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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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2
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Ujcikova H, Lee YS, Roubalova L, Svoboda P. The impact of multifunctional enkephalin analogs and morphine on the protein changes in crude membrane fractions isolated from the rat brain cortex and hippocampus. Peptides 2024; 174:171165. [PMID: 38307418 DOI: 10.1016/j.peptides.2024.171165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Endogenous opioid peptides serve as potent analgesics through the opioid receptor (OR) activation. However, they often suffer from poor metabolic stability, low lipophilicity, and low blood-brain barrier permeability. Researchers have developed many strategies to overcome the drawbacks of current pain medications and unwanted biological effects produced by the interaction with opioid receptors. Here, we tested multifunctional enkephalin analogs LYS739 (MOR/DOR agonist and KOR partial antagonist) and LYS744 (MOR/DOR agonist and KOR full antagonist) under in vivo conditions in comparison with MOR agonist, morphine. We applied 2D electrophoretic resolution to investigate differences in proteome profiles of crude membrane (CM) fractions isolated from the rat brain cortex and hippocampus exposed to the drugs (10 mg/kg, seven days). Our results have shown that treatment with analog LYS739 induced the most protein changes in cortical and hippocampal samples. The identified proteins were mainly associated with energy metabolism, cell shape and movement, apoptosis, protein folding, regulation of redox homeostasis, and signal transduction. Among these, the isoform of mitochondrial ATP synthase subunit beta (ATP5F1B) was the only protein upregulation in the hippocampus but not in the brain cortex. Contrarily, the administration of analog LYS744 caused a small number of protein alterations in both brain parts. Our results indicate that the KOR full antagonism, together with MOR/DOR agonism of multifunctional opioid ligands, can be beneficial in treating chronic pain states by reducing changes in protein expression levels but retaining analgesic efficacy.
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Affiliation(s)
- Hana Ujcikova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic.
| | - Yeon Sun Lee
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
| | - Lenka Roubalova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic
| | - Petr Svoboda
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic
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3
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Wei H, Weaver YM, Yang C, Zhang Y, Hu G, Karner CM, Sieber M, DeBerardinis RJ, Weaver BP. Proteolytic activation of fatty acid synthase signals pan-stress resolution. Nat Metab 2024; 6:113-126. [PMID: 38167727 PMCID: PMC10822777 DOI: 10.1038/s42255-023-00939-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Chronic stress and inflammation are both outcomes and major drivers of many human diseases. Sustained responsiveness despite mitigation suggests a failure to sense resolution of the stressor. Here we show that a proteolytic cleavage event of fatty acid synthase (FASN) activates a global cue for stress resolution in Caenorhabditis elegans. FASN is well established for biosynthesis of the fatty acid palmitate. Our results demonstrate FASN promoting an anti-inflammatory profile apart from palmitate synthesis. Redox-dependent proteolysis of limited amounts of FASN by caspase activates a C-terminal fragment sufficient to downregulate multiple aspects of stress responsiveness, including gene expression, metabolic programs and lipid droplets. The FASN C-terminal fragment signals stress resolution in a cell non-autonomous manner. Consistent with these findings, FASN processing is also seen in well-fed but not fasted male mouse liver. As downregulation of stress responses is critical to health, our findings provide a potential pathway to control diverse aspects of stress responses.
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Affiliation(s)
- Hai Wei
- Department of Pharmacology, UT Southwestern, Dallas, TX, USA
| | - Yi M Weaver
- Department of Pharmacology, UT Southwestern, Dallas, TX, USA
| | - Chendong Yang
- Children's Medical Center Research Institute, UT Southwestern, Dallas, TX, USA
| | - Yuan Zhang
- Department of Pharmacology, UT Southwestern, Dallas, TX, USA
| | - Guoli Hu
- Department of Internal Medicine, UT Southwestern, Dallas, TX, USA
| | | | - Matthew Sieber
- Department of Physiology, UT Southwestern, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, UT Southwestern, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern, Dallas, TX, USA
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4
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Okoye CN, Koren SA, Wojtovich AP. Mitochondrial complex I ROS production and redox signaling in hypoxia. Redox Biol 2023; 67:102926. [PMID: 37871533 PMCID: PMC10598411 DOI: 10.1016/j.redox.2023.102926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.
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Affiliation(s)
- Chidozie N Okoye
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Shon A Koren
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Wojtovich
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA; Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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5
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Cao L, Yoo H, Chen T, Mwimba M, Zhang X, Dong X. H 2O 2 sulfenylates CHE linking local infection to establishment of systemic acquired resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550865. [PMID: 37546937 PMCID: PMC10402168 DOI: 10.1101/2023.07.27.550865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
In plants, a local infection can lead to systemic acquired resistance (SAR) through increased production of salicylic acid (SA). For 30 years, the identity of the mobile signal and its direct transduction mechanism for systemic SA synthesis in initiating SAR have been hotly debated. We found that, upon pathogen challenge, the cysteine residue of transcription factor CHE undergoes sulfenylation in systemic tissues, enhancing its binding to the promoter of SA-synthesis gene, ICS1, and increasing SA production. This occurs independently of previously reported pipecolic acid (Pip) signal. Instead, H2O2 produced by NADPH oxidase, RBOHD, is the mobile signal that sulfenylates CHE in a concentration-dependent manner. This modification serves as a molecular switch that activates CHE-mediated SA-increase and subsequent Pip-accumulation in systemic tissues to synergistically induce SAR.
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Affiliation(s)
- Lijun Cao
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Heejin Yoo
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Tianyuan Chen
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Musoki Mwimba
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Xing Zhang
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Xinnian Dong
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
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6
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Stanhope SC, Brandwine-Shemmer T, Blum HR, Doud EH, Jannasch A, Mosley AL, Minke B, Weake VM. Proteome-wide quantitative analysis of redox cysteine availability in the Drosophila melanogaster eye reveals oxidation of phototransduction machinery during blue light exposure and age. Redox Biol 2023; 63:102723. [PMID: 37146512 DOI: 10.1016/j.redox.2023.102723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
The retina is one of the highest oxygen-consuming tissues because visual transduction and light signaling processes require large amounts of ATP. Thus, because of the high energy demand, oxygen-rich environment, and tissue transparency, the eye is susceptible to excess production of reactive oxygen species (ROS) resulting in oxidative stress. Oxidative stress in the eye is associated with the development and progression of ocular diseases including cataracts, glaucoma, age-related macular degeneration, and diabetic retinopathy. ROS can modify and damage cellular proteins, but can also be involved in redox signaling. In particular, the thiol groups of cysteines can undergo reversible or irreversible oxidative post-translational modifications (PTMs). Identifying the redox-sensitive cysteines on a proteome-wide scale provides insight into those proteins that act as redox sensors or become irreversibly damaged upon exposure to oxidative stress. In this study, we profiled the redox proteome of the Drosophila eye under prolonged, high intensity blue light exposure and age using iodoacetamide isobaric label sixplex reagents (iodo-TMT) to identify changes in cysteine availability. Although redox metabolite analysis of the major antioxidant, glutathione, revealed similar ratios of its oxidized and reduced form in aged or light-stressed eyes, we observed different changes in the redox proteome under these conditions. Both conditions resulted in significant oxidation of proteins involved in phototransduction and photoreceptor maintenance but affected distinct targets and cysteine residues. Moreover, redox changes induced by blue light exposure were accompanied by a large reduction in light sensitivity that did not arise from a reduction in the photopigment level, suggesting that the redox-sensitive cysteines we identified in the phototransduction machinery might contribute to light adaptation. Our data provide a comprehensive description of the redox proteome of Drosophila eye tissue under light stress and aging and suggest how redox signaling might contribute to light adaptation in response to acute light stress.
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Affiliation(s)
- Sarah C Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Tal Brandwine-Shemmer
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada (IMRIC), Edmond and Lily Safra Center for Brain Sciences (ELSC), Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Hannah R Blum
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Emma H Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Amber Jannasch
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Amber L Mosley
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Baruch Minke
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada (IMRIC), Edmond and Lily Safra Center for Brain Sciences (ELSC), Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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7
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Korkola NC, Stillman MJ. Structural Role of Cadmium and Zinc in Metallothionein Oxidation by Hydrogen Peroxide: The Resilience of Metal-Thiolate Clusters. J Am Chem Soc 2023; 145:6383-6397. [PMID: 36914167 DOI: 10.1021/jacs.2c13578] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Oxidative stress is a state involving an imbalance of reactive oxygen species in a cell and is linked to a variety of diseases. The metal-binding protein metallothionein (MT) may play a role in protection due to its high cysteine content. Many studies have shown that oxidative stress will cause MT to both form disulfide bonds and release bound metals. However, studies on the more biologically relevant partially metalated MTs have been largely neglected. Additionally, most studies to date have used spectroscopic methods that cannot detect specific intermediate species. In this paper, we describe the oxidation and the subsequent metal displacement pathway of fully and partially metalated MTs with hydrogen peroxide. The rates of the reactions were monitored using electrospray ionization mass spectrometry (ESI-MS) techniques, which resolved and characterized the individual intermediate Mx(SH)yMT species. The rate constants were calculated for each species formation. Through ESI-MS and circular dichroism spectroscopy, it was found that the three metals in the β-domain were the first to be released from the fully metalated MTs. The Cd(II) in the partially metalated Cd(II)-bound MTs rearranged to form a protective Cd4MT cluster structure upon exposure to oxidation. The partially metalated Zn(II)-bound MTs oxidized at a faster rate as the Zn(II) did not rearrange in response to oxidation. Additionally, density functional theory calculations showed that the terminally bound cysteines were more negative and thus more susceptible to oxidation than the bridging cysteines. The results of this study highlight the importance of metal-thiolate structures and metal identity in MT's response to oxidation.
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Affiliation(s)
- Natalie C Korkola
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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8
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He B, Zhang Z, Huang Z, Duan X, Wang Y, Cao J, Li L, He K, Nice EC, He W, Gao W, Shen Z. Protein persulfidation: Rewiring the hydrogen sulfide signaling in cell stress response. Biochem Pharmacol 2023; 209:115444. [PMID: 36736962 DOI: 10.1016/j.bcp.2023.115444] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
The past few decades have witnessed significant progress in the discovery of hydrogen sulfide (H2S) as a ubiquitous gaseous signaling molecule in mammalian physiology, akin to nitric oxide and carbon monoxide. As the third gasotransmitter, H2S is now known to exert a wide range of physiological and cytoprotective functions in the biological systems. However, endogenous H2S concentrations are usually low, and its potential biologic mechanisms responsible have not yet been fully clarified. Recently, a growing body of evidence has demonstrated that protein persulfidation, a posttranslational modification of cysteine residues (RSH) to persulfides (RSSH) elicited by H2S, is a fundamental mechanism of H2S-mediated signaling pathways. Persulfidation, as a biological switch for protein function, plays an important role in the maintenance of cell homeostasis in response to various internal and external stress stimuli and is also implicated in numerous diseases, such as cardiovascular and neurodegenerative diseases and cancer. In this review, the biological significance of protein persulfidation by H2S in cell stress response is reviewed providing a framework for understanding the multifaceted roles of H2S. A mechanism-guided perspective can help open novel avenues for the exploitation of therapeutics based on H2S-induced persulfidation in the context of diseases.
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Affiliation(s)
- Bo He
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Zhe Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Zhao Huang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Xirui Duan
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Jiangjun Cao
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Lei Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Kai He
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Weifeng He
- Institute of Burn Research, Southwest Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Military Medical University, Chongqing 400038, China.
| | - Wei Gao
- Clinical Genetics Laboratory, Affiliated Hospital & Clinical Medical College of Chengdu University, Chengdu 610081, China.
| | - Zhisen Shen
- Department of Otorhinolaryngology and Head and Neck Surgery, Affiliated Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China.
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9
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Ren X, Léveillard T. Modulating antioxidant systems as a therapeutic approach to retinal degeneration. Redox Biol 2022; 57:102510. [PMID: 36274523 PMCID: PMC9596747 DOI: 10.1016/j.redox.2022.102510] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/21/2022] Open
Abstract
The human retina is facing a big challenge of reactive oxygen species (ROS) from endogenous and exogenous sources. Excessive ROS can cause damage to DNA, lipids, and proteins, triggering abnormal redox signaling, and ultimately lead to cell death. Thus, oxidative stress has been observed in inherited retinal diseases as a common hallmark. To counteract the detrimental effect of ROS, cells are equipped with various antioxidant defenses. In this review, we will focus on the antioxidant systems in the retina and how they can protect retina from oxidative stress. Both small antioxidants and antioxidant enzymes play a role in ROS removal. Particularly, the thioredoxin and glutaredoxin systems, as the major antioxidant systems in mammalian cells, exert functions in redox signaling regulation via modifying cysteines in proteins. In addition, the thioredoxin-like rod-derived cone viability factor (RdCVFL) and thioredoxin interacting protein (TXNIP) can modulate metabolism in photoreceptors and promote their survival. In conclusion, elevating the antioxidant capacity in retina is a promising therapy to curb the progress of inherited retinal degeneration.
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Affiliation(s)
- Xiaoyuan Ren
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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10
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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Salovska B, Kondelova A, Pimkova K, Liblova Z, Pribyl M, Fabrik I, Bartek J, Vajrychova M, Hodny Z. Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape. Redox Biol 2021; 49:102212. [PMID: 34923300 PMCID: PMC8688892 DOI: 10.1016/j.redox.2021.102212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Cellular senescence is a complex stress response defined as an essentially irreversible cell cycle arrest mediated by the inhibition of cell cycle-specific cyclin dependent kinases. The imbalance in redox homeostasis and oxidative stress have been repeatedly observed as one of the hallmarks of the senescent phenotype. However, a large-scale study investigating protein oxidation and redox signaling in senescent cells in vitro has been lacking. Here we applied a proteome-wide analysis using SILAC-iodoTMT workflow to quantitatively estimate the level of protein sulfhydryl oxidation and proteome level changes in ionizing radiation-induced senescence (IRIS) in hTERT-RPE-1 cells. We observed that senescent cells mobilized the antioxidant system to buffer the increased oxidation stress. Among the antioxidant proteins with increased relative abundance in IRIS, a unique 1-Cys peroxiredoxin family member, peroxiredoxin 6 (PRDX6), was identified as an important contributor to protection against oxidative stress. PRDX6 silencing increased ROS production in senescent cells, decreased their resistance to oxidative stress-induced cell death, and impaired their viability. Subsequent SILAC-iodoTMT and secretome analysis after PRDX6 silencing showed the downregulation of PRDX6 in IRIS affected protein secretory pathways, decreased expression of extracellular matrix proteins, and led to unexpected attenuation of senescence-associated secretory phenotype (SASP). The latter was exemplified by decreased secretion of pro-inflammatory cytokine IL-6 which was also confirmed after treatment with an inhibitor of PRDX6 iPLA2 activity, MJ33. In conclusion, by combining different methodological approaches we discovered a novel role of PRDX6 in senescent cell viability and SASP development. Our results suggest PRDX6 could have a potential as a drug target for senolytic or senomodulatory therapy. SILAC-iodoTMT is a powerful tool to quantify redox imbalance in IRIS. Senescence in hTERT-RPE-1 cells is not accompanied by bulk cysteine oxidation. Antioxidant proteins are upregulated in senescent hTERT-RPE-1 cells. PRDX6 silencing affects redox homeostasis and viability of senescent cells. PRDX6 silencing alters secretome of senescent RPE-1 cells and suppresses IL-6.
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Affiliation(s)
- Barbora Salovska
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alexandra Kondelova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kristyna Pimkova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic; BIOCEV, 1st Medical Faculty, Charles University, Vestec, Czech Republic
| | - Zuzana Liblova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslav Pribyl
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Danish Cancer Society Research Center, Copenhagen, Denmark; Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Marie Vajrychova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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12
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Wdowiak AP, Duong MN, Joyce RD, Boyatzis AE, Walkey MC, Nealon GL, Arthur PG, Piggott MJ. Isotope-Coded Maleimide Affinity Tags for Proteomics Applications. Bioconjug Chem 2021; 32:1652-1666. [PMID: 34160215 DOI: 10.1021/acs.bioconjchem.1c00206] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotope-coded affinity tags (ICATs) are valuable tools for mass spectrometry-based quantitative proteomics, in particular, for comparison of protein (cysteine-residue) thiol oxidation state in normal, stressed, and diseased tissue. However, the iodoacetamido electrophile used in most commercial ICATs suffers from poor thiol-selectivity and modest rates of adduct formation, which can lead to spurious results. Hence, we designed and synthesized three ICATs containing thiol-selective N-alkylmaleimide electrophiles (isotope-coded maleimide affinity tags = ICMATs) and assessed these as mass spectrometry probes for ratiometric analysis of lysozyme and muscle proteomes. Two ICMAT pairs containing butylene/D8-butylene linkers were effective MS probes, but not ideal for typical proteomics workflows, because peptides bearing these tags frequently did not coelute with HPLC. A switch to a phenylene/13C6-phenylene linker solved this issue without compromising the efficiency of adduct formation.
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13
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Pham TK, Buczek WA, Mead RJ, Shaw PJ, Collins MO. Proteomic Approaches to Study Cysteine Oxidation: Applications in Neurodegenerative Diseases. Front Mol Neurosci 2021; 14:678837. [PMID: 34177463 PMCID: PMC8219902 DOI: 10.3389/fnmol.2021.678837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 11/15/2022] Open
Abstract
Oxidative stress appears to be a key feature of many neurodegenerative diseases either as a cause or consequence of disease. A range of molecules are subject to oxidation, but in particular, proteins are an important target and measure of oxidative stress. Proteins are subject to a range of oxidative modifications at reactive cysteine residues, and depending on the level of oxidative stress, these modifications may be reversible or irreversible. A range of experimental approaches has been developed to characterize cysteine oxidation of proteins. In particular, mass spectrometry-based proteomic methods have emerged as a powerful means to identify and quantify cysteine oxidation sites on a proteome scale; however, their application to study neurodegenerative diseases is limited to date. Here we provide a guide to these approaches and highlight the under-exploited utility of these methods to measure oxidative stress in neurodegenerative diseases for biomarker discovery, target engagement and to understand disease mechanisms.
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Affiliation(s)
- Trong Khoa Pham
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Weronika A. Buczek
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Richard J. Mead
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Mark O. Collins
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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14
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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15
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Zhang X, Zhang Z, Chen XL. The Redox Proteome of Thiol Proteins in the Rice Blast Fungus Magnaporthe oryzae. Front Microbiol 2021; 12:648894. [PMID: 33776980 PMCID: PMC7987659 DOI: 10.3389/fmicb.2021.648894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
Redox modification, a post-translational modification, has been demonstrated to be significant for many physiological pathways and biological processes in both eukaryotes and prokaryotes. However, little is known about the global profile of protein redox modification in fungi. To explore the roles of redox modification in the plant pathogenic fungi, a global thiol proteome survey was performed in the model fungal pathogen Magnaporthe oryzae. A total of 3713 redox modification sites from 1899 proteins were identified through a mix sample containing mycelia with or without oxidative stress, conidia, appressoria, and invasive hyphae of M. oryzae. The identified thiol-modified proteins were performed with protein domain, subcellular localization, functional classification, metabolic pathways, and protein–protein interaction network analyses, indicating that redox modification is associated with a wide range of biological and cellular functions. These results suggested that redox modification plays important roles in fungal growth, conidium formation, appressorium formation, as well as invasive growth. Interestingly, a large number of pathogenesis-related proteins were redox modification targets, suggesting the significant roles of redox modification in pathogenicity of M. oryzae. This work provides a global insight into the redox proteome of the pathogenic fungi, which built a groundwork and valuable resource for future studies of redox modification in fungi.
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Affiliation(s)
- Xinrong Zhang
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Zhenhua Zhang
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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16
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Tomin T, Schittmayer M, Sedej S, Bugger H, Gollmer J, Honeder S, Darnhofer B, Liesinger L, Zuckermann A, Rainer PP, Birner-Gruenberger R. Mass Spectrometry-Based Redox and Protein Profiling of Failing Human Hearts. Int J Mol Sci 2021; 22:ijms22041787. [PMID: 33670142 PMCID: PMC7916846 DOI: 10.3390/ijms22041787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of the antioxidative defense, dysregulation of redox signaling, and protein damage. In order to precisely dissect the changes of the myocardial redox state correlated with oxidative stress and heart failure, we subjected left-ventricular tissue specimens collected from control or failing human hearts to comprehensive mass spectrometry-based redox and quantitative proteomics, as well as glutathione status analyses. As a result, we report that failing hearts have lower glutathione to glutathione disulfide ratios and increased oxidation of a number of different proteins, including constituents of the contractile machinery as well as glycolytic enzymes. Furthermore, quantitative proteomics of failing hearts revealed a higher abundance of proteins responsible for extracellular matrix remodeling and reduced abundance of several ion transporters, corroborating contractile impairment. Similar effects were recapitulated by an in vitro cell culture model under a controlled oxygen atmosphere. Together, this study provides to our knowledge the most comprehensive report integrating analyses of protein abundance and global and peptide-level redox state in end-stage failing human hearts as well as oxygen-dependent redox and global proteome profiles of cultured human cardiomyocytes.
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Affiliation(s)
- Tamara Tomin
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Matthias Schittmayer
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Simon Sedej
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Heiko Bugger
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Johannes Gollmer
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Sophie Honeder
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Andreas Zuckermann
- Cardiac Transplantation, Department of Cardiac Surgery, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria;
| | - Peter P. Rainer
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Ruth Birner-Gruenberger
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
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17
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Zhang T, Gaffrey MJ, Li X, Qian WJ. Characterization of cellular oxidative stress response by stoichiometric redox proteomics. Am J Physiol Cell Physiol 2020; 320:C182-C194. [PMID: 33264075 DOI: 10.1152/ajpcell.00040.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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18
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Speciale A, Saija A, Bashllari R, Molonia MS, Muscarà C, Occhiuto C, Cimino F, Cristani M. Anthocyanins As Modulators of Cell Redox-Dependent Pathways in Non-Communicable Diseases. Curr Med Chem 2020; 27:1955-1996. [PMID: 30417771 DOI: 10.2174/0929867325666181112093336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/22/2018] [Accepted: 11/04/2018] [Indexed: 12/15/2022]
Abstract
Chronic Noncommunicable Diseases (NCDs), mostly represented by cardiovascular diseases, diabetes, chronic pulmonary diseases, cancers, and several chronic pathologies, are one of the main causes of morbidity and mortality, and are mainly related to the occurrence of metabolic risk factors. Anthocyanins (ACNs) possess a wide spectrum of biological activities, such as anti-inflammatory, antioxidant, cardioprotective and chemopreventive properties, which are able to promote human health. Although ACNs present an apparent low bioavailability, their metabolites may play an important role in the in vivo protective effects observed. This article directly addresses the scientific evidences supporting that ACNs could be useful to protect human population against several NCDs not only acting as antioxidant but through their capability to modulate cell redox-dependent signaling. In particular, ACNs interact with the NF-κB and AP-1 signal transduction pathways, which respond to oxidative signals and mediate a proinflammatory effect, and the Nrf2/ARE pathway and its regulated cytoprotective proteins (GST, NQO, HO-1, etc.), involved in both cellular antioxidant defenses and elimination/inactivation of toxic compounds, so countering the alterations caused by conditions of chemical/oxidative stress. In addition, supposed crosstalks could contribute to explain the protective effects of ACNs in different pathological conditions characterized by an altered balance among these pathways. Thus, this review underlines the importance of specific nutritional molecules for human health and focuses on the molecular targets and the underlying mechanisms of ACNs against various diseases.
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Affiliation(s)
- Antonio Speciale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Antonella Saija
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Romina Bashllari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Maria Sofia Molonia
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Claudia Muscarà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.,"Prof. Antonio Imbesi" Foundation, University of Messina, Messina, Italy
| | - Cristina Occhiuto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Francesco Cimino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Mariateresa Cristani
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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19
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Karimi M, Crossett B, Cordwell SJ, Pattison DI, Davies MJ. Characterization of disulfide (cystine) oxidation by HOCl in a model peptide: Evidence for oxygen addition, disulfide bond cleavage and adduct formation with thiols. Free Radic Biol Med 2020; 154:62-74. [PMID: 32370994 DOI: 10.1016/j.freeradbiomed.2020.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/19/2023]
Abstract
Disulfide bonds play a key role in stabilizing proteins by cross-linking secondary structures. Whilst many disulfides are effectively unreactive, it is increasingly clear that some disulfides are redox active, participate in enzymatic reactions and/or regulate protein function by allosteric mechanisms. Previously (Karimi et al., Sci. Rep. 2016, 6, 38752) we have shown that some disulfides react rapidly with biological oxidants due to favourable interactions with available lone-pairs of electrons. Here we present data from kinetic, mechanistic and product studies for HOCl-mediated oxidation of a protected nine-amino acid model peptide containing a N- to C-terminal disulfide bond. This peptide reacts with HOCl with k2 1.8 × 106 M-1 s-1, similar to other highly-reactive disulfide-containing compounds. With low oxidant excesses, oxidation yields multiple oxidation products from the disulfide, with reaction predominating at the N-terminal Cys to give sulfenic, sulfinic and sulfonic acids, and disulfide bond cleavage. Limited oxidation occurs, with higher oxidant excesses, at Trp and His residues to give mono- and di- (for Trp) oxygenated products. Site-specific backbone cleavage also occurs between Arg and Trp, probably via initial side-chain modification. Treatment of the previously-oxidised peptide with thiols (GSH, N-Ac-Cys), results in adduction of the thiol to the oxidised peptide, with this occurring at the original disulfide bond. This gives an open-chain peptide, and a new mixed disulfide containing GSH or N-Ac-Cys as determined by mass spectrometry. Disulfide bond oxidation may therefore markedly alter the structure, activity and function of disulfide-containing proteins, and provides a potential mechanism for protein glutathionylation.
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Affiliation(s)
- Maryam Karimi
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia
| | - Ben Crossett
- Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart J Cordwell
- Faculty of Medicine, The University of Sydney, NSW, 2006, Australia; Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - David I Pattison
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia
| | - Michael J Davies
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia; Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
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20
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Chung NC, Choi H, Wang D, Mirza B, Pelletier AR, Sigdel D, Wang W, Ping P. Identifying temporal molecular signatures underlying cardiovascular diseases: A data science platform. J Mol Cell Cardiol 2020; 145:54-58. [PMID: 32504647 PMCID: PMC7583079 DOI: 10.1016/j.yjmcc.2020.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/18/2020] [Accepted: 05/31/2020] [Indexed: 11/26/2022]
Abstract
OBJECTIVE During cardiovascular disease progression, molecular systems of myocardium (e.g., a proteome) undergo diverse and distinct changes. Dynamic, temporally-regulated alterations of individual molecules underlie the collective response of the heart to pathological drivers and the ultimate development of pathogenesis. Advances in high-throughput omics technologies have enabled cost-effective, temporal profiling of targeted systems in animal models of human diseases. However, computational analysis of temporal patterns from omics data remains challenging. In particular, bioinformatic pipelines involving unsupervised statistical approaches to support cardiovascular investigations are lacking, which hinders one's ability to extract biomedical insights from these complex datasets. APPROACH AND RESULTS We developed a non-parametric data analysis platform to resolve computational challenges unique to temporal omics datasets. Our platform consists of three modules. Module I preprocesses the temporal data using either cubic splines or principal component analysis (PCA), and it simultaneously accomplishes the tasks on missing data imputation and denoising. Module II performs an unsupervised classification by K-means or hierarchical clustering. Module III evaluates and identifies biological entities (e.g., molecular events) that exhibit strong associations to specific temporal patterns. The jackstraw method for cluster membership has been applied to estimate p-values and posterior inclusion probabilities (PIPs), both of which guided feature selection. To demonstrate the utility of the analysis platform, we employed a temporal proteomics dataset that captured the proteome-wide dynamics of oxidative stress induced post-translational modifications (O-PTMs) in mouse hearts undergoing isoproterenol (ISO)-induced hypertrophy. CONCLUSION We have created a platform, CV.Signature.TCP, to identify distinct temporal clusters in omics datasets. We presented a cardiovascular use case to demonstrate its utility in unveiling biological insights underlying O-PTM regulations in cardiac remodeling. This platform is implemented in an open source R package (https://github.com/UCLA-BD2K/CV.Signature.TCP).
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Affiliation(s)
- Neo Christopher Chung
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA; Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics University of Warsaw, Warsaw, Poland.
| | - Howard Choi
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA; Bioinformatics and Medical Informatics at UCLA School of Engineering, Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi) at UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Ding Wang
- Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA
| | - Bilal Mirza
- Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA
| | - Alexander R Pelletier
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Bioinformatics and Medical Informatics at UCLA School of Engineering, Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi) at UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Dibakar Sigdel
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA
| | - Wei Wang
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Bioinformatics and Medical Informatics at UCLA School of Engineering, Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi) at UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Peipei Ping
- NHLBI Integrated Cardiovascular Data Science Training Program at University of California (UCLA), Los Angeles, USA; Departments of Physiology and Medicine (Cardiology) at UCLA School of Medicine, USA; Bioinformatics and Medical Informatics at UCLA School of Engineering, Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi) at UCLA School of Engineering, Los Angeles, CA 90095, USA.
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21
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Reina S, Pittalà MGG, Guarino F, Messina A, De Pinto V, Foti S, Saletti R. Cysteine Oxidations in Mitochondrial Membrane Proteins: The Case of VDAC Isoforms in Mammals. Front Cell Dev Biol 2020; 8:397. [PMID: 32582695 PMCID: PMC7287182 DOI: 10.3389/fcell.2020.00397] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Cysteine residues are reactive amino acids that can undergo several modifications driven by redox reagents. Mitochondria are the source of an abundant production of radical species, and it is surprising that such a large availability of highly reactive chemicals is compatible with viable and active organelles, needed for the cell functions. In this work, we review the results highlighting the modifications of cysteines in the most abundant proteins of the outer mitochondrial membrane (OMM), that is, the voltage-dependent anion selective channel (VDAC) isoforms. This interesting protein family carries several cysteines exposed to the oxidative intermembrane space (IMS). Through mass spectrometry (MS) analysis, cysteine posttranslational modifications (PTMs) were precisely determined, and it was discovered that such cysteines can be subject to several oxidization degrees, ranging from the disulfide bridge to the most oxidized, the sulfonic acid, one. The large spectra of VDAC cysteine oxidations, which is unique for OMM proteins, indicate that they have both a regulative function and a buffering capacity able to counteract excess of mitochondrial reactive oxygen species (ROS) load. The consequence of these peculiar cysteine PTMs is discussed.
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Affiliation(s)
- Simona Reina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Maria Gaetana Giovanna Pittalà
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Francesca Guarino
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Foti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Rosaria Saletti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
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22
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ZN148 Is a Modular Synthetic Metallo-β-Lactamase Inhibitor That Reverses Carbapenem Resistance in Gram-Negative Pathogens In Vivo. Antimicrob Agents Chemother 2020; 64:AAC.02415-19. [PMID: 32179522 PMCID: PMC7269481 DOI: 10.1128/aac.02415-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenem-resistant Gram-negative pathogens are a critical public health threat and there is an urgent need for new treatments. Carbapenemases (β-lactamases able to inactivate carbapenems) have been identified in both serine β-lactamase (SBL) and metallo-β-lactamase (MBL) families. The recent introduction of SBL carbapenemase inhibitors has provided alternative therapeutic options. Unfortunately, there are no approved inhibitors of MBL-mediated carbapenem-resistance and treatment options for infections caused by MBL-producing Gram-negatives are limited. Carbapenem-resistant Gram-negative pathogens are a critical public health threat and there is an urgent need for new treatments. Carbapenemases (β-lactamases able to inactivate carbapenems) have been identified in both serine β-lactamase (SBL) and metallo-β-lactamase (MBL) families. The recent introduction of SBL carbapenemase inhibitors has provided alternative therapeutic options. Unfortunately, there are no approved inhibitors of MBL-mediated carbapenem-resistance and treatment options for infections caused by MBL-producing Gram-negatives are limited. Here, we present ZN148, a zinc-chelating MBL-inhibitor capable of restoring the bactericidal effect of meropenem and in vitro clinical susceptibility to carbapenems in >98% of a large international collection of MBL-producing clinical Enterobacterales strains (n = 234). Moreover, ZN148 was able to potentiate the effect of meropenem against NDM-1-producing Klebsiella pneumoniae in a murine neutropenic peritonitis model. ZN148 showed no inhibition of the human zinc-containing enzyme glyoxylase II at 500 μM, and no acute toxicity was observed in an in vivo mouse model with cumulative dosages up to 128 mg/kg. Biochemical analysis showed a time-dependent inhibition of MBLs by ZN148 and removal of zinc ions from the active site. Addition of exogenous zinc after ZN148 exposure only restored MBL activity by ∼30%, suggesting an irreversible mechanism of inhibition. Mass-spectrometry and molecular modeling indicated potential oxidation of the active site Cys221 residue. Overall, these results demonstrate the therapeutic potential of a ZN148-carbapenem combination against MBL-producing Gram-negative pathogens and that ZN148 is a highly promising MBL inhibitor that is capable of operating in a functional space not presently filled by any clinically approved compound.
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23
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The crosstalk of NAD, ROS and autophagy in cellular health and ageing. Biogerontology 2020; 21:381-397. [PMID: 32124104 PMCID: PMC7196094 DOI: 10.1007/s10522-020-09864-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Cellular adaptation to various types of stress requires a complex network of steps that altogether lead to reconstitution of redox balance, degradation of damaged macromolecules and restoration of cellular metabolism. Advances in our understanding of the interplay between cellular signalling and signal translation paint a complex picture of multi-layered paths of regulation. In this review we explore the link between cellular adaptation to metabolic and oxidative stresses by activation of autophagy, a crucial cellular catabolic pathway. Metabolic stress can lead to changes in the redox state of nicotinamide adenine dinucleotide (NAD), a co-factor in a variety of enzymatic reactions and thus trigger autophagy that acts to sequester intracellular components for recycling to support cellular growth. Likewise, autophagy is activated by oxidative stress to selectively recycle damaged macromolecules and organelles and thus maintain cellular viability. Multiple proteins that help regulate or execute autophagy are targets of post-translational modifications (PTMs) that have an effect on their localization, binding affinity or enzymatic activity. These PTMs include acetylation, a reversible enzymatic modification of a protein’s lysine residues, and oxidation, a set of reversible and irreversible modifications by free radicals. Here we highlight the latest findings and outstanding questions on the interplay of autophagy with metabolic stress, presenting as changes in NAD levels, and oxidative stress, with a focus on autophagy proteins that are regulated by both, oxidation and acetylation. We further explore the relevance of this multi-layered signalling to healthy human ageing and their potential role in human disease.
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24
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Su Z, Burchfield JG, Yang P, Humphrey SJ, Yang G, Francis D, Yasmin S, Shin SY, Norris DM, Kearney AL, Astore MA, Scavuzzo J, Fisher-Wellman KH, Wang QP, Parker BL, Neely GG, Vafaee F, Chiu J, Yeo R, Hogg PJ, Fazakerley DJ, Nguyen LK, Kuyucak S, James DE. Global redox proteome and phosphoproteome analysis reveals redox switch in Akt. Nat Commun 2019; 10:5486. [PMID: 31792197 PMCID: PMC6889415 DOI: 10.1038/s41467-019-13114-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 10/18/2019] [Indexed: 01/04/2023] Open
Abstract
Protein oxidation sits at the intersection of multiple signalling pathways, yet the magnitude and extent of crosstalk between oxidation and other post-translational modifications remains unclear. Here, we delineate global changes in adipocyte signalling networks following acute oxidative stress and reveal considerable crosstalk between cysteine oxidation and phosphorylation-based signalling. Oxidation of key regulatory kinases, including Akt, mTOR and AMPK influences the fidelity rather than their absolute activation state, highlighting an unappreciated interplay between these modifications. Mechanistic analysis of the redox regulation of Akt identified two cysteine residues in the pleckstrin homology domain (C60 and C77) to be reversibly oxidized. Oxidation at these sites affected Akt recruitment to the plasma membrane by stabilizing the PIP3 binding pocket. Our data provide insights into the interplay between oxidative stress-derived redox signalling and protein phosphorylation networks and serve as a resource for understanding the contribution of cellular oxidation to a range of diseases. Crosstalk between protein oxidation and other post-translational modifications remains unexplored. Here, the authors map the phosphoproteome, cysteine redox proteome and total proteome of adipocytes under acute oxidative stress and reveal crosstalk between cysteine oxidation and phosphorylation-based signalling.
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Affiliation(s)
- Zhiduan Su
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - James G Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Pengyi Yang
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Guang Yang
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Deanne Francis
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Sabina Yasmin
- School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Sung-Young Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.,Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Dougall M Norris
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Alison L Kearney
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Miro A Astore
- School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jonathan Scavuzzo
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kelsey H Fisher-Wellman
- Brody School of Medicine, Physiology Department, East Carolina University, Greenville, NC, USA.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, USA
| | - Qiao-Ping Wang
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.,The Dr. John and Anne Chong Laboratory for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Benjamin L Parker
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - G Gregory Neely
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.,The Dr. John and Anne Chong Laboratory for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Fatemeh Vafaee
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Joyce Chiu
- The Centenary Institute, Newtown, NSW, 2042, Australia.,National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Reichelle Yeo
- The Centenary Institute, Newtown, NSW, 2042, Australia.,National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Philip J Hogg
- The Centenary Institute, Newtown, NSW, 2042, Australia.,National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Daniel J Fazakerley
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.,Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Serdar Kuyucak
- School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - David E James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia. .,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia. .,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.
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25
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Allawzi A, Nozik-Grayck E. S-nitrosylation of surfactant protein-D: a proinflammatory posttranslational modification. Am J Physiol Lung Cell Mol Physiol 2019; 317:L537-L538. [PMID: 31508980 DOI: 10.1152/ajplung.00359.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Ayed Allawzi
- Cardiovascular Pulmonary Research Laboratory, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Eva Nozik-Grayck
- Cardiovascular Pulmonary Research Laboratory, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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26
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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27
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Tomin T, Schittmayer M, Honeder S, Heininger C, Birner-Gruenberger R. Irreversible oxidative post-translational modifications in heart disease. Expert Rev Proteomics 2019; 16:681-693. [PMID: 31361162 PMCID: PMC6816499 DOI: 10.1080/14789450.2019.1645602] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Development of specific biomarkers aiding early diagnosis of heart failure is an ongoing challenge. Biomarkers commonly used in clinical routine usually act as readouts of an already existing acute condition rather than disease initiation. Functional decline of cardiac muscle is greatly aggravated by increased oxidative stress and damage of proteins. Oxidative post-translational modifications occur already at early stages of tissue damage and are thus regarded as potential up-coming disease markers. Areas covered: Clinical practice regarding commonly used biomarkers for heart disease is briefly summarized. The types of oxidative post-translational modification in cardiac pathologies are discussed with a special focus on available quantitative techniques and characteristics of individual modifications with regard to their stability and analytical accessibility. As irreversible oxidative modifications trigger protein degradation pathways or cause protein aggregation, both influencing biomarker abundance, a chapter is dedicated to their regulation in the heart.
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Affiliation(s)
- Tamara Tomin
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Matthias Schittmayer
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Sophie Honeder
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Christoph Heininger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Ruth Birner-Gruenberger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
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28
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Anjo SI, Melo MN, Loureiro LR, Sabala L, Castanheira P, Grãos M, Manadas B. oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening. Redox Biol 2019; 22:101130. [PMID: 30737169 PMCID: PMC6435957 DOI: 10.1016/j.redox.2019.101130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation without considering the variation in the total levels of the proteins. However, protein synthesis and protein degradation also belong to the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in PTMs-focused analyses, such as cysteine redox characterization. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using a combination of commonly available alkylating reagents (oxSWATH) is presented, by which it is possible to integrate the information regarding relative cysteine oxidation with the analysis of the total protein levels in a cost-effective high-throughput approach. The proposed method was tested using a redox-regulated protein and further applied to a comparative analysis of secretomes obtained from cells cultured under control or oxidative stress conditions to strengthen the importance of considering the overall proteome changes. Using the OxSWATH method it was possible to determine both the relative proportion of reduced and reversible oxidized oxoforms, as well as the total levels of each oxoform by taking into consideration the total levels of the protein. Therefore, using OxSWATH the comparative analyses can be performed at two different levels by considering the relative proportion or the total levels at both peptide and protein level. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can also be performed, allowing a truly comprehensive evaluation of proteomics changes upon the oxidative stimulus. Data are available via ProteomeXchange and SWATHAtlas with the identifiers PXD006802, PXD006802, and PASS01210. Determination of redox changes considering protein total levels. Integrative redoxomics and common differential proteomics in a single analysis. Differential alkylation strategy using commonly available alkylating agents. First untargeted label-free quantitative method to study cysteine oxidation.
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Affiliation(s)
- Sandra I Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
| | - Matilde N Melo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Liliana R Loureiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Lúcia Sabala
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | | | - Mário Grãos
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Biocant, Technology Transfer Association, Cantanhede, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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29
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Prakash AS, Kabli AMF, Bulleid N, Burchmore R. Mix-and-Match Proteomics: Using Advanced Iodoacetyl Tandem Mass Tag Multiplexing To Investigate Cysteine Oxidation Changes with Respect to Protein Expression. Anal Chem 2018; 90:14173-14180. [DOI: 10.1021/acs.analchem.8b02517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aruna S. Prakash
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Glasgow, United Kingdom G61 1QH
| | - Abdulbaset M. F. Kabli
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Glasgow, United Kingdom G61 1QH
| | - Neil Bulleid
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Davidson Building, Glasgow, United Kingdom G12 8QQ
| | - Richard Burchmore
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Glasgow, United Kingdom G61 1QH
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30
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Alcaraz-Quiles J, Casulleras M, Oettl K, Titos E, Flores-Costa R, Duran-Güell M, López-Vicario C, Pavesi M, Stauber RE, Arroyo V, Clària J. Oxidized Albumin Triggers a Cytokine Storm in Leukocytes Through P38 Mitogen-Activated Protein Kinase: Role in Systemic Inflammation in Decompensated Cirrhosis. Hepatology 2018; 68:1937-1952. [PMID: 30070728 DOI: 10.1002/hep.30135] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/22/2018] [Accepted: 05/20/2018] [Indexed: 12/22/2022]
Abstract
Decompensated cirrhosis is characterized by exuberant systemic inflammation. Although the inducers of this feature remain unknown, the presence of circulating forms of oxidized albumin, namely human nonmercaptalbumin 1 (HNA1) and HNA2, is a common finding in cirrhosis. The aim of this study was to explore the ability of these oxidized albumin forms to induce systemic inflammation by triggering the activation of peripheral leukocytes. We observed significantly higher plasma levels of HNA1 and HNA2 in patients with cirrhosis (n = 256) compared to healthy volunteers (n = 48), which gradually increased during the course from compensated to decompensated to acute-on-chronic liver failure. Plasma HNA1 and HNA2 levels significantly correlated with inflammatory markers (i.e., interleukin-6 [IL-6], IL-1β, tumor necrosis factor-alpha [TNF-α] and IL-8) in patients with cirrhosis. To directly test the inflammatory effects of HNA1 and HNA2 on leukocytes, these oxidized albumin forms were prepared ex vivo and their posttranslational modifications monitored by liquid chromatography (LC)-quadrupole time-of-flight/mass spectrometry (MS). HNA1, but not HNA2, increased IL-1β, IL-6, and TNF-α mRNA and protein expression in leukocytes from both healthy volunteers and patients with cirrhosis. Moreover, HNA1 up-regulated the expression of eicosanoid-generating enzymes (i.e., cyclooxygenase-2 [COX-2] and microsomal prostaglandin E [PGE] synthase 1) and the production of inflammatory eicosanoids (PGE2 , PGF2α , thromboxane B2 , and leukotriene B4 ), as determined by LC-electrospray ionization-MS/MS. The inflammatory response to HNA1 was more pronounced in peripheral blood mononuclear cells (PBMCs) and marginal in polymorphonuclear neutrophils. Kinome analysis of PBMCs revealed that HNA1 induced the phosphorylation of p38 mitogen-activated protein kinase, the inhibition of which blocked HNA1-induced cytokine and COX-2 induction. Conclusion: HNA1 triggers an inflammatory response in PBMCs, providing a rationale for its removal and replacement by reduced albumin in the prevention of systemic inflammation in patients with advanced liver disease.
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Affiliation(s)
- José Alcaraz-Quiles
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Mireia Casulleras
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Karl Oettl
- Institute of Physiological Chemistry, Center of Physiological Medicine, Medical University of Graz, Graz, Austria
| | - Esther Titos
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Roger Flores-Costa
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Marta Duran-Güell
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Cristina López-Vicario
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Marco Pavesi
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain
| | - Rudolf E Stauber
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Vicente Arroyo
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain
| | - Joan Clària
- Department of Biochemistry and Molecular Genetics, Hospital Clínic-IDIBAPS, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.,European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain.,Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
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31
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Wang RS, Oldham WM, Maron BA, Loscalzo J. Systems Biology Approaches to Redox Metabolism in Stress and Disease States. Antioxid Redox Signal 2018; 29:953-972. [PMID: 29121773 PMCID: PMC6104248 DOI: 10.1089/ars.2017.7256] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/12/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE All cellular metabolic processes are tied to the cellular redox environment. Therefore, maintaining redox homeostasis is critically important for normal cell function. Indeed, redox stress contributes to the pathobiology of many human diseases. The cellular redox response system is composed of numerous interconnected components, including free radicals, redox couples, protein thiols, enzymes, metabolites, and transcription factors. Moreover, interactions between and among these factors are regulated in time and space. Owing to their complexity, systems biology approaches to the characterization of the cellular redox response system may provide insights into novel homeostatic mechanisms and methods of therapeutic reprogramming. Recent Advances: The emergence and development of systems biology has brought forth a set of innovative technologies that provide new avenues for studying redox metabolism. This article will review these systems biology approaches and their potential application to the study of redox metabolism in stress and disease states. CRITICAL ISSUES Clarifying the scope of biological intermediaries affected by dysregulated redox metabolism requires methods that are suitable for analyzing big datasets as classical methods that do not account for multiple interactions are unlikely to portray the totality of perturbed metabolic systems. FUTURE DIRECTIONS Given the diverse redox microenvironments within cells, it will be important to improve the spatial resolution of omic approaches. Futures studies on the integration of multiple systems-based methods and heterogeneous omics data for redox metabolism are required to accelerate the development of the field of redox systems biology. Antioxid. Redox Signal. 29, 953-972.
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Affiliation(s)
- Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - William M. Oldham
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley A. Maron
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Section of Cardiology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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32
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Abstract
The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology and Toxicology, College of
Pharmacy, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Jesse R. Poganik
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
- Department of Biochemistry, Weill Cornell Medicine, New
York, New York, 10065, USA
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33
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Zhang T, Gaffrey MJ, Thrall BD, Qian WJ. Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials. Anal Bioanal Chem 2018; 410:6067-6077. [PMID: 29947897 PMCID: PMC6119095 DOI: 10.1007/s00216-018-1168-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/17/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
The widespread use of engineered nanomaterials or nanotechnology makes the characterization of biological responses to nanomaterials an important area of research. The application of omics approaches, such as mass spectrometry-based proteomics, has revealed new insights into the cellular responses of exposure to nanomaterials, including how nanomaterials interact and alter cellular pathways. In addition, exposure to engineered nanomaterials often leads to the generation of reactive oxygen species and cellular oxidative stress, which implicates a redox-dependent regulation of cellular responses under such conditions. In this review, we discuss quantitative proteomics-based approaches, with an emphasis on redox proteomics, as a tool for system-level characterization of the biological responses induced by engineered nanomaterials. Graphical abstract ᅟ.
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Affiliation(s)
- Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Wang J, Choi H, Chung NC, Cao Q, Ng DCM, Mirza B, Scruggs SB, Wang D, Garlid AO, Ping P. Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy. J Proteome Res 2018; 17:4243-4257. [PMID: 30141336 DOI: 10.1021/acs.jproteome.8b00372] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cysteine oxidative modification of cellular proteins is crucial for many aspects of cardiac hypertrophy development. However, integrated dissection of multiple types of cysteine oxidative post-translational modifications (O-PTM) of proteomes in cardiac hypertrophy is currently missing. Here we developed a novel discovery platform that encompasses a customized biotin switch-based quantitative proteomics pipeline and an advanced analytic workflow to comprehensively profile the landscape of cysteine O-PTM in an ISO-induced cardiac hypertrophy mouse model. Specifically, we identified a total of 1655 proteins containing 3324 oxidized cysteine sites by at least one of the following three modifications: reversible cysteine O-PTM, cysteine sulfinylation (CysSO2H), and cysteine sulfonylation (CysSO3H). Analyzing the hypertrophy signatures that are reproducibly discovered from this computational workflow unveiled four biological processes with increased cysteine O-PTM. Among them, protein phosphorylation, creatine metabolism, and response to elevated Ca2+ pathways exhibited an elevation of cysteine O-PTM in early stages, whereas glucose metabolism enzymes were increasingly modified in later stages, illustrating a temporal regulatory map in cardiac hypertrophy. Our cysteine O-PTM platform depicts a dynamic and integrated landscape of the cysteine oxidative proteome, through the extracted molecular signatures, and provides critical mechanistic insights in cardiac hypertrophy. Data are available via ProteomeXchange with identifier PXD010336.
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Wani R, Murray BW. Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology. Methods Mol Biol 2018; 1558:191-212. [PMID: 28150239 DOI: 10.1007/978-1-4939-6783-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Reversible cysteine oxidation is an emerging class of protein post-translational modification (PTM) that regulates catalytic activity, modulates conformation, impacts protein-protein interactions, and affects subcellular trafficking of numerous proteins. Redox PTMs encompass a broad array of cysteine oxidation reactions with different half-lives, topographies, and reactivities such as S-glutathionylation and sulfoxidation. Recent studies from our group underscore the lesser known effect of redox protein modifications on drug binding. To date, biological studies to understand mechanistic and functional aspects of redox regulation are technically challenging. A prominent issue is the lack of tools for labeling proteins oxidized to select chemotype/oxidant species in cells. Predictive computational tools and curated databases of oxidized proteins are facilitating structural and functional insights into regulation of the network of oxidized proteins or redox proteome. In this chapter, we discuss analytical platforms for studying protein oxidation, suggest computational tools currently available in the field to determine redox sensitive proteins, and begin to illuminate roles of cysteine redox PTMs in drug pharmacology.
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Affiliation(s)
- Revati Wani
- Oncology Research Unit, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Brion W Murray
- Oncology Research Unit, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA, 92121, USA.
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Winter M, Bretschneider T, Kleiner C, Ries R, Hehn JP, Redemann N, Luippold AH, Bischoff D, Büttner FH. Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction. SLAS DISCOVERY 2018; 23:561-573. [DOI: 10.1177/2472555218759267] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.
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Affiliation(s)
- Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jörg P. Hehn
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Norbert Redemann
- Cardio-Metabolic Diseases, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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Chung HS, Murray CI, Van Eyk JE. A Proteomics Workflow for Dual Labeling Biotin Switch Assay to Detect and Quantify Protein S-Nitroylation. Methods Mol Biol 2018; 1747:89-101. [PMID: 29600453 DOI: 10.1007/978-1-4939-7695-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
S-nitrosylation (or S-nitrosation, SNO) is an oxidative posttranslational modification to the thiol group of a cysteine amino acid residue. There are several methods to detect SNO modifications, mostly based on the classic biotin-switch assay, where the labile SNO sites are replaced with a stable biotin moiety to facilitate enrichment of the modified proteins. As the technique has evolved, new and more advanced thiol-reactive reagents have been introduced in the protocol to improve the identification of modified peptides or to quantify the level of modification at individual cysteine residues. However, the growing diversity of thiol-reactive affinity tags has not produced a consistent set of protein modifications, suggesting incomplete coverage using a single tag. Here, we present a parallel dual labeling strategy followed by an optimized proteomics workflow, which maximizes the overall detection of SNO by reducing the labeling bias derived from the use of a single tag-capture approach.
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Affiliation(s)
| | | | - Jennifer E Van Eyk
- Medicine and Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
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Pinto G, Radulovic M, Godovac-Zimmermann J. Spatial perspectives in the redox code-Mass spectrometric proteomics studies of moonlighting proteins. MASS SPECTROMETRY REVIEWS 2018; 37:81-100. [PMID: 27186965 DOI: 10.1002/mas.21508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
The Redox Code involves specific, reversible oxidative changes in proteins that modulate protein tertiary structure, interactions, trafficking, and activity, and hence couple the proteome to the metabolic/oxidative state of cells. It is currently a major focus of study in cell biology. Recent studies of dynamic cellular spatial reorganization with MS-based subcellular-spatial-razor proteomics reveal that protein constituents of many subcellular structures, including mitochondria, the endoplasmic reticulum, the plasma membrane, and the extracellular matrix, undergo changes in their subcellular abundance/distribution in response to oxidative stress. These proteins are components of a diverse variety of functional processes spatially distributed across cells. Many of the same proteins are involved in response to suppression of DNA replication indicate that oxidative stress is strongly intertwined with DNA replication/proliferation. Both are replete with networks of moonlighting proteins that show coordinated changes in subcellular location and that include primary protein actuators of the redox code involved in the processing of NAD+ /NADH, NADP+ /NADPH, Cys/CySS, and GSH/GSSG redox couples. Small groups of key proteins such as {KPNA2, KPNB1, PCNA, PTMA, SET} constitute "spatial switches" that modulate many nuclear processes. Much of the functional response involves subcellular protein trafficking, including nuclear import/export processes, vesicle-mediated trafficking, the endoplasmic reticulum/Golgi pathway, chaperone-assisted processes, and other transport systems. This is not visible to measurements of total protein abundance by transcriptomics or proteomics. Comprehensive pictures of cellular function will require collection of data on the subcellular transport and local functions of many moonlighting proteins, especially of those with critical roles in spatial coordination across cells. The proteome-wide analysis of coordinated changes in abundance and trafficking of proteins offered by MS-based proteomics has a unique, crucial role to play in deciphering the complex adaptive systems that underlie cellular function. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Gabriella Pinto
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
| | - Marko Radulovic
- Insitute of Oncology and Radiology, Pasterova 14, Belgrade, 11000, Serbia
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
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Elucidation of Plasma-induced Chemical Modifications on Glutathione and Glutathione Disulphide. Sci Rep 2017; 7:13828. [PMID: 29062059 PMCID: PMC5653798 DOI: 10.1038/s41598-017-13041-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/12/2017] [Indexed: 12/25/2022] Open
Abstract
Cold atmospheric pressure plasmas are gaining increased interest in the medical sector and clinical trials to treat skin diseases are underway. Plasmas are capable of producing several reactive oxygen and nitrogen species (RONS). However, there are open questions how plasma-generated RONS interact on a molecular level in a biological environment, e.g. cells or cell components. The redox pair glutathione (GSH) and glutathione disulphide (GSSG) forms the most important redox buffer in organisms responsible for detoxification of intracellular reactive species. We apply Raman spectroscopy, mass spectrometry, and molecular dynamics simulations to identify the time-dependent chemical modifications on GSH and GSSG that are caused by dielectric barrier discharge under ambient conditions. We find GSSG, S-oxidised glutathione species, and S-nitrosoglutathione as oxidation products with the latter two being the final products, while glutathione sulphenic acid, glutathione sulphinic acid, and GSSG are rather reaction intermediates. Experiments using stabilized pH conditions revealed the same main oxidation products as were found in unbuffered solution, indicating that the dominant oxidative or nitrosative reactions are not influenced by acidic pH. For more complex systems these results indicate that too long treatment times can cause difficult-to-handle modifications to the cellular redox buffer which can impair proper cellular function.
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40
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Keng CL, Lin YC, Tseng WL, Lu CY. Design of Peptide-Based Probes for the Microscale Detection of Reactive Oxygen Species. Anal Chem 2017; 89:10883-10888. [PMID: 28976728 DOI: 10.1021/acs.analchem.7b02544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Reactive oxygen species (ROS) can induce oxidative stress and are associated with cell death and chronic diseases in organisms. In the treatment of disease, drugs that induce ROS are associated with many side effects and unpleasant symptoms. Therefore, during the assessment of new drugs and candidate compounds, ROS generation is an issue of concern, because ROS can modify proteins, lipids, and nucleic acids within organisms and alter their biological functions. In this work, we designed a peptide-based probe for the rapid (<10 min) high-throughput survey of oxidative stress induced by clinical drugs at the microliter level. Using menadione and H2O2 as positive controls, just 100 μg/mL of the test compound and 100 μg/mL of the probe were sufficient to effectively monitor the generation of ROS, which is important as many active compounds are rare and difficult to isolate or purify. This in vitro evaluation could be used to effectively generate preliminary data before pharmacologically active candidate compounds are processed in cell-line or animal tests. Furthermore, we demonstrated that this peptide probe successfully detects ROS in biological samples.
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Affiliation(s)
- Chun-Lan Keng
- Research Center for Environmental Medicine, Kaohsiung Medical University , Kaohsiung 80708, Taiwan
| | - Ying-Chi Lin
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University , Kaohsiung 80708, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, College of Science, National Sun Yat-sen University , Kaohsiung 80424, Taiwan
| | - Chi-Yu Lu
- Research Center for Environmental Medicine, Kaohsiung Medical University , Kaohsiung 80708, Taiwan.,Department of Biochemistry, College of Medicine, Kaohsiung Medical University , Kaohsiung 80708, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-sen University , Kaohsiung 80424, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital , Kaohsiung 80708, Taiwan
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41
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Schattauer SS, Land BB, Reichard KL, Abraham AD, Burgeno LM, Kuhar JR, Phillips PEM, Ong SE, Chavkin C. Peroxiredoxin 6 mediates Gαi protein-coupled receptor inactivation by cJun kinase. Nat Commun 2017; 8:743. [PMID: 28963507 PMCID: PMC5622097 DOI: 10.1038/s41467-017-00791-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
Inactivation of opioid receptors limits the therapeutic efficacy of morphine-like analgesics and mediates the long duration of kappa opioid antidepressants by an uncharacterized, arrestin-independent mechanism. Here we use an iterative, discovery-based proteomic approach to show that following opioid administration, peroxiredoxin 6 (PRDX6) is recruited to the opioid receptor complex by c-Jun N-terminal kinase (JNK) phosphorylation. PRDX6 activation generates reactive oxygen species via NADPH oxidase, reducing the palmitoylation of receptor-associated Gαi in a JNK-dependent manner. Selective inhibition of PRDX6 blocks Gαi depalmitoylation, prevents the enhanced receptor G-protein association and blocks acute analgesic tolerance to morphine and kappa opioid receptor inactivation in vivo. Opioid stimulation of JNK also inactivates dopamine D2 receptors in a PRDX6-dependent manner. We show that the loss of this lipid modification distorts the receptor G-protein association, thereby preventing agonist-induced guanine nucleotide exchange. These findings establish JNK-dependent PRDX6 recruitment and oxidation-induced Gαi depalmitoylation as an additional mechanism of Gαi-G-protein-coupled receptor inactivation. Opioid receptors are important modulators of nociceptive pain. Here the authors show that opioid receptor activation recruits peroxiredoxin 6 (PRDX6) to the receptor-Gαi complex by c-Jun N-terminal kinase, resulting in Gαi depalmitoylation and enhanced receptor-Gαi association.
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Affiliation(s)
- Selena S Schattauer
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Benjamin B Land
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Kathryn L Reichard
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Antony D Abraham
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Lauren M Burgeno
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA.,Department of Psychiatry, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Jamie R Kuhar
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Paul E M Phillips
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA.,Department of Psychiatry, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Shao En Ong
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Charles Chavkin
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, 98195, USA.
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Periyasamy P, Shinohara T. Age-related cataracts: Role of unfolded protein response, Ca 2+ mobilization, epigenetic DNA modifications, and loss of Nrf2/Keap1 dependent cytoprotection. Prog Retin Eye Res 2017; 60:1-19. [PMID: 28864287 PMCID: PMC5600869 DOI: 10.1016/j.preteyeres.2017.08.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 12/11/2022]
Abstract
Age-related cataracts are closely associated with lens chronological aging, oxidation, calcium imbalance, hydration and crystallin modifications. Accumulating evidence indicates that misfolded proteins are generated in the endoplasmic reticulum (ER) by most cataractogenic stresses. To eliminate misfolded proteins from cells before they can induce senescence, the cells activate a clean-up machinery called the ER stress/unfolded protein response (UPR). The UPR also activates the nuclear factor-erythroid-2-related factor 2 (Nrf2), a central transcriptional factor for cytoprotection against stress. Nrf2 activates nearly 600 cytoprotective target genes. However, if ER stress reaches critically high levels, the UPR activates destructive outputs to trigger programmed cell death. The UPR activates mobilization of ER-Ca2+ to the cytoplasm and results in activation of Ca2+-dependent proteases to cleave various enzymes and proteins which cause the loss of normal lens function. The UPR also enhances the overproduction of reactive oxygen species (ROS), which damage lens constituents and induce failure of the Nrf2 dependent cytoprotection. Kelch-like ECH-associated protein 1 (Keap1) is an oxygen sensor protein and regulates the levels of Nrf2 by the proteasomal degradation. A significant loss of DNA methylation in diabetic cataracts was found in the Keap1 promoter, which overexpresses the Keap1 protein. Overexpressed Keap1 significantly decreases the levels of Nrf2. Lower levels of Nrf2 induces loss of the redox balance toward to oxidative stress thereby leading to failure of lens cytoprotection. Here, this review summarizes the overall view of ER stress, increases in Ca2+ levels, protein cleavage, and loss of the well-established stress protection in somatic lens cells.
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Affiliation(s)
- Palsamy Periyasamy
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Toshimichi Shinohara
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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H₂S-Mediated Protein S-Sulfhydration: A Prediction for Its Formation and Regulation. Molecules 2017; 22:molecules22081334. [PMID: 28800080 PMCID: PMC6152389 DOI: 10.3390/molecules22081334] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/26/2017] [Accepted: 08/04/2017] [Indexed: 11/27/2022] Open
Abstract
Protein S-sulfhydration is a newly discovered post-translational modification of specific cysteine residue(s) in target proteins, which is involved in a broad range of cellular functions and metabolic pathways. By changing local conformation and the final activity of target proteins, S-sulfhydration is believed to mediate most cellular responses initiated by H2S, a novel gasotransmitter. In comparison to protein S-sulfhydration, nitric oxide-mediated protein S-nitrosylation has been extensively investigated, including its formation, regulation, transfer and metabolism. Although the investigation on the regulatory mechanisms associated with protein S-sulfhydration is still in its infancy, accumulated evidence suggested that protein S-sulfhydration may share similar chemical features with protein S-nitrosylation. Glutathione persulfide acts as a major donor for protein S-sulfhydration. Here, we review the present knowledge on protein S-sulfhydration, and also predict its formation and regulation mechanisms based on the knowledge from protein S-nitrosylation.
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Borotto NB, McClory PJ, Martin BR, Håkansson K. Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 2017; 89:8304-8310. [PMID: 28708386 DOI: 10.1021/acs.analchem.7b01461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein S-sulfinylation (R-SO2-) and S-sulfonylation (R-SO3-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Phillip J McClory
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brent R Martin
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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45
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Abstract
Kinase-mediated phosphorylation is a pivotal regulatory process in stomatal responses to stresses. Through a redox proteomics study, a sucrose non-fermenting 1-related protein kinase (SnRK2.4) was identified to be redox-regulated in Brassica napus guard cells upon abscisic acid treatment. There are six genes encoding SnRK2.4 paralogs in B. napus Here, we show that recombinant BnSnRK2.4-1C exhibited autophosphorylation activity and preferentially phosphorylated the N-terminal region of B. napus slow anion channel (BnSLAC1-NT) over generic substrates. The in vitro activity of BnSnRK2.4-1C requires the presence of manganese (Mn2+). Phosphorylation sites of autophosphorylated BnSnRK2.4-1C were mapped, including serine and threonine residues in the activation loop. In vitro BnSnRK2.4-1C autophosphorylation activity was inhibited by oxidants such as H2O2 and recovered by active thioredoxin isoforms, indicating redox regulation of BnSnRK2.4-1C. Thiol-specific isotope tagging followed by mass spectrometry analysis revealed specific cysteine residues responsive to oxidant treatments. The in vivo activity of BnSnRK2.4-1C is inhibited by 15 min of H2O2 treatment. Taken together, these data indicate that BnSnRK2.4-1C, an SnRK preferentially expressed in guard cells, is redox-regulated with potential roles in guard cell signal transduction.
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46
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Sommer N, Hüttemann M, Pak O, Scheibe S, Knoepp F, Sinkler C, Malczyk M, Gierhardt M, Esfandiary A, Kraut S, Jonas F, Veith C, Aras S, Sydykov A, Alebrahimdehkordi N, Giehl K, Hecker M, Brandes RP, Seeger W, Grimminger F, Ghofrani HA, Schermuly RT, Grossman LI, Weissmann N. Mitochondrial Complex IV Subunit 4 Isoform 2 Is Essential for Acute Pulmonary Oxygen Sensing. Circ Res 2017; 121:424-438. [PMID: 28620066 DOI: 10.1161/circresaha.116.310482] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 12/14/2016] [Accepted: 06/14/2017] [Indexed: 12/17/2022]
Abstract
RATIONALE Acute pulmonary oxygen sensing is essential to avoid life-threatening hypoxemia via hypoxic pulmonary vasoconstriction (HPV) which matches perfusion to ventilation. Hypoxia-induced mitochondrial superoxide release has been suggested as a critical step in the signaling pathway underlying HPV. However, the identity of the primary oxygen sensor and the mechanism of superoxide release in acute hypoxia, as well as its relevance for chronic pulmonary oxygen sensing, remain unresolved. OBJECTIVES To investigate the role of the pulmonary-specific isoform 2 of subunit 4 of the mitochondrial complex IV (Cox4i2) and the subsequent mediators superoxide and hydrogen peroxide for pulmonary oxygen sensing and signaling. METHODS AND RESULTS Isolated ventilated and perfused lungs from Cox4i2-/- mice lacked acute HPV. In parallel, pulmonary arterial smooth muscle cells (PASMCs) from Cox4i2-/- mice showed no hypoxia-induced increase of intracellular calcium. Hypoxia-induced superoxide release which was detected by electron spin resonance spectroscopy in wild-type PASMCs was absent in Cox4i2-/- PASMCs and was dependent on cysteine residues of Cox4i2. HPV could be inhibited by mitochondrial superoxide inhibitors proving the functional relevance of superoxide release for HPV. Mitochondrial hyperpolarization, which can promote mitochondrial superoxide release, was detected during acute hypoxia in wild-type but not Cox4i2-/- PASMCs. Downstream signaling determined by patch-clamp measurements showed decreased hypoxia-induced cellular membrane depolarization in Cox4i2-/- PASMCs compared with wild-type PASMCs, which could be normalized by the application of hydrogen peroxide. In contrast, chronic hypoxia-induced pulmonary hypertension and pulmonary vascular remodeling were not or only slightly affected by Cox4i2 deficiency, respectively. CONCLUSIONS Cox4i2 is essential for acute but not chronic pulmonary oxygen sensing by triggering mitochondrial hyperpolarization and release of mitochondrial superoxide which, after conversion to hydrogen peroxide, contributes to cellular membrane depolarization and HPV. These findings provide a new model for oxygen-sensing processes in the lung and possibly also in other organs.
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Affiliation(s)
- Natascha Sommer
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Maik Hüttemann
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Oleg Pak
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Susan Scheibe
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Fenja Knoepp
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Christopher Sinkler
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Monika Malczyk
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Mareike Gierhardt
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Azadeh Esfandiary
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Simone Kraut
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Felix Jonas
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Christine Veith
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Siddhesh Aras
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Akylbek Sydykov
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Nasim Alebrahimdehkordi
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Klaudia Giehl
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Matthias Hecker
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Ralf P Brandes
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Werner Seeger
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Friedrich Grimminger
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Hossein A Ghofrani
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Ralph T Schermuly
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
| | - Lawrence I Grossman
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.).
| | - Norbert Weissmann
- From the Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany (N.S., O.P., S.S., F.K., M.M., M.G., A.E., S.K., F.J., C.V., A.S., N.A., K.G., M.H., W.S., F.G., H.A.G., R.T.S., N.W.); Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI (M.H., C.S., S.A., L.I.G.); Institut für Kardiovaskuläre Physiologie, Goethe-Universität, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany (R.P.B.); and Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (W.S.)
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Duan J, Gaffrey MJ, Qian WJ. Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines. MOLECULAR BIOSYSTEMS 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] [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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Parker L, Shaw CS, Stepto NK, Levinger I. Exercise and Glycemic Control: Focus on Redox Homeostasis and Redox-Sensitive Protein Signaling. Front Endocrinol (Lausanne) 2017; 8:87. [PMID: 28529499 PMCID: PMC5418238 DOI: 10.3389/fendo.2017.00087] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/04/2017] [Indexed: 12/16/2022] Open
Abstract
Physical inactivity, excess energy consumption, and obesity are associated with elevated systemic oxidative stress and the sustained activation of redox-sensitive stress-activated protein kinase (SAPK) and mitogen-activated protein kinase signaling pathways. Sustained SAPK activation leads to aberrant insulin signaling, impaired glycemic control, and the development and progression of cardiometabolic disease. Paradoxically, acute exercise transiently increases oxidative stress and SAPK signaling, yet postexercise glycemic control and skeletal muscle function are enhanced. Furthermore, regular exercise leads to the upregulation of antioxidant defense, which likely assists in the mitigation of chronic oxidative stress-associated disease. In this review, we explore the complex spatiotemporal interplay between exercise, oxidative stress, and glycemic control, and highlight exercise-induced reactive oxygen species and redox-sensitive protein signaling as important regulators of glucose homeostasis.
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Affiliation(s)
- Lewan Parker
- Institute of Sport, Exercise and Active Living (ISEAL), College of Sport and Exercise Science, Victoria University, Melbourne, VIC, Australia
- *Correspondence: Lewan Parker, ,
| | - Christopher S. Shaw
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, VIC, Australia
| | - Nigel K. Stepto
- Institute of Sport, Exercise and Active Living (ISEAL), College of Sport and Exercise Science, Victoria University, Melbourne, VIC, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventative Medicine, Monash University, Clayton, VIC, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Victoria University and Western Health, St. Albans, VIC, Australia
| | - Itamar Levinger
- Institute of Sport, Exercise and Active Living (ISEAL), College of Sport and Exercise Science, Victoria University, Melbourne, VIC, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Victoria University and Western Health, St. Albans, VIC, Australia
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Abstract
Redox homeostasis is crucial for proper cellular functions, including receptor tyrosine kinase signaling, protein folding, and xenobiotic detoxification. Under basal conditions, there is a balance between oxidants and antioxidants. This balance facilitates the ability of oxidants, such as reactive oxygen species, to play critical regulatory functions through a direct modification of a small number of amino acids (e.g. cysteine) on signaling proteins. These signaling functions leverage tight spatial, amplitude, and temporal control of oxidant concentrations. However, when oxidants overwhelm the antioxidant capacity, they lead to a harmful condition of oxidative stress. Oxidative stress has long been held to be one of the key players in disease progression for Huntington's disease (HD). In this review, we will critically review this evidence, drawing some intermediate conclusions, and ultimately provide a framework for thinking about the role of oxidative stress in the pathophysiology of HD.
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Affiliation(s)
- Amit Kumar
- Burke Medical Research Institute, White Plains, NY, USA
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY, USA
- Department of Neurology, Weill Medical College of Cornell University, New York, NY, USA
| | - Rajiv R. Ratan
- Burke Medical Research Institute, White Plains, NY, USA
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY, USA
- Department of Neurology, Weill Medical College of Cornell University, New York, NY, USA
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50
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Ni CL, Seth D, Fonseca FV, Wang L, Xiao TS, Gruber P, Sy MS, Stamler JS, Tartakoff AM. Polyglutamine Tract Expansion Increases S-Nitrosylation of Huntingtin and Ataxin-1. PLoS One 2016; 11:e0163359. [PMID: 27658206 PMCID: PMC5033456 DOI: 10.1371/journal.pone.0163359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
Expansion of the polyglutamine (polyQ) tract in the huntingtin (Htt) protein causes Huntington’s disease (HD), a fatal inherited movement disorder linked to neurodegeneration in the striatum and cortex. S-nitrosylation and S-acylation of cysteine residues regulate many functions of cytosolic proteins. We therefore used a resin-assisted capture approach to identify these modifications in Htt. In contrast to many proteins that have only a single S-nitrosylation or S-acylation site, we identified sites along much of the length of Htt. Moreover, analysis of cells expressing full-length Htt or a large N-terminal fragment of Htt shows that polyQ expansion strongly increases Htt S-nitrosylation. This effect appears to be general since it is also observed in Ataxin-1, which causes spinocerebellar ataxia type 1 (SCA1) when its polyQ tract is expanded. Overexpression of nitric oxide synthase increases the S-nitrosylation of normal Htt and the frequency of conspicuous juxtanuclear inclusions of Htt N-terminal fragments in transfected cells. Taken together with the evidence that S-nitrosylation of Htt is widespread and parallels polyQ expansion, these subcellular changes show that S-nitrosylation affects the biology of this protein in vivo.
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Affiliation(s)
- Chun-Lun Ni
- Cell Biology Program, Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Divya Seth
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Fabio Vasconcelos Fonseca
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Liwen Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Phillip Gruber
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Man-Sun Sy
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Jonathan S. Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Alan M. Tartakoff
- Cell Biology Program, Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, United States of America
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, United States of America
- * E-mail:
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