinetics of movement and morphological changes in postnatal bone marrow-derived mesenchymal stem cells (MSCs). Cellular migration kinetics and morphological changes of the migrating MSCs were measured in the presence of an NO donor (S-Nitroso-N-Acetyl-D,L-Penicillamine, SNAP), especially, to track the dynamics of single-cell responses. Two experimental conditions were assessed, in which SNAP (200 μM) was applied to the MSCs. In the first experimental group (SN-1), SNAP was applied immediately following wound formation, and migration kinetics were determined for 24 h. In the second experimental group (SN-2), MSCs were pretreated for 7 days with SNAP prior to wound formation and the determination of migration kinetics. The generated displacement curves were further analyzed by non-linear regression analysis. The migration displacement of the controls and NO treated MSCs (SN-1 and SN-2) was best described by a two parameter exponential functions expressing difference constant coefficients. Additionally, changes in the fractal dimension (D) of migrating MSCs were correlated with their displacement kinetics for all the three groups. Overall, these data suggest that NO may evidently function as a stop migration signal by disordering the cytoskeletal elements required for cell movement and proliferation of MSCs.
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Affiliation(s)
- John W Fuseler
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina Columbia, SC, USA
| | - Mani T Valarmathi
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign Urbana, IL, USA
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38
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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39
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Wilson C, Terman JR, González-Billault C, Ahmed G. Actin filaments-A target for redox regulation. Cytoskeleton (Hoboken) 2016; 73:577-595. [PMID: 27309342 DOI: 10.1002/cm.21315] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022]
Abstract
Actin and its ability to polymerize into dynamic filaments is critical for the form and function of cells throughout the body. While multiple proteins have been characterized as affecting actin dynamics through noncovalent means, actin and its protein regulators are also susceptible to covalent modifications of their amino acid residues. In this regard, oxidation-reduction (Redox) intermediates have emerged as key modulators of the actin cytoskeleton with multiple different effects on cellular form and function. Here, we review work implicating Redox intermediates in post-translationally altering actin and discuss what is known regarding how these alterations affect the properties of actin. We also focus on two of the best characterized enzymatic sources of these Redox intermediates-the NADPH oxidase NOX and the flavoprotein monooxygenase MICAL-and detail how they have both been identified as altering actin, but share little similarity and employ different means to regulate actin dynamics. Finally, we discuss the role of these enzymes and redox signaling in regulating the actin cytoskeleton in vivo and highlight their importance for neuronal form and function in health and disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Carlos Wilson
- Department of Biology, Faculty of Sciences, Universidad De Chile, Las Palmeras 3425, Santiago, 7800024, Chile.,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Jonathan R Terman
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390. .,Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.
| | - Christian González-Billault
- Department of Biology, Faculty of Sciences, Universidad De Chile, Las Palmeras 3425, Santiago, 7800024, Chile. .,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile. .,The Buck Institute for Research on Aging, Novato, California 94945.
| | - Giasuddin Ahmed
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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40
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Gu L, Robinson RAS. High-throughput endogenous measurement of S-nitrosylation in Alzheimer's disease using oxidized cysteine-selective cPILOT. Analyst 2016; 141:3904-15. [PMID: 27152368 DOI: 10.1039/c6an00417b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible cysteine modifications play important physiological roles such as modulating enzymatic catalysis, maintaining redox homeostasis and conducting cellular signaling. These roles can be critical in the context of disease. Oxidative modifications such as S-nitrosylation (SNO) are signatures of neurodestruction in conditions of oxidative stress however are also indicators of neuroprotection and normal signaling in cellular environments with low concentrations of reactive oxygen and nitrogen species. SNO is a dynamic and low abundance modification and requires sensitive and selective analytical methods for its detection in biological tissues. Here we present an enhanced multiplexing strategy to study SNO in complex mixtures arising from tissues. This method, termed oxidized cysteine-selective cPILOT (OxcyscPILOT), allows simultaneous analysis of SNO-modified peptides in 12 samples. OxcyscPILOT has three primary steps: (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing SNO on a solid phase resin, and (3) isotopic labeling and isobaric tagging of enriched peptides on the solid phase resin. This approach offers the advantage of allowing total protein abundance levels to be measured simultaneously with endogenous SNO levels and measurement of SNO levels across four biological replicates in a single analysis. Furthermore, the relative amount of SNO on a specific cysteine site can also be determined. A well-known model of Alzheimer's disease, the APP/PS-1 transgenic mouse model, was selected for demonstration of the method as several SNO-modified proteins have previously been reported in brain and synaptosomes from AD subjects. OxcyscPILOT analysis resulted in identification of 138 SNO-modified cysteines in brain homogenates that correspond to 135 proteins. Many of these SNO-modified proteins were only present in wild-type or AD mice, whereas 93 proteins had SNO signals in both WT and AD. Pathway analysis links SNO-modified proteins to various biological pathways especially metabolism and signal transduction, consistent with previous reports in the literature. The OxcyscPILOT strategy provides enhanced multiplexing capability to current redox proteomics methods to study oxidative modifications of cysteine.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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41
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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. Biochim Biophys Acta 2016; 1864:952-66. [PMID: 26861774 DOI: 10.1016/j.bbapap.2016.02.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Duan J, Kodali VK, Gaffrey MJ, Guo J, Chu RK, Camp DG, Smith RD, Thrall BD, Qian WJ. Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function during Nanoparticle-Induced Oxidative Stress. ACS Nano 2016; 10:524-38. [PMID: 26700264 PMCID: PMC4762218 DOI: 10.1021/acsnano.5b05524] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Engineered nanoparticles (ENPs) are increasingly utilized for commercial and medical applications; thus, understanding their potential adverse effects is an important societal issue. Herein, we investigated protein S-glutathionylation (SSG) as an underlying regulatory mechanism by which ENPs may alter macrophage innate immune functions, using a quantitative redox proteomics approach for site-specific measurement of SSG modifications. Three high-volume production ENPs (SiO2, Fe3O4, and CoO) were selected as representatives which induce low, moderate, and high propensity, respectively, to stimulate cellular reactive oxygen species (ROS) and disrupt macrophage function. The SSG modifications identified highlighted a broad set of redox sensitive proteins and specific Cys residues which correlated well with the overall level of cellular redox stress and impairment of macrophage phagocytic function (CoO > Fe3O4 ≫ SiO2). Moreover, our data revealed pathway-specific differences in susceptibility to SSG between ENPs which induce moderate versus high levels of ROS. Pathways regulating protein translation and protein stability indicative of ER stress responses and proteins involved in phagocytosis were among the most sensitive to SSG in response to ENPs that induce subcytoxic levels of redox stress. At higher levels of redox stress, the pattern of SSG modifications displayed reduced specificity and a broader set pathways involving classical stress responses and mitochondrial energetics (e.g., glycolysis) associated with apoptotic mechanisms. An important role for SSG in regulation of macrophage innate immune function was also confirmed by RNA silencing of glutaredoxin, a major enzyme which reverses SSG modifications. Our results provide unique insights into the protein signatures and pathways that serve as ROS sensors and may facilitate cellular adaption to ENPs, versus intracellular targets of ENP-induced oxidative stress that are linked to irreversible cell outcomes.
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Affiliation(s)
- Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vamsi K. Kodali
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew J. Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jia Guo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian D. Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Corresponding Authors: .
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Corresponding Authors: .
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Gu L, Robinson RAS. A simple isotopic labeling method to study cysteine oxidation in Alzheimer's disease: oxidized cysteine-selective dimethylation (OxcysDML). Anal Bioanal Chem 2016; 408:2993-3004. [PMID: 26800981 DOI: 10.1007/s00216-016-9307-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 02/01/2023]
Abstract
Cysteine is widely involved in redox signaling pathways through a number of reversible and irreversible modifications. Reversible modifications (e.g., S-glutathionylation, S-nitrosylation, disulfide bonds, and sulfenic acid) are used to protect proteins from oxidative attack and maintain cellular homeostasis, while irreversible oxidations (e.g., sulfinic acid and sulfonic acid) serve as hallmarks of oxidative stress. Proteomic analysis of cysteine-enriched peptides coupled with reduction of oxidized thiols can be used to measure the oxidation states of cysteine, which is helpful for elucidating the role that oxidative stress plays in biology and disease. As an extension of our previously reported cysDML method, we have developed oxidized cysteine-selective dimethylation (OxcysDML), to investigate the site-specific total oxidation of cysteine residues in biologically relevant samples. OxcysDML employs (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing reversibly oxidized cysteine by a solid phase resin, and (3) isotopic labeling of peptide amino groups to quantify cysteine modifications arising from different biological conditions. On-resin enrichment and labeling minimizes sample handing time and improves efficiency in comparison with other redox proteomic methods. OxcysDML is also inexpensive and flexible, as it can accommodate the exploration of various cysteine modifications. Here, we applied the method to liver tissues from a late-stage Alzheimer's disease (AD) mouse model and wild-type (WT) controls. Because we have previously characterized this proteome using the cysDML approach, we are able here to probe deeper into the redox status of cysteine in AD. OxcysDML identified 1129 cysteine sites (from 527 proteins), among which 828 cysteine sites underwent oxidative modifications. Nineteen oxidized cysteine sites had significant alteration levels in AD and represent proteins involved in metabolic processes. Overall, we have demonstrated OxcysDML as a simple, rapid, robust, and inexpensive redox proteomic approach that is useful for gaining deeper insight into the proteome of AD.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA.
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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: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Figueiredo-Freitas C, Dulce RA, Foster MW, Liang J, Yamashita AMS, Lima-Rosa FL, Thompson JW, Moseley MA, Hare JM, Nogueira L, Sorenson MM, Pinto JR. S-Nitrosylation of Sarcomeric Proteins Depresses Myofilament Ca2+)Sensitivity in Intact Cardiomyocytes. Antioxid Redox Signal 2015; 23:1017-34. [PMID: 26421519 PMCID: PMC4649751 DOI: 10.1089/ars.2015.6275] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AIMS The heart responds to physiological and pathophysiological stress factors by increasing its production of nitric oxide (NO), which reacts with intracellular glutathione to form S-nitrosoglutathione (GSNO), a protein S-nitrosylating agent. Although S-nitrosylation protects some cardiac proteins against oxidative stress, direct effects on myofilament performance are unknown. We hypothesize that S-nitrosylation of sarcomeric proteins will modulate the performance of cardiac myofilaments. RESULTS Incubation of intact mouse cardiomyocytes with S-nitrosocysteine (CysNO, a cell-permeable low-molecular-weight nitrosothiol) significantly decreased myofilament Ca(2+) sensitivity. In demembranated (skinned) fibers, S-nitrosylation with 1 μM GSNO also decreased Ca(2+) sensitivity of contraction and 10 μM reduced maximal isometric force, while inhibition of relaxation and myofibrillar ATPase required higher concentrations (≥ 100 μM). Reducing S-nitrosylation with ascorbate partially reversed the effects on Ca(2+) sensitivity and ATPase activity. In live cardiomyocytes treated with CysNO, resin-assisted capture of S-nitrosylated protein thiols was combined with label-free liquid chromatography-tandem mass spectrometry to quantify S-nitrosylation and determine the susceptible cysteine sites on myosin, actin, myosin-binding protein C, troponin C and I, tropomyosin, and titin. The ability of sarcomere proteins to form S-NO from 10-500 μM CysNO in intact cardiomyocytes was further determined by immunoblot, with actin, myosin, myosin-binding protein C, and troponin C being the more susceptible sarcomeric proteins. INNOVATION AND CONCLUSIONS Thus, specific physiological effects are associated with S-nitrosylation of a limited number of cysteine residues in sarcomeric proteins, which also offer potential targets for interventions in pathophysiological situations.
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Affiliation(s)
- Cícero Figueiredo-Freitas
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University , Tallahassee, Florida.,2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil .,3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
| | - Raul A Dulce
- 4 Interdisciplinary Stem Cell Institute, University of Miami , Miami, Florida
| | - Matthew W Foster
- 5 Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center , Durham, North Carolina.,6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - Jingsheng Liang
- 3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
| | - Aline M S Yamashita
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - Frederico L Lima-Rosa
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - J Will Thompson
- 6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - M Arthur Moseley
- 6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - Joshua M Hare
- 4 Interdisciplinary Stem Cell Institute, University of Miami , Miami, Florida
| | - Leonardo Nogueira
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - Martha M Sorenson
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - José Renato Pinto
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University , Tallahassee, Florida.,3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
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Abstract
Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO(2)H), S-sulfonylation (-SO(3)H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications.
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Affiliation(s)
- Jing Yang
- From the ‡National Center for Protein Sciences · Beijing, Beijing, 102206, China; §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China;
| | - Kate S Carroll
- ¶Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
| | - Daniel C Liebler
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Wojdyla K, Rogowska-Wrzesinska A. Differential alkylation-based redox proteomics--Lessons learnt. Redox Biol 2015; 6:240-52. [PMID: 26282677 DOI: 10.1016/j.redox.2015.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023] Open
Abstract
Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms.
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Abstract
Cancer cells are characterized by higher levels of intracellular reactive oxygen species (ROS) due to metabolic aberrations. ROS are widely accepted as second messengers triggering pivotal signaling pathways involved in the process of cell metabolism, cell cycle, apoptosis, and autophagy. However, the underlying cellular mechanisms remain largely unknown. Recently, accumulating evidence has demonstrated that ROS initiate redox signaling through direct oxidative modification of the cysteines of key redox-sensitive proteins (termed redox sensors). Uncovering the functional changes underlying redox regulation of redox sensors is urgently required, and the role of different redox sensors in distinct disease states still remains to be identified. To assist this, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for cancer treatment. Highlighted here are recent advances in redox proteomics approaches and their applications in identifying redox sensors involved in tumor development.
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Affiliation(s)
- Jingwen Jiang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
| | - Kui Wang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- c 3 Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Tao Zhang
- d 4 School of Biomedical Sciences, Chengdu Medical College, Chengdu 610500, PR China
| | - Canhua Huang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
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49
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Yang J, Gupta V, Tallman KA, Porter NA, Carroll KS, Liebler DC. Global, in situ, site-specific analysis of protein S-sulfenylation. Nat Protoc 2015; 10:1022-37. [PMID: 26086405 DOI: 10.1038/nprot.2015.062] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein S-sulfenylation is the reversible oxidative modification of cysteine thiol groups to form cysteine S-sulfenic acids. Mapping the specific sites of protein S-sulfenylation onto complex proteomes is crucial to understanding the molecular mechanisms controlling redox signaling and regulation. This protocol describes global, in situ, site-specific analysis of protein S-sulfenylation using sulfenic acid-specific chemical probes and mass spectrometry (MS)-based proteomics. The major steps in this protocol are as follows: (i) optimization of conditions for selective labeling of cysteine S-sulfenic acids in intact cells with the commercially available dimedone-based probe, DYn-2; (ii) tagging the modified cysteines with a functionalized biotin reagent containing a cleavable linker via Cu(I)-catalyzed azide-alkyne cycloaddition reaction; (iii) enrichment of the biotin-tagged tryptic peptides with streptavidin; (iv) liquid chromatography-tandem MS (LC-MS/MS)-based shotgun proteomics; and (v) computational data analysis. We also outline strategies for quantitative analysis of this modification in cells responding to redox perturbations and discuss special issues pertaining to experimental design of thiol redox studies. Our chemoproteomic platform should be broadly applicable to the investigation of other bio-orthogonal chemically engineered post-translational modifications. The entire analysis protocol takes ∼1 week to complete.
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50
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. J Am Soc Mass Spectrom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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