1
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Qiu F, Liu Y, Liu Z. The Role of Protein S-Nitrosylation in Mitochondrial Quality Control in Central Nervous System Diseases. Aging Dis 2024:AD.2024.0099. [PMID: 38739938 DOI: 10.14336/ad.2024.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/25/2024] [Indexed: 05/16/2024] Open
Abstract
S-Nitrosylation is a reversible covalent post-translational modification. Under physiological conditions, S-nitrosylation plays a dynamic role in a wide range of biological processes by regulating the function of substrate proteins. Like other post-translational modifications, S-nitrosylation can affect protein conformation, activity, localization, aggregation, and protein interactions. Aberrant S-nitrosylation can lead to protein misfolding, mitochondrial fragmentation, synaptic damage, and autophagy. Mitochondria are essential organelles in energy production, metabolite biosynthesis, cell death, and immune responses, among other processes. Mitochondrial dysfunction can result in cell death and has been implicated in the development of many human diseases. Recent evidence suggests that S-nitrosylation and mitochondrial dysfunction are important modulators of the progression of several diseases. In this review, we highlight recent findings regarding the aberrant S- nitrosylation of mitochondrial proteins that regulate mitochondrial biosynthesis, fission and fusion, and autophagy. Specifically, we discuss the mechanisms by which S-nitrosylated mitochondrial proteins exercise mitochondrial quality control under pathological conditions, thereby influencing disease. A better understanding of these pathological events may provide novel therapeutic targets to mitigate the development of neurological diseases.
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Affiliation(s)
- Fang Qiu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yuqiang Liu
- Department of Anesthesiology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiheng Liu
- Department of Anesthesiology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
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2
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Belenichev I, Popazova O, Bukhtiyarova N, Savchenko D, Oksenych V, Kamyshnyi O. Modulating Nitric Oxide: Implications for Cytotoxicity and Cytoprotection. Antioxidants (Basel) 2024; 13:504. [PMID: 38790609 PMCID: PMC11118938 DOI: 10.3390/antiox13050504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the significant progress in the fields of biology, physiology, molecular medicine, and pharmacology; the designation of the properties of nitrogen monoxide in the regulation of life-supporting functions of the organism; and numerous works devoted to this molecule, there are still many open questions in this field. It is widely accepted that nitric oxide (•NO) is a unique molecule that, despite its extremely simple structure, has a wide range of functions in the body, including the cardiovascular system, the central nervous system (CNS), reproduction, the endocrine system, respiration, digestion, etc. Here, we systematize the properties of •NO, contributing in conditions of physiological norms, as well as in various pathological processes, to the mechanisms of cytoprotection and cytodestruction. Current experimental and clinical studies are contradictory in describing the role of •NO in the pathogenesis of many diseases of the cardiovascular system and CNS. We describe the mechanisms of cytoprotective action of •NO associated with the regulation of the expression of antiapoptotic and chaperone proteins and the regulation of mitochondrial function. The most prominent mechanisms of cytodestruction-the initiation of nitrosative and oxidative stresses, the production of reactive oxygen and nitrogen species, and participation in apoptosis and mitosis. The role of •NO in the formation of endothelial and mitochondrial dysfunction is also considered. Moreover, we focus on the various ways of pharmacological modulation in the nitroxidergic system that allow for a decrease in the cytodestructive mechanisms of •NO and increase cytoprotective ones.
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Affiliation(s)
- Igor Belenichev
- Department of Pharmacology and Medical Formulation with Course of Normal Physiology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Olena Popazova
- Department of Histology, Cytology and Embryology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Nina Bukhtiyarova
- Department of Clinical Laboratory Diagnostics, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Dmytro Savchenko
- Department of Pharmacy and Industrial Drug Technology, Bogomolets National Medical University, 01601 Kyiv, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology and Immunology, I. Horbachevsky Ternopil State Medical University, 46001 Ternopil, Ukraine;
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3
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Cho B, Shin M, Chang E, Son S, Shin I, Shim J. S-nitrosylation-triggered unfolded protein response maintains hematopoietic progenitors in Drosophila. Dev Cell 2024; 59:1075-1090.e6. [PMID: 38521056 DOI: 10.1016/j.devcel.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/27/2023] [Accepted: 02/29/2024] [Indexed: 03/25/2024]
Abstract
The Drosophila lymph gland houses blood progenitors that give rise to myeloid-like blood cells. Initially, blood progenitors proliferate, but later, they become quiescent to maintain multipotency before differentiation. Despite the identification of various factors involved in multipotency maintenance, the cellular mechanism controlling blood progenitor quiescence remains elusive. Here, we identify the expression of nitric oxide synthase in blood progenitors, generating nitric oxide for post-translational S-nitrosylation of protein cysteine residues. S-nitrosylation activates the Ire1-Xbp1-mediated unfolded protein response, leading to G2 cell-cycle arrest. Specifically, we identify the epidermal growth factor receptor as a target of S-nitrosylation, resulting in its retention within the endoplasmic reticulum and blockade of its receptor function. Overall, our findings highlight developmentally programmed S-nitrosylation as a critical mechanism that induces protein quality control in blood progenitors, maintaining their undifferentiated state by inhibiting cell-cycle progression and rendering them unresponsive to paracrine factors.
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Affiliation(s)
- Bumsik Cho
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Mingyu Shin
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Eunji Chang
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Seogho Son
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Incheol Shin
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jiwon Shim
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea.
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4
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Zhu L, Wang L, Yang Z, Xu P, Yang S. PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information. Interdiscip Sci 2024; 16:192-217. [PMID: 38206557 DOI: 10.1007/s12539-023-00595-7] [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: 07/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological function mechanisms. In this document, we have constructed a predictor, named PPSNO, forecasting protein SNO sites using stacked integrated learning. PPSNO integrates multiple machine learning techniques into an ensemble model, enhancing its predictive accuracy. First, we established benchmark datasets by collecting SNO sites from various sources, including literature, databases, and other predictors. Second, various techniques for feature extraction are applied to derive characteristics from protein sequences, which are subsequently amalgamated into the PPSNO predictor for training. Five-fold cross-validation experiments show that PPSNO outperformed existing predictors, such as PSNO, PreSNO, pCysMod, DeepNitro, RecSNO, and Mul-SNO. The PPSNO predictor achieved an impressive accuracy of 92.8%, an area under the curve (AUC) of 96.1%, a Matthews correlation coefficient (MCC) of 81.3%, an F1-score of 85.6%, an SN of 79.3%, an SP of 97.7%, and an average precision (AP) of 92.2%. We also employed ROC curves, PR curves, and radar plots to show the superior performance of PPSNO. Our study shows that fused protein sequence features and two-layer stacked ensemble models can improve the accuracy of predicting SNO sites, which can aid in comprehending cellular processes and disease mechanisms. The codes and data are available at https://github.com/serendipity-wly/PPSNO .
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Affiliation(s)
- Lun Zhu
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Liuyang Wang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Zexi Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Piao Xu
- College of Economics and Management, Nanjing Forestry University, Nanjing, 210037, China
| | - Sen Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China.
- The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, 213164, China.
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5
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Clark GC, Lai A, Agarwal A, Liu Z, Wang XY. Biopterin metabolism and nitric oxide recoupling in cancer. Front Oncol 2024; 13:1321326. [PMID: 38469569 PMCID: PMC10925643 DOI: 10.3389/fonc.2023.1321326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/26/2023] [Indexed: 03/13/2024] Open
Abstract
Tetrahydrobiopterin is a cofactor necessary for the activity of several enzymes, the most studied of which is nitric oxide synthase. The role of this cofactor-enzyme relationship in vascular biology is well established. Recently, tetrahydrobiopterin metabolism has received increasing attention in the field of cancer immunology and immunotherapy due to its involvement in the cytotoxic T cell response. Past research has demonstrated that when the availability of BH4 is low, as it is in chronic inflammatory conditions and tumors, electron transfer in the active site of nitric oxide synthase becomes uncoupled from the oxidation of arginine. This results in the production of radical species that are capable of a direct attack on tetrahydrobiopterin, further depleting its local availability. This feedforward loop may act like a molecular switch, reinforcing low tetrahydrobiopterin levels leading to altered NO signaling, restrained immune effector activity, and perpetual vascular inflammation within the tumor microenvironment. In this review, we discuss the evidence for this underappreciated mechanism in different aspects of tumor progression and therapeutic responses. Furthermore, we discuss the preclinical evidence supporting a clinical role for tetrahydrobiopterin supplementation to enhance immunotherapy and radiotherapy for solid tumors and the potential safety concerns.
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Affiliation(s)
- Gene Chatman Clark
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, United States
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Alan Lai
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | | | - Zheng Liu
- Department of Human Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Xiang-Yang Wang
- Department of Human Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, United States
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6
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Falco JA, Wynia-Smith SL, McCoy J, Smith BC, Weerapana E. Identification of Protein Targets of S-Nitroso-Coenzyme A-Mediated S-Nitrosation Using Chemoproteomics. ACS Chem Biol 2024; 19:193-207. [PMID: 38159293 PMCID: PMC11154738 DOI: 10.1021/acschembio.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
S-Nitrosation is a cysteine post-translational modification fundamental to cellular signaling. This modification regulates protein function in numerous biological processes in the nervous, cardiovascular, and immune systems. Small molecule or protein nitrosothiols act as mediators of NO signaling by transferring the NO group (formally NO+) to a free thiol on a target protein through a transnitrosation reaction. The protein targets of specific transnitrosating agents and the extent and functional effects of S-nitrosation on these target proteins have been poorly characterized. S-nitroso-coenzyme A (CoA-SNO) was recently identified as a mediator of endogenous S-nitrosation. Here, we identified direct protein targets of CoA-SNO-mediated transnitrosation using a competitive chemical-proteomic approach that quantified the extent of modification on 789 cysteine residues in response to CoA-SNO. A subset of cysteines displayed high susceptibility to modification by CoA-SNO, including previously uncharacterized sites of S-nitrosation. We further validated and functionally characterized the functional effects of S-nitrosation on the protein targets phosphofructokinase (platelet type), ATP citrate synthase, and ornithine aminotransferase.
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Affiliation(s)
- Julia A. Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James McCoy
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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7
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Zhou HL, Grimmett ZW, Venetos NM, Stomberski CT, Qian Z, McLaughlin PJ, Bansal PK, Zhang R, Reynolds JD, Premont RT, Stamler JS. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling. Cell 2023; 186:5812-5825.e21. [PMID: 38056462 PMCID: PMC10794992 DOI: 10.1016/j.cell.2023.11.009] [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] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/01/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
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Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhaoxia Qian
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Precious J McLaughlin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Puneet K Bansal
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rongli Zhang
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Anesthesiology and Perioperative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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8
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Lualdi M, Casale F, Rizzone MG, Zibetti M, Monti C, Colugnat I, Calvo A, De Marco G, Moglia C, Fuda G, Comi C, Chiò A, Lopiano L, Fasano M, Alberio T. Shared and Unique Disease Pathways in Amyotrophic Lateral Sclerosis and Parkinson's Disease Unveiled in Peripheral Blood Mononuclear Cells. ACS Chem Neurosci 2023; 14:4240-4251. [PMID: 37939393 DOI: 10.1021/acschemneuro.3c00629] [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: 11/10/2023] Open
Abstract
Recent evidence supports an association between amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). Indeed, prospective population-based studies demonstrated that about one-third of ALS patients develop parkinsonian (PK) signs, even though different neuronal circuitries are involved. In this context, proteomics represents a valuable tool to identify unique and shared pathological pathways. Here, we used two-dimensional electrophoresis to obtain the proteomic profile of peripheral blood mononuclear cells (PBMCs) from PD and ALS patients including a small cohort of ALS patients with parkinsonian signs (ALS-PK). After the removal of protein spots correlating with confounding factors, we applied a sparse partial least square discriminant analysis followed by recursive feature elimination to obtain two protein classifiers able to discriminate (i) PD and ALS patients (30 spots) and (ii) ALS-PK patients among all ALS subjects (20 spots). Functionally, the glycolysis pathway was significantly overrepresented in the first signature, while extracellular interactions and intracellular signaling were enriched in the second signature. These results represent molecular evidence at the periphery for the classification of ALS-PK as ALS patients that manifest parkinsonian signs, rather than comorbid patients suffering from both ALS and PD. Moreover, we confirmed that low levels of fibrinogen in PBMCs is a characteristic feature of PD, also when compared with another movement disorder. Collectively, we provide evidence that peripheral protein signatures are a tool to differentially investigate neurodegenerative diseases and highlight altered biochemical pathways.
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Affiliation(s)
- Marta Lualdi
- Department of Science and High Technology and Center for Research in Neuroscience, University of Insubria, I-21052 Busto Arsizio, Varese, Italy
| | - Federico Casale
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Mario Giorgio Rizzone
- "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Maurizio Zibetti
- "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Chiara Monti
- Department of Science and High Technology and Center for Research in Neuroscience, University of Insubria, I-21052 Busto Arsizio, Varese, Italy
| | - Ilaria Colugnat
- Department of Science and High Technology and Center for Research in Neuroscience, University of Insubria, I-21052 Busto Arsizio, Varese, Italy
| | - Andrea Calvo
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Giovanni De Marco
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Cristina Moglia
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Giuseppe Fuda
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Cristoforo Comi
- Department of Translational Medicine, University of Piemonte Orientale, and Sant'Andrea Hospital, I-13100 Vercelli, Italy
| | - Adriano Chiò
- Neurology 1, ALS Expert Center, "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Leonardo Lopiano
- "Rita Levi Montalcini" Department of Neuroscience, University of Torino, and AOU Città della Salute e della Scienza, I-10126 Torino, Italy
| | - Mauro Fasano
- Department of Science and High Technology and Center for Research in Neuroscience, University of Insubria, I-21052 Busto Arsizio, Varese, Italy
| | - Tiziana Alberio
- Department of Science and High Technology and Center for Research in Neuroscience, University of Insubria, I-21052 Busto Arsizio, Varese, Italy
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9
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Moltó E, Pintado C, Louzada RA, Bernal-Mizrachi E, Andrés A, Gallardo N, Bonzon-Kulichenko E. Unbiased Phosphoproteome Mining Reveals New Functional Sites of Metabolite-Derived PTMs Involved in MASLD Development. Int J Mol Sci 2023; 24:16172. [PMID: 38003361 PMCID: PMC10671570 DOI: 10.3390/ijms242216172] [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: 09/12/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are paramount in health and disease. Phosphoproteome analysis by enrichment techniques is becoming increasingly attractive for biomedical research. Recent findings show co-enrichment of other phosphate-containing biologically relevant PTMs, but these results were obtained by closed searches focused on the modifications sought. Open searches are a breakthrough in high-throughput PTM analysis (OS-PTM), identifying practically all PTMs detectable by mass spectrometry, even unknown ones, with their modified sites, in a hypothesis-free and deep manner. Here we reanalyze liver phosphoproteome by OS-PTM, demonstrating its extremely complex nature. We found extensive Lys glycerophosphorylations (pgK), as well as modification with glycerylphosphorylethanolamine on Glu (gpetE) and flavin mononucleotide on His (fmnH). The functionality of these metabolite-derived PTMs is demonstrated during metabolic dysfunction-associated steatotic liver disease (MASLD) development in mice. MASLD elicits specific alterations in pgK, epgE and fmnH in the liver, mainly on glycolytic enzymes and mitochondrial proteins, suggesting an increase in glycolysis and mitochondrial ATP production from the early insulin-resistant stages. Thus, we show new possible mechanisms based on metabolite-derived PTMs leading to intrahepatic lipid accumulation during MASLD development and reinforce phosphoproteome enrichment as a valuable tool with which to study the functional implications of a variety of low-abundant phosphate-containing PTMs in cell physiology.
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Affiliation(s)
- Eduardo Moltó
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
| | - Cristina Pintado
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
| | - Ruy Andrade Louzada
- Department of Internal Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ernesto Bernal-Mizrachi
- Department of Internal Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Antonio Andrés
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain
| | - Nilda Gallardo
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain
| | - Elena Bonzon-Kulichenko
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
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10
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Seth D, Stomberski CT, McLaughlin PJ, Premont RT, Lundberg K, Stamler JS. Comparison of the Nitric Oxide Synthase Interactomes and S-Nitroso-Proteomes: Furthering the Case for Enzymatic S-Nitrosylation. Antioxid Redox Signal 2023; 39:621-634. [PMID: 37053107 PMCID: PMC10619892 DOI: 10.1089/ars.2022.0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/13/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Aims: S-nitrosylation of proteins is the main mechanism through which nitric oxide (NO) regulates cellular function and likely represents the archetype redox-based signaling system across aerobic and anaerobic organisms. How NO generated by different nitric oxide synthase (NOS) isoforms leads to specificity of S-nitrosylation remains incompletely understood. This study aimed to identify proteins interacting with, and whose S-nitrosylation is mediated by, human NOS isoforms in the same cellular system, thereby illuminating the contribution of individual NOSs to specificity. Results: Of the hundreds of proteins interacting with each NOS, many were also S-nitrosylated. However, a large proportion of S-nitrosylated proteins (SNO-proteins) did not associate with NOS. Moreover, most NOS interactors and SNO-proteins were unique to each isoform. The amount of NO produced by each NOS isoform was unrelated to the numbers of SNO-proteins. Thus, NOSs promoted S-nitrosylation of largely distinct sets of target proteins. Different signaling pathways were enriched downstream of each NOS. Innovation and Conclusion: The interactomes and SNOomes of individual NOS isoforms were largely distinct. Only a small fraction of SNO-proteins interacted with their respective NOS. Amounts of S-nitrosylation were unrelated to the amount of NO generated by NOSs. These data argue against free diffusion of NO or NOS interactions as being necessary or sufficient for S-nitrosylation and favor roles for additional enzymes and/or regulatory elements in imparting SNO-protein specificity. Antioxid. Redox Signal. 39, 621-634.
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Affiliation(s)
- Divya Seth
- Department of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Colin T. Stomberski
- Department of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Precious J. McLaughlin
- Department of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Richard T. Premont
- Department of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Kathleen Lundberg
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jonathan S. Stamler
- Department of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
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11
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Andrabi SM, Sharma NS, Karan A, Shahriar SMS, Cordon B, Ma B, Xie J. Nitric Oxide: Physiological Functions, Delivery, and Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303259. [PMID: 37632708 PMCID: PMC10602574 DOI: 10.1002/advs.202303259] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Indexed: 08/28/2023]
Abstract
Nitric oxide (NO) is a gaseous molecule that has a central role in signaling pathways involved in numerous physiological processes (e.g., vasodilation, neurotransmission, inflammation, apoptosis, and tumor growth). Due to its gaseous form, NO has a short half-life, and its physiology role is concentration dependent, often restricting its function to a target site. Providing NO from an external source is beneficial in promoting cellular functions and treatment of different pathological conditions. Hence, the multifaceted role of NO in physiology and pathology has garnered massive interest in developing strategies to deliver exogenous NO for the treatment of various regenerative and biomedical complexities. NO-releasing platforms or donors capable of delivering NO in a controlled and sustained manner to target tissues or organs have advanced in the past few decades. This review article discusses in detail the generation of NO via the enzymatic functions of NO synthase as well as from NO donors and the multiple biological and pathological processes that NO modulates. The methods for incorporating of NO donors into diverse biomaterials including physical, chemical, or supramolecular techniques are summarized. Then, these NO-releasing platforms are highlighted in terms of advancing treatment strategies for various medical problems.
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Affiliation(s)
- Syed Muntazir Andrabi
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Navatha Shree Sharma
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Anik Karan
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - S. M. Shatil Shahriar
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Brent Cordon
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Bing Ma
- Cell Therapy Manufacturing FacilityMedStar Georgetown University HospitalWashington, DC2007USA
| | - Jingwei Xie
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
- Department of Mechanical and Materials EngineeringCollege of EngineeringUniversity of Nebraska LincolnLincolnNE68588USA
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12
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Moshfegh CM, Elkhatib SK, Watson GF, Drake J, Taylor ZN, Reed EC, Lauten TH, Clopp AJ, Vladimirov VI, Case AJ. S100a9 Protects Against the Effects of Repeated Social Defeat Stress. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:919-929. [PMID: 37881565 PMCID: PMC10593888 DOI: 10.1016/j.bpsgos.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Background Posttraumatic stress disorder, a consequence of psychological trauma, is associated with increased inflammation and an elevated risk of developing comorbid inflammatory diseases. However, the mechanistic link between this mental health disorder and inflammation remains elusive. We previously found that S100a8 and S100a9 messenger RNA, genes that encode the protein calprotectin, were significantly upregulated in T lymphocytes and positively correlated with inflammatory gene expression and the mitochondrial redox environment in these cells. Therefore, we hypothesized that genetic deletion of calprotectin would attenuate the inflammatory and redox phenotype displayed after psychological trauma. Methods We used a preclinical mouse model of posttraumatic stress disorder known as repeated social defeat stress (RSDS) combined with pharmacological and genetic manipulation of S100a9 (which functionally eliminates calprotectin). A total of 186 animals (93 control, 93 RSDS) were used in these studies. Results Unexpectedly, we observed worsening of behavioral pathology, inflammation, and the mitochondrial redox environment in mice after RSDS compared with wild-type animals. Furthermore, loss of calprotectin significantly enhanced the metabolic demand on T lymphocytes, suggesting that this protein may play an undescribed role in mitochondrial regulation. This was further supported by single-cell RNA sequencing analysis demonstrating that RSDS and loss of S100a9 primarily altered genes associated with mitochondrial function and oxidative phosphorylation. Conclusions These data demonstrate that the loss of calprotectin potentiates the RSDS-induced phenotype, which suggests that its observed upregulation after psychological trauma may provide previously unexplored protective functions.
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Affiliation(s)
- Cassandra M. Moshfegh
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Safwan K. Elkhatib
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gabrielle F. Watson
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
| | - Zachary N. Taylor
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
| | - Emily C. Reed
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
- Department of Medical Physiology, Texas A&M University, Bryan, Texas
| | - Tatlock H. Lauten
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
- Department of Medical Physiology, Texas A&M University, Bryan, Texas
| | - Amelia J. Clopp
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
- Department of Medical Physiology, Texas A&M University, Bryan, Texas
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
- Department of Psychiatry, University of Arizona, Phoenix, Arizona
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, Maryland
| | - Adam J. Case
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, Texas
- Department of Medical Physiology, Texas A&M University, Bryan, Texas
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13
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Mollace R, Scarano F, Bava I, Carresi C, Maiuolo J, Tavernese A, Gliozzi M, Musolino V, Muscoli S, Palma E, Muscoli C, Salvemini D, Federici M, Macrì R, Mollace V. Modulation of the nitric oxide/cGMP pathway in cardiac contraction and relaxation: Potential role in heart failure treatment. Pharmacol Res 2023; 196:106931. [PMID: 37722519 DOI: 10.1016/j.phrs.2023.106931] [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: 05/31/2023] [Revised: 09/09/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Evidence exists that heart failure (HF) has an overall impact of 1-2 % in the global population being often associated with comorbidities that contribute to increased disease prevalence, hospitalization, and mortality. Recent advances in pharmacological approaches have significantly improved clinical outcomes for patients with vascular injury and HF. Nevertheless, there remains an unmet need to clarify the crucial role of nitric oxide/cyclic guanosine 3',5'-monophosphate (NO/cGMP) signalling in cardiac contraction and relaxation, to better identify the key mechanisms involved in the pathophysiology of myocardial dysfunction both with reduced (HFrEF) as well as preserved ejection fraction (HFpEF). Indeed, NO signalling plays a crucial role in cardiovascular homeostasis and its dysregulation induces a significant increase in oxidative and nitrosative stress, producing anatomical and physiological cardiac alterations that can lead to heart failure. The present review aims to examine the molecular mechanisms involved in the bioavailability of NO and its modulation of downstream pathways. In particular, we focus on the main therapeutic targets and emphasize the recent evidence of preclinical and clinical studies, describing the different emerging therapeutic strategies developed to counteract NO impaired signalling and cardiovascular disease (CVD) development.
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Affiliation(s)
- Rocco Mollace
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy; Department of Systems Medicine, University of Rome Tor Vergata, Italy
| | - Federica Scarano
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Irene Bava
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Cristina Carresi
- Veterinary Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Jessica Maiuolo
- Pharmaceutical Biology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Annamaria Tavernese
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Micaela Gliozzi
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Vincenzo Musolino
- Pharmaceutical Biology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Saverio Muscoli
- Division of Cardiology, Foundation PTV Polyclinic Tor Vergata, Rome 00133, Italy
| | - Ernesto Palma
- Veterinary Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Carolina Muscoli
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Daniela Salvemini
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Massimo Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Italy
| | - Roberta Macrì
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy.
| | - Vincenzo Mollace
- Pharmacology Laboratory, Institute of Research for Food Safety and Health IRC-FSH, Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy; Renato Dulbecco Institute, Lamezia Terme, Catanzaro 88046, Italy.
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14
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Bodnar Y, Lillig CH. Cysteinyl and methionyl redox switches: Structural prerequisites and consequences. Redox Biol 2023; 65:102832. [PMID: 37536083 PMCID: PMC10412846 DOI: 10.1016/j.redox.2023.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
Redox modifications of specific cysteinyl and methionyl residues regulate key enzymes and signal-transducing proteins in various pathways. Here, we analyzed the effect of redox modifications on protein structure screening the RCSB protein data bank for oxidative modifications of proteins, i.e. protein disulfides, mixed disulfides with glutathione, cysteinyl sulfenic acids, cysteinyl S-nitrosylation, and methionyl sulfoxide residues. When available, these structures were compared to the structures of the same proteins in the reduced state with respect to both pre-requirements for the oxidative modifications as well as the structural consequences of the modifications. In general, the conformational changes induced by the redox modification are small, i.e. within the range of normal fluctuations. Some redox modifications, disulfides in particular, induces alterations in the electrostatic properties of the proteins. Solvent accessibility does not seem to be a strict pre-requirement for the redox modification of a particular residue. We identified an enrichment of certain other amino acid residues in the vicinity of the susceptible residues, for disulfide and sulfenic acid modifications, for instance, histidyl and tyrosyl residues. These motifs, as well as the specific features of the susceptible sulfur-containing amino acids, may become helpful for the prediction of redox modifications.
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Affiliation(s)
- Yana Bodnar
- Institut for Physics, University of Greifswald, Germany; Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.
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15
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Kalinina EV, Novichkova MD. S-Glutathionylation and S-Nitrosylation as Modulators of Redox-Dependent Processes in Cancer Cell. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:924-943. [PMID: 37751864 DOI: 10.1134/s0006297923070064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 09/28/2023]
Abstract
Development of oxidative/nitrosative stress associated with the activation of oncogenic pathways results from the increase in the generation of reactive oxygen and nitrogen species (ROS/RNS) in tumor cells, where they can have a dual effect. At high concentrations, ROS/RNS cause cell death and limit tumor growth at certain phases of its development, while their low amounts promote oxidative/nitrosative modifications of key redox-dependent residues in regulatory proteins. The reversibility of such modifications as S-glutathionylation and S-nitrosylation that proceed through the electrophilic attack of ROS/RNS on nucleophilic Cys residues ensures the redox-dependent switch in the activity of signaling proteins, as well as the ability of these compounds to control cell proliferation and programmed cell death. The content of S-glutathionylated and S-nitrosylated proteins is controlled by the balance between S-glutathionylation/deglutathionylation and S-nitrosylation/denitrosylation, respectively, and depends on the cellular redox status. The extent of S-glutathionylation and S-nitrosylation of protein targets and their ratio largely determine the status and direction of signaling pathways in cancer cells. The review discusses the features of S-glutathionylation and S-nitrosylation reactions and systems that control them in cancer cells, as well as their relationship with redox-dependent processes and tumor growth.
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16
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Tripathi SJ, Chakraborty S, Miller E, Pieper AA, Paul BD. Hydrogen sulfide signalling in neurodegenerative diseases. Br J Pharmacol 2023:10.1111/bph.16170. [PMID: 37338307 PMCID: PMC10730776 DOI: 10.1111/bph.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023] Open
Abstract
The gaseous neurotransmitter hydrogen sulfide (H2 S) exerts neuroprotective efficacy in the brain via post-translational modification of cysteine residues by sulfhydration, also known as persulfidation. This process is comparable in biological impact to phosphorylation and mediates a variety of signalling events. Unlike conventional neurotransmitters, H2 S cannot be stored in vesicles due to its gaseous nature. Instead, it is either locally synthesized or released from endogenous stores. Sulfhydration affords both specific and general neuroprotective effects and is critically diminished in several neurodegenerative disorders. Conversely, some forms of neurodegenerative disease are linked to excessive cellular H2 S. Here, we review the signalling roles of H2 S across the spectrum of neurodegenerative diseases, including Huntington's disease, Parkinson's disease, Alzheimer's disease, Down syndrome, traumatic brain injury, the ataxias, and amyotrophic lateral sclerosis, as well as neurodegeneration generally associated with ageing.
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Affiliation(s)
- Sunil Jamuna Tripathi
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Suwarna Chakraborty
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emiko Miller
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Andrew A Pieper
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center; Cleveland, Ohio, USA
- School of Medicine, Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Translational Therapeutics Core, Cleveland Alzheimer's Disease Research Center, Cleveland, Ohio, USA
| | - Bindu D Paul
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
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17
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Wang K, Moore A, Grayson C, Mailloux RJ. S-nitroso-glutathione (GSNO) inhibits hydrogen peroxide production by alpha-ketoglutarate dehydrogenase: An investigation into sex and diet effects. Free Radic Biol Med 2023; 204:287-300. [PMID: 37225107 DOI: 10.1016/j.freeradbiomed.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/06/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
Pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGDH) are vital sources of hydrogen peroxide (H2O2) and key sites for redox regulation. Here, we report KGDH is more sensitive to inhibition by S-nitroso-glutathione (GSNO) when compared to PDH and deactivation of both enzymes by nitro modification is affected by sex and diet. Liver mitochondria from male C57BL/6N mice displayed a robust inhibition of H2O2 production after exposure to 500-2000 μM GSNO. H2O2 genesis by PDH was not significantly affected by GSNO. Purified KGDH of porcine heart origin displayed a ∼82% decrease in H2O2 generating activity at 500 μM GSNO, which was mirrored by a decrease in NADH production. By contrast, H2O2- and NADH-producing activity of purified PDH was only minimally affected by an incubation in 500 μM GSNO. Incubations in GSNO had no significant effect on the H2O2-generating activity of KGDH and PDH in female liver mitochondria when compared to samples collected from males, which was attributed to higher GSNO reductase (GSNOR) activity. High fat feeding augmented the GSNO-mediated inhibition of KGDH in liver mitochondria from male mice. Exposure of male mice to a HFD also resulted in a significant decrease in the GSNO-mediated inhibition of H2O2 genesis by PDH, an effect not observed in mice fed a control-matched diet (CD). Female mice displayed higher resistance to the GSNO-induced inhibition of H2O2 production, regardless of being fed a CD or HFD. However, exposure to a HFD did result in a small but significant decrease in H2O2 production by KGDH and PDH when female liver mitochondria were treated with GSNO. Although, the effect was less when compared to their male counterparts. Collectively, we show for the first time GSNO deactivates H2O2 production by α-keto acid dehydrogenases and we demonstrate that sex and diet are determinants for the nitro-inhibition of both KGDH and PDH.
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Affiliation(s)
- Kevin Wang
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada
| | - Amanda Moore
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada
| | - Cathryn Grayson
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada
| | - Ryan J Mailloux
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada.
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18
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Li Y, Hook JS, Ding Q, Xiao X, Chung SS, Mettlen M, Xu L, Moreland JG, Agathocleous M. Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation. Nat Commun 2023; 14:2610. [PMID: 37147288 PMCID: PMC10162006 DOI: 10.1038/s41467-023-37567-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/20/2023] [Indexed: 05/07/2023] Open
Abstract
Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in patients with COVID-19. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19 and healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism. Metabolic changes in neutrophils from patients with severe COVID-19 were consistent with reduced activity of the glycolytic enzyme GAPDH. Inhibition of GAPDH blocked glycolysis and promoted pentose phosphate pathway activity but blunted the neutrophil respiratory burst. Inhibition of GAPDH was sufficient to cause neutrophil extracellular trap (NET) formation which required neutrophil elastase activity. GAPDH inhibition increased neutrophil pH, and blocking this increase prevented cell death and NET formation. These findings indicate that neutrophils in severe COVID-19 have an aberrant metabolism which can contribute to their dysfunction. Our work also shows that NET formation, a pathogenic feature of many inflammatory diseases, is actively suppressed in neutrophils by a cell-intrinsic mechanism controlled by GAPDH.
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Affiliation(s)
- Yafeng Li
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jessica S Hook
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing Ding
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xue Xiao
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen S Chung
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marcel Mettlen
- Department of Cell Biology, Quantitative Light Microscopy Core, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lin Xu
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jessica G Moreland
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michalis Agathocleous
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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19
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Post-translational modifications on the metal-sequestering protein calprotectin. Biometals 2023:10.1007/s10534-023-00493-x. [PMID: 36826733 PMCID: PMC10393864 DOI: 10.1007/s10534-023-00493-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
Human calprotectin (CP, S100A8/S100A9 oligomer) is an abundant neutrophil protein that contributes to innate immunity by sequestering nutrient metal ions in the extracellular space. This process starves invading microbial pathogens of essential metal nutrients, which can inhibit growth and colonization. Over the past decade, fundamental and clinical studies have revealed that the S100A8 and S100A9 subunits of CP exhibit a variety of post-translational modifications (PTMs). This review summarizes PTMs on the CP subunits that have been detected and highlights two recent studies that evaluated the structural and functional consequences of methionine and cysteine oxidation on CP. Collectively, these investigations indicate that the molecular speciation of extracellular CP is complex and composed of multiple proteoforms. Moreover, PTMs may impact biological function and the lifetime of the protein. It is therefore important that post-translationally modified CP species receive consideration and integration into the current working model for how CP functions in nutritional immunity.
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20
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Martin EA, Fulcher JM, Zhou M, Monroe ME, Petyuk VA. TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis. J Proteome Res 2023; 22:399-409. [PMID: 36631391 DOI: 10.1021/acs.jproteome.2c00570] [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] [Indexed: 01/13/2023]
Abstract
Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with the interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. We extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across data sets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS data sets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.
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Affiliation(s)
- Evan A Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - James M Fulcher
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Mowei Zhou
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
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21
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Polakowska M, Steczkiewicz K, Szczepanowski RH, Wysłouch-Cieszyńska A. Toward an understanding of the conformational plasticity of S100A8 and S100A9 Ca 2+-binding proteins. J Biol Chem 2023; 299:102952. [PMID: 36731796 PMCID: PMC10124908 DOI: 10.1016/j.jbc.2023.102952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
S100A8 and S100A9 are small, human, Ca2+-binding proteins with multiple intracellular and extracellular functions in signaling, regulation, and defense. The two proteins are not detected as monomers but form various noncovalent homo- or hetero-oligomers related to specific activities in human physiology. Because of their significant roles in numerous medical conditions, there has been intense research on the conformational properties of various S100A8 and S100A9 proteoforms as essential targets of drug discovery. NMR or crystal structures are currently available only for mutated or truncated protein complexes, mainly with bound metal ions, that may well reflect the proteins' properties outside cells but not in other biological contexts in which they perform. Here, we used structural mass spectrometry methods combined with molecular dynamics simulations to compare the conformations of wild-type full-length S100A8 and S100A9 subunits in biologically relevant homo- and hetero-dimers and in higher oligomers formed in the presence of calcium or zinc ions. We provide, first, rationales for their functional response to changing environmental conditions, by elucidating differences between proteoforms in flexible protein regions that may provide the plasticity of the binding sites for the multiple targets, and second, the key factors contributing to the variable stability of the oligomers. The described methods and a systematic view of the conformational properties of S100A8 and S100A9 complexes provide a basis for further research to characterize and modulate their functions for basic science and therapies.
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Affiliation(s)
- Magdalena Polakowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Księcia Trojdena Street, 02-109 Warsaw, Poland
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22
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Verde C, Giordano D, Bruno S. NO and Heme Proteins: Cross-Talk between Heme and Cysteine Residues. Antioxidants (Basel) 2023; 12:antiox12020321. [PMID: 36829880 PMCID: PMC9952723 DOI: 10.3390/antiox12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Heme proteins are a diverse group that includes several unrelated families. Their biological function is mainly associated with the reactivity of the heme group, which-among several other reactions-can bind to and react with nitric oxide (NO) and other nitrogen compounds for their production, scavenging, and transport. The S-nitrosylation of cysteine residues, which also results from the reaction with NO and other nitrogen compounds, is a post-translational modification regulating protein activity, with direct effects on a variety of signaling pathways. Heme proteins are unique in exhibiting this dual reactivity toward NO, with reported examples of cross-reactivity between the heme and cysteine residues within the same protein. In this work, we review the literature on this interplay, with particular emphasis on heme proteins in which heme-dependent nitrosylation has been reported and those for which both heme nitrosylation and S-nitrosylation have been associated with biological functions.
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Affiliation(s)
- Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
- Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
- Correspondence:
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23
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Taylor S, Murray A, Francis M, Abramova E, Guo C, Laskin DL, Gow AJ. Regulation of macrophage activation by S-Nitrosothiols following ozone-induced lung injury. Toxicol Appl Pharmacol 2022; 457:116281. [PMID: 36244437 PMCID: PMC10250783 DOI: 10.1016/j.taap.2022.116281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/01/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
Abstract
Acute exposure to ozone causes oxidative stress, characterized by increases in nitric oxide (NO) and other reactive nitrogen species in the lung. NO has been shown to modify thiols generating S-nitrosothiols (SNOs); this results in altered protein function. In macrophages this can lead to changes in inflammatory activity which impact the resolution of inflammation. As SNO formation is dependent on the redox state of both the NO donor and the recipient thiol, the local microenvironment plays a key role in its regulation. This dictates not only the chemical feasibility of SNO formation but also mechanisms by which they may form. In these studies, we compared the ability of the SNO donors, ethyl nitrite (ENO), which targets both hydrophobic and hydrophilic thiols, SNO-propanamide (SNOPPM) which targets hydrophobic thiols, and S-nitroso-N-acetylcysteine. (SNAC) which targets hydrophilic thiols. to modify macrophage activation following ozone exposure. Mice were treated with air or ozone (0.8 ppm, 3 h) followed 1 h later by intranasal administration of ENO, SNOPPM or SNAC (1-500 μM) or appropriate controls. Mice were euthanized 48 h later. Each of the SNO donors reduced ozone-induced inflammation and modified the phenotype of macrophages both within the lung lining fluid and the tissue. ENO and SNOPPM were more effective than SNAC. These findings suggest that the hydrophobic SNO thiol pool targeted by SNOPPM and ENO plays a major role in regulating macrophage phenotype following ozone induced injury.
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Affiliation(s)
- Sheryse Taylor
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Alexa Murray
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Mary Francis
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Elena Abramova
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Changjiang Guo
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Debra L Laskin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America
| | - Andrew J Gow
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States of America.
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24
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Stomberski CT, Venetos NM, Zhou HL, Qian Z, Collison BR, Field SJ, Premont RT, Stamler JS. A multienzyme S-nitrosylation cascade regulates cholesterol homeostasis. Cell Rep 2022; 41:111538. [PMID: 36288700 PMCID: PMC9667709 DOI: 10.1016/j.celrep.2022.111538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 11/03/2022] Open
Abstract
Accumulating evidence suggests that protein S-nitrosylation is enzymatically regulated and that specificity in S-nitrosylation derives from dedicated S-nitrosylases and denitrosylases that conjugate and remove S-nitrosothiols, respectively. Here, we report that mice deficient in the protein denitrosylase SCoR2 (S-nitroso-Coenzyme A Reductase 2; AKR1A1) exhibit marked reductions in serum cholesterol due to reduced secretion of the cholesterol-regulating protein PCSK9. SCoR2 associates with endoplasmic reticulum (ER) secretory machinery to control an S-nitrosylation cascade involving ER cargo-selection proteins SAR1 and SURF4, which moonlight as S-nitrosylases. SAR1 acts as a SURF4 nitrosylase and SURF4 as a PCSK9 nitrosylase to inhibit PCSK9 secretion, while SCoR2 counteracts nitrosylase activity by promoting PCSK9 denitrosylation. Inhibition of PCSK9 by an NO-based drug requires nitrosylase activity, and small-molecule inhibition of SCoR2 phenocopies the PCSK9-mediated reductions in cholesterol observed in SCoR2-deficient mice. Our results reveal enzymatic machinery controlling cholesterol levels through S-nitrosylation and suggest a distinct treatment paradigm for cardiovascular disease.
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Affiliation(s)
- Colin T Stomberski
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nicholas M Venetos
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Zhaoxia Qian
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Bryce R Collison
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Seth J Field
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA.
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25
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Wang J, Wang X, Zhang C, Zhou X. Microplastics induce immune suppression via S100A8 downregulation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113905. [PMID: 35868177 DOI: 10.1016/j.ecoenv.2022.113905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Microplastic (MP) pollution has been largely reported in the daily consumption of water and food, however, the toxicities of MPs to human beings remain largely uncovered. We found that MPs in drinking water significantly impaired mouse immune function by reducing spleen weight, CD8+ T cell amount and raising CD4+ to CD8+ T cell ratio. We performed proteomics and phosphoproteomics by LC-MS/MS and found MPs significantly induced 130 and 57 proteins upregulated in proteome and phosphoproteome, and 191 and 37 proteins downregulated in proteome and phosphoproteome, separately. Bioinformatic analysis show that asthma, mineral absorption, and the IL-17 signaling pathway were significantly enriched and may be involved in MP-induced spleen damage and immune suppression. We verified the top 3 differentially expressed proteins and phosphoproteins by western blot, and we further showed that S100A8 was significantly downregulated by MPs via histochemistry staining. Our results revealed that MPs can induce spleen damage and immune suppression by reducing S100A8 expression, suggesting an underestimated influence and mechanism of MPs on the mammalian immune system.
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Affiliation(s)
- Juan Wang
- Henan Institute for Food and Drug Control, Zhengzhou, Henan 450000, China
| | - Xiaojuan Wang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, China
| | - Conghui Zhang
- Department of clinical laboratory medicine, Xiangya Medical School of Central South University, Changsha, Hunan 410013, China; Department of clinical laboratory medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Xiao Zhou
- Department of clinical laboratory medicine, Xiangya Medical School of Central South University, Changsha, Hunan 410013, China; Department of clinical laboratory medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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26
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Cui C, Wu C, Shu P, Liu T, Li H, Beuve A. Soluble guanylyl cyclase mediates noncanonical nitric oxide signaling by nitrosothiol transfer under oxidative stress. Redox Biol 2022; 55:102425. [PMID: 35961098 PMCID: PMC9372771 DOI: 10.1016/j.redox.2022.102425] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022] Open
Abstract
Soluble guanylyl cyclase (GC1) is an α/β heterodimer producing cGMP when stimulated by nitric oxide (NO). The NO-GC1-cGMP pathway is essential for cardiovascular homeostasis but is disrupted by oxidative stress, which causes GC1 desensitization to NO by heme oxidation and S-nitrosation (SNO) of specific cysteines. We discovered that under these conditions, GC1-α subunit increases cellular S-nitrosation via transfer of nitrosothiols to other proteins (transnitrosation) in cardiac and smooth muscle cells. One of the GC1 SNO-targets was the oxidized form of Thioredoxin1 (oTrx1), which is unidirectionally transnitrosated by GC1 with αC610 as a SNO-donor. Because oTrx1 itself drives transnitrosation, we sought and identified SNO-proteins targeted by both GC1 and Trx1. We found that transnitrosation of the small GTPase RhoA by SNO-GC1 requires oTrx1 as a nitrosothiol relay, suggesting a SNO-GC1→oTrx1→RhoA cascade. The RhoA signaling pathway, which is antagonized by the canonical NO-cGMP pathway, was alternatively inhibited by GC1-α-dependent S-nitrosation under oxidative conditions. We propose that SNO-GC1, via transnitrosation, mediates adaptive responses triggered by oxidation of the canonical NO-cGMP pathway.
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Affiliation(s)
- Chuanlong Cui
- Rutgers School of Graduate Studies, Newark Health Science, Newark, NJ, 07103, USA; Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School at Rutgers, Newark, NJ, 07103, USA
| | - Changgong Wu
- Thermo Fisher Scientific, Somerset, NJ, 08873, USA
| | - Ping Shu
- Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School at Rutgers, Newark, NJ, 07103, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School at Rutgers, Newark, NJ, 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School at Rutgers, Newark, NJ, 07103, USA
| | - Annie Beuve
- Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School at Rutgers, Newark, NJ, 07103, USA.
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27
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Fonseca FV, Raffay TM, Xiao K, McLaughlin PJ, Qian Z, Grimmett ZW, Adachi N, Wang B, Hausladen A, Cobb BA, Zhang R, Hess DT, Gaston B, Lambert NA, Reynolds JD, Premont RT, Stamler JS. S-nitrosylation is required for β 2AR desensitization and experimental asthma. Mol Cell 2022; 82:3089-3102.e7. [PMID: 35931084 PMCID: PMC9391322 DOI: 10.1016/j.molcel.2022.06.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/18/2022] [Accepted: 06/28/2022] [Indexed: 12/22/2022]
Abstract
The β2-adrenergic receptor (β2AR), a prototypic G-protein-coupled receptor (GPCR), is a powerful driver of bronchorelaxation, but the effectiveness of β-agonist drugs in asthma is limited by desensitization and tachyphylaxis. We find that during activation, the β2AR is modified by S-nitrosylation, which is essential for both classic desensitization by PKA as well as desensitization of NO-based signaling that mediates bronchorelaxation. Strikingly, S-nitrosylation alone can drive β2AR internalization in the absence of traditional agonist. Mutant β2AR refractory to S-nitrosylation (Cys265Ser) exhibits reduced desensitization and internalization, thereby amplifying NO-based signaling, and mice with Cys265Ser mutation are resistant to bronchoconstriction, inflammation, and the development of asthma. S-nitrosylation is thus a central mechanism in β2AR signaling that may be operative widely among GPCRs and targeted for therapeutic gain.
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Affiliation(s)
- Fabio V Fonseca
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Thomas M Raffay
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kunhong Xiao
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Precious J McLaughlin
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhaoxia Qian
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Naoko Adachi
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Brian A Cobb
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Rongli Zhang
- Cardiovascular Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Douglas T Hess
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Benjamin Gaston
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Richard T Premont
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.
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28
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Brücksken KA, Loreto Palacio P, Hanschmann EM. Thiol Modifications in the Extracellular Space—Key Proteins in Inflammation and Viral Infection. Front Immunol 2022; 13:932525. [PMID: 35833136 PMCID: PMC9271835 DOI: 10.3389/fimmu.2022.932525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Posttranslational modifications (PTMs) allow to control molecular and cellular functions in response to specific signals and changes in the microenvironment of cells. They regulate structure, localization, stability, and function of proteins in a spatial and temporal manner. Among them, specific thiol modifications of cysteine (Cys) residues facilitate rapid signal transduction. In fact, Cys is unique because it contains the highly reactive thiol group that can undergo different reversible and irreversible modifications. Upon inflammation and changes in the cellular microenvironment, many extracellular soluble and membrane proteins undergo thiol modifications, particularly dithiol–disulfide exchange, S-glutathionylation, and S-nitrosylation. Among others, these thiol switches are essential for inflammatory signaling, regulation of gene expression, cytokine release, immunoglobulin function and isoform variation, and antigen presentation. Interestingly, also the redox state of bacterial and viral proteins depends on host cell-mediated redox reactions that are critical for invasion and infection. Here, we highlight mechanistic thiol switches in inflammatory pathways and infections including cholera, diphtheria, hepatitis, human immunodeficiency virus (HIV), influenza, and coronavirus disease 2019 (COVID-19).
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29
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Barik GK, Sahay O, Paul D, Santra MK. Ezrin gone rogue in cancer progression and metastasis: An enticing therapeutic target. Biochim Biophys Acta Rev Cancer 2022; 1877:188753. [PMID: 35752404 DOI: 10.1016/j.bbcan.2022.188753] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 12/12/2022]
Abstract
Cancer metastasis is the primary cause of morbidity and mortality in cancer as it remains the most complicated, devastating, and enigmatic aspect of cancer. Several decades of extensive research have identified several key players closely associated with metastasis. Among these players, cytoskeletal linker Ezrin (the founding member of the ERM (Ezrin-Radixin-Moesin) family) was identified as a critical promoter of metastasis in pediatric cancers in the early 21st century. Ezrin was discovered 40 years ago as a aminor component of intestinal epithelial microvillus core protein, which is enriched in actin-containing cell surface structures. It controls gastric acid secretion and plays diverse physiological roles including maintaining cell polarity, regulating cell adhesion, cell motility and morphogenesis. Extensive research for more than two decades evinces that Ezrin is frequently dysregulated in several human cancers. Overexpression, altered subcellular localization and/or aberrant activation of Ezrin are closely associated with higher metastatic incidence and patient mortality, thereby justifying Ezrin as a valuable prognostic biomarker in cancer. Ezrin plays multifaceted role in multiple aspects of cancer, with its significant contribution in the complex metastatic cascade, through reorganizing the cytoskeleton and deregulating various cellular signaling pathways. Current preclinical studies using genetic and/or pharmacological approaches reveal that inactivation of Ezrin results in significant inhibition of Ezrin-mediated tumor growth and metastasis as well as increase in the sensitivity of cancer cells to various chemotherapeutic drugs. In this review, we discuss the recent advances illuminating the molecular mechanisms responsible for Ezrin dysregulation in cancer and its pleiotropic role in cancer progression and metastasis. We also highlight its potential as a prognostic biomarker and therapeutic target in various cancers. More importantly, we put forward some potential questions, which we strongly believe, will stimulate both basic and translational research to better understand Ezrin-mediated malignancy, ultimately leading to the development of Ezrin-targeted cancer therapy for the betterment of human life.
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Affiliation(s)
- Ganesh Kumar Barik
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Osheen Sahay
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, Centre for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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30
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The Breast Cancer Protooncogenes HER2, BRCA1 and BRCA2 and Their Regulation by the iNOS/NOS2 Axis. Antioxidants (Basel) 2022; 11:antiox11061195. [PMID: 35740092 PMCID: PMC9227079 DOI: 10.3390/antiox11061195] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
The expression of inducible nitric oxide synthase (iNOS; NOS2) and derived NO in various cancers was reported to exert pro- and anti-tumorigenic effects depending on the levels of expression and the tumor types. In humans, the breast cancer level of iNOS was reported to be overexpressed, to exhibit pro-tumorigenic activities, and to be of prognostic significance. Likewise, the expression of the oncogenes HER2, BRCA1, and BRCA2 has been associated with malignancy. The interrelationship between the expression of these protooncogenes and oncogenes and the expression of iNOS is not clear. We have hypothesized that there exist cross-talk signaling pathways between the breast cancer protooncogenes, the iNOS axis, and iNOS-mediated NO mutations of these protooncogenes into oncogenes. We review the molecular regulation of the expression of the protooncogenes in breast cancer and their interrelationships with iNOS expression and activities. In addition, we discuss the roles of iNOS, HER2, BRCA1/2, and NO metabolism in the pathophysiology of cancer stem cells. Bioinformatic analyses have been performed and have found suggested molecular alterations responsible for breast cancer aggressiveness. These include the association of BRCA1/2 mutations and HER2 amplifications with the dysregulation of the NOS pathway. We propose that future studies should be undertaken to investigate the regulatory mechanisms underlying the expression of iNOS and various breast cancer oncogenes, with the aim of identifying new therapeutic targets for the treatment of breast cancers that are refractory to current treatments.
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31
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Ye H, Wu J, Liang Z, Zhang Y, Huang Z. Protein S-Nitrosation: Biochemistry, Identification, Molecular Mechanisms, and Therapeutic Applications. J Med Chem 2022; 65:5902-5925. [PMID: 35412827 DOI: 10.1021/acs.jmedchem.1c02194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein S-nitrosation (SNO), a posttranslational modification (PTM) of cysteine (Cys) residues elicited by nitric oxide (NO), regulates a wide range of protein functions. As a crucial form of redox-based signaling by NO, SNO contributes significantly to the modulation of physiological functions, and SNO imbalance is closely linked to pathophysiological processes. Site-specific identification of the SNO protein is critical for understanding the underlying molecular mechanisms of protein function regulation. Although careful verification is needed, SNO modification data containing numerous functional proteins are a potential research direction for druggable target identification and drug discovery. Undoubtedly, SNO-related research is meaningful not only for the development of NO donor drugs but also for classic target-based drug design. Herein, we provide a comprehensive summary of SNO, including its origin and transport, identification, function, and potential contribution to drug discovery. Importantly, we propose new views to develop novel therapies based on potential protein SNO-sourced targets.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Zhuangzhuang Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Zhangjian Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, P.R. China
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Premont RT, Singel DJ, Stamler JS. The enzymatic function of the honorary enzyme: S-nitrosylation of hemoglobin in physiology and medicine. Mol Aspects Med 2022; 84:101056. [PMID: 34852941 PMCID: PMC8821404 DOI: 10.1016/j.mam.2021.101056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
The allosteric transition within tetrameric hemoglobin (Hb) that allows both full binding to four oxygen molecules in the lung and full release of four oxygens in hypoxic tissues would earn Hb the moniker of 'honorary enzyme'. However, the allosteric model for oxygen binding in hemoglobin overlooked the essential role of blood flow in tissue oxygenation that is essential for life (aka autoregulation of blood flow). That is, blood flow, not oxygen content of blood, is the principal determinant of oxygen delivery under most conditions. With the discovery that hemoglobin carries a third biologic gas, nitric oxide (NO) in the form of S-nitrosothiol (SNO) at β-globin Cys93 (βCys93), and that formation and export of SNO to dilate blood vessels are linked to hemoglobin allostery through enzymatic activity, this title is honorary no more. This chapter reviews evidence that hemoglobin formation and release of SNO is a critical mediator of hypoxic autoregulation of blood flow in tissues leading to oxygen delivery, considers the physiological implications of a 3-gas respiratory cycle (O2/NO/CO2) and the pathophysiological consequences of its dysfunction. Opportunities for therapeutic intervention to optimize oxygen delivery at the level of tissue blood flow are highlighted.
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Affiliation(s)
- Richard T Premont
- Institute for Transformative Molecular Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - David J Singel
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA.
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Retamal MA, Altenberg GA. Role and Posttranslational Regulation of Cx46 Hemichannels and Gap Junction Channels in the Eye Lens. Front Physiol 2022; 13:864948. [PMID: 35431975 PMCID: PMC9006113 DOI: 10.3389/fphys.2022.864948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022] Open
Abstract
Connexins are a family of proteins that can form two distinct types of channels: hemichannels and gap junction channels. Hemichannels are composed of six connexin subunits and when open allow for exchanges between the cytoplasm and the extracellular milieu. Gap junction channels are formed by head-to-head docking of two hemichannels in series, each one from one of two adjacent cells. These channels allow for exchanges between the cytoplasms of contacting cells. The lens is a transparent structure located in the eye that focuses light on the retina. The transparency of the lens depends on its lack of blood irrigation and the absence of organelles in its cells. To survive such complex metabolic scenario, lens cells express Cx43, Cx46 and Cx50, three connexins isoforms that form hemichannels and gap junction channels that allow for metabolic cooperation between lens cells. This review focuses on the roles of Cx46 hemichannels and gap junction channels in the lens under physiological conditions and in the formation of cataracts, with emphasis on the modulation by posttranslational modifications.
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Affiliation(s)
- Mauricio A. Retamal
- Universidad del Desarrollo, Centro de Fisiología Celular e Integrativa, Clínica Alemana Facultad de Medicina, Santiago, Chile
- Universidad del Desarrollo, Programa de Comunicación Celular en Cáncer, Clínica Alemana Facultad de Medicina, Santiago, Chile
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- *Correspondence: Mauricio A. Retamal, ; Guillermo A. Altenberg,
| | - Guillermo A. Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- *Correspondence: Mauricio A. Retamal, ; Guillermo A. Altenberg,
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De Jesus A, Keyhani-Nejad F, Pusec CM, Goodman L, Geier JA, Stoolman JS, Stanczyk PJ, Nguyen T, Xu K, Suresh KV, Chen Y, Rodriguez AE, Shapiro JS, Chang HC, Chen C, Shah KP, Ben-Sahra I, Layden BT, Chandel NS, Weinberg SE, Ardehali H. Hexokinase 1 cellular localization regulates the metabolic fate of glucose. Mol Cell 2022; 82:1261-1277.e9. [PMID: 35305311 PMCID: PMC8995391 DOI: 10.1016/j.molcel.2022.02.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 10/12/2021] [Accepted: 02/22/2022] [Indexed: 12/24/2022]
Abstract
The product of hexokinase (HK) enzymes, glucose-6-phosphate, can be metabolized through glycolysis or directed to alternative metabolic routes, such as the pentose phosphate pathway (PPP) to generate anabolic intermediates. HK1 contains an N-terminal mitochondrial binding domain (MBD), but its physiologic significance remains unclear. To elucidate the effect of HK1 mitochondrial dissociation on cellular metabolism, we generated mice lacking the HK1 MBD (ΔE1HK1). These mice produced a hyper-inflammatory response when challenged with lipopolysaccharide. Additionally, there was decreased glucose flux below the level of GAPDH and increased upstream flux through the PPP. The glycolytic block below GAPDH is mediated by the binding of cytosolic HK1 with S100A8/A9, resulting in GAPDH nitrosylation through iNOS. Additionally, human and mouse macrophages from conditions of low-grade inflammation, such as aging and diabetes, displayed increased cytosolic HK1 and reduced GAPDH activity. Our data indicate that HK1 mitochondrial binding alters glucose metabolism through regulation of GAPDH.
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Affiliation(s)
- Adam De Jesus
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Farnaz Keyhani-Nejad
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Carolina M Pusec
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lauren Goodman
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Justin A Geier
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Joshua S Stoolman
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paulina J Stanczyk
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Tivoli Nguyen
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Kai Xu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Krishna V Suresh
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Yihan Chen
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Arianne E Rodriguez
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jason S Shapiro
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Hsiang-Chun Chang
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Chunlei Chen
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kriti P Shah
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian T Layden
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Navdeep S Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Samuel E Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hossein Ardehali
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA.
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35
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Endogenous S-nitrosocysteine proteomic inventories identify a core of proteins in heart metabolic pathways. Redox Biol 2021; 47:102153. [PMID: 34610554 PMCID: PMC8497991 DOI: 10.1016/j.redox.2021.102153] [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: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022] Open
Abstract
Protein cysteine residues are essential for protein folding, participate in enzymatic catalysis, and coordinate the binding of metal ions to proteins. Enzymatically catalyzed and redox-dependent post-translational modifications of cysteine residues are also critical for signal transduction and regulation of protein function and localization. S-nitrosylation, the addition of a nitric oxide equivalent to a cysteine residue, is a redox-dependent modification. In this study, we curated and analyzed four different studies that employed various chemoselective platforms coupled to mass spectrometry to precisely identify S-nitrosocysteine residues in mouse heart proteins. Collectively 1974 S-nitrosocysteine residues in 761 proteins were identified and 33.4% were identified in two or more studies. A core of 75 S-nitrosocysteine residues in 44 proteins were identified in all four studies. Bioinformatic analysis of each study indicated a significant enrichment of mitochondrial proteins participating in metabolism. Regulatory proteins in glycolysis, TCA cycle, oxidative phosphorylation and ATP production, long chain fatty acid β-oxidation, and ketone and amino acid metabolism constitute the major functional pathways impacted by protein S-nitrosylation. In the cardiovascular system, nitric oxide signaling regulates vasodilation and cardiac muscle contractility. The meta-analysis of the proteomic data supports the hypothesis that nitric oxide signaling via protein S-nitrosylation is also a regulator of cardiomyocyte metabolism that coordinates fuel utilization to maximize ATP production. As such, protein cysteine S-nitrosylation represents a third functional dimension of nitric oxide signaling in the cardiovascular system to ensure optimal cardiac function.
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Monteith AJ, Miller JM, Maxwell CN, Chazin WJ, Skaar EP. Neutrophil extracellular traps enhance macrophage killing of bacterial pathogens. SCIENCE ADVANCES 2021; 7:eabj2101. [PMID: 34516771 PMCID: PMC8442908 DOI: 10.1126/sciadv.abj2101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/20/2021] [Indexed: 05/16/2023]
Abstract
Neutrophils and macrophages are critical to the innate immune response, but cooperative mechanisms used by these cells to combat extracellular pathogens are not well understood. This study reveals that S100A9-deficient neutrophils produce higher levels of mitochondrial superoxide in response to Staphylococcus aureus and, as a result, form neutrophil extracellular traps (suicidal NETosis). Increased suicidal NETosis does not improve neutrophil killing of S. aureus in isolation but augments macrophage killing. NET formation enhances antibacterial activity by increasing phagocytosis by macrophages and by transferring neutrophil-specific antimicrobial peptides to them. Similar results were observed in response to other phylogenetically distinct bacterial pathogens including Streptococcus pneumoniae and Pseudomonas aeruginosa, implicating this as an immune defense mechanism that broadly enhances antibacterial activity. These results demonstrate that achieving maximal bactericidal activity through NET formation requires macrophages and that accelerated and more robust suicidal NETosis makes neutrophils adept at increasing antibacterial activity, especially when A9 deficient.
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Affiliation(s)
- Andrew J. Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeanette M. Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C. Noel Maxwell
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Walter J. Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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37
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Chatterji A, Sengupta R. Stability of S-nitrosothiols and S-nitrosylated proteins: A struggle for cellular existence! J Cell Biochem 2021; 122:1579-1593. [PMID: 34472139 DOI: 10.1002/jcb.30139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/29/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Nitric oxide is a well-known gasotransmitter molecule that covalently docks to sulfhydryl groups of proteins resulting in S-nitrosylation of proteins and nonprotein thiols that serve a variety of cellular processes including cGMP signaling, vasodilatation, neurotransmission, ion-channel modulation, and cardiac signaling. S-nitrosylation is an indispensable modification like phosphorylation that directly regulates the functionality of numerous proteins. However, recently there has been a controversy over the stability of S-nitrosylated proteins (PSNOs) within the cell. It has been argued that PSNOs formed within the cell is a transient intermediate step to more stable disulfide formation and disulfides are the predominant end effector modifications in NO-mediated signaling. The present article accumulates state-of-the-art evidence from numerous research that strongly supports the very existence of PSNOs within the cell and attempts to put an end to the controversy. This review illustrates critical points including comparative bond dissociation energies of S-NO bond, the half-life of S-nitrosothiols and PSNOs, cellular concentrations of PSNOs, X ray crystallographic studies on PSNOs, and stability of PSNOs at physiological concentration of antioxidants. These logical evidence cumulatively support the endogenous stability and inevitable existence of PSNOs/RSNOs within the cell that directly regulate the functionality of proteins and provide valuable insight into understanding stable S-nitrosylation mediated cell signaling.
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Affiliation(s)
- Ajanta Chatterji
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Kolkata, India
| | - Rajib Sengupta
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Kolkata, India
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38
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Nakamura T, Oh CK, Zhang X, Tannenbaum SR, Lipton SA. Protein Transnitrosylation Signaling Networks Contribute to Inflammaging and Neurodegenerative Disorders. Antioxid Redox Signal 2021; 35:531-550. [PMID: 33957758 PMCID: PMC8388249 DOI: 10.1089/ars.2021.0081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Significance: Physiological concentrations of nitric oxide (NO•) and related reactive nitrogen species (RNS) mediate multiple signaling pathways in the nervous system. During inflammaging (chronic low-grade inflammation associated with aging) and in neurodegenerative diseases, excessive RNS contribute to synaptic and neuronal loss. "NO signaling" in both health and disease is largely mediated through protein S-nitrosylation (SNO), a redox-based posttranslational modification with "NO" (possibly in the form of nitrosonium cation [NO+]) reacting with cysteine thiol (or, more properly, thiolate anion [R-S-]). Recent Advances: Emerging evidence suggests that S-nitrosylation occurs predominantly via transnitros(yl)ation. Mechanistically, the reaction involves thiolate anion, as a nucleophile, performing a reversible nucleophilic attack on a nitroso nitrogen to form an SNO-protein adduct. Prior studies identified transnitrosylation reactions between glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-nuclear proteins, thioredoxin-caspase-3, and X-linked inhibitor of apoptosis (XIAP)-caspase-3. Recently, we discovered that enzymes previously thought to act in completely disparate biochemical pathways can transnitrosylate one another during inflammaging in an unexpected manner to mediate neurodegeneration. Accordingly, we reported a concerted tricomponent transnitrosylation network from Uch-L1-to-Cdk5-to-Drp1 that mediates synaptic damage in Alzheimer's disease. Critical Issues: Transnitrosylation represents a critical chemical mechanism for transduction of redox-mediated events to distinct subsets of proteins. Although thousands of thiol-containing proteins undergo S-nitrosylation, how transnitrosylation regulates a myriad of neuronal attributes is just now being uncovered. In this review, we highlight recent progress in the study of the chemical biology of transnitrosylation between proteins as a mechanism of disease. Future Directions: We discuss future areas of study of protein transnitrosylation that link our understanding of aging, inflammation, and neurodegenerative diseases. Antioxid. Redox Signal. 35, 531-550.
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Affiliation(s)
- Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, California, USA
| | - Chang-Ki Oh
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, California, USA
| | - Xu Zhang
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, California, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stuart A Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, California, USA.,Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, California, USA
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Chatterji A, Banerjee D, Billiar TR, Sengupta R. Understanding the role of S-nitrosylation/nitrosative stress in inflammation and the role of cellular denitrosylases in inflammation modulation: Implications in health and diseases. Free Radic Biol Med 2021; 172:604-621. [PMID: 34245859 DOI: 10.1016/j.freeradbiomed.2021.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/22/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
S-nitrosylation is a very fundamental post-translational modification of protein and non-protein thiols due the involvement of it in a variety of cellular processes including activation/inhibition of several ion channels such as ryanodine receptor in the cardiovascular system; blood vessel dilation; cGMP signaling and neurotransmission. S-nitrosothiol homeostasis in the cell is tightly regulated and perturbations in homeostasis result in an altered redox state leading to a plethora of disease conditions. However, the exact role of S-nitrosylated proteins and nitrosative stress metabolites in inflammation and in inflammation modulation is not well-reviewed. The cell utilizes its intricate defense mechanisms i.e. cellular denitrosylases such as Thioredoxin (Trx) and S-nitrosoglutathione reductase (GSNOR) systems to combat nitric oxide (NO) pathology which has also gained current attraction as novel anti-inflammatory molecules. This review attempts to provide state-of-the-art knowledge from past and present research on the mechanistic role of nitrosative stress intermediates (RNS, OONO-, PSNO) in pulmonary and autoimmune diseases and how cellular denitrosylases particularly GSNOR and Trx via imparting opposing effects can modulate and reduce inflammation in several health and disease conditions. This review would also bring into notice the existing gaps in current research where denitrosylases can be utilized for ameliorating inflammation that would leave avenues for future therapeutic interventions.
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Affiliation(s)
- Ajanta Chatterji
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Action Area II, Rajarhat, Newtown, Kolkata, West Bengal, 700135, India
| | - Debasmita Banerjee
- Department of Molecular Biology and Biotechnology, University of Kalyani, Block C, Nadia, Kalyani, West Bengal, 741235, India
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 5213, USA
| | - Rajib Sengupta
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Action Area II, Rajarhat, Newtown, Kolkata, West Bengal, 700135, India.
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40
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Nakamura T, Oh CK, Zhang X, Lipton SA. Protein S-nitrosylation and oxidation contribute to protein misfolding in neurodegeneration. Free Radic Biol Med 2021; 172:562-577. [PMID: 34224817 PMCID: PMC8579830 DOI: 10.1016/j.freeradbiomed.2021.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Neurodegenerative disorders like Alzheimer's disease and Parkinson's disease are characterized by progressive degeneration of synapses and neurons. Accumulation of misfolded/aggregated proteins represents a pathological hallmark of most neurodegenerative diseases, potentially contributing to synapse loss and neuronal damage. Emerging evidence suggests that misfolded proteins accumulate in the diseased brain at least in part as a consequence of excessively generated reactive oxygen species (ROS) and reactive nitrogen species (RNS). Mechanistically, not only disease-linked genetic mutations but also known risk factors for neurodegenerative diseases, such as aging and exposure to environmental toxins, can accelerate production of ROS/RNS, which contribute to protein misfolding - in many cases mimicking the effect of rare genetic mutations known to be linked to the disease. This review will focus on the role of RNS-dependent post-translational modifications, such as S-nitrosylation and tyrosine nitration, in protein misfolding and aggregation. Specifically, we will discuss molecular mechanisms whereby RNS disrupt the activity of the cellular protein quality control machinery, including molecular chaperones, autophagy/lysosomal pathways, and the ubiquitin-proteasome system (UPS). Because chronic accumulation of misfolded proteins can trigger mitochondrial dysfunction, synaptic damage, and neuronal demise, further characterization of RNS-mediated protein misfolding may establish these molecular events as therapeutic targets for intervention in neurodegenerative diseases.
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Affiliation(s)
- Tomohiro Nakamura
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Chang-Ki Oh
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xu Zhang
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Stuart A Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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41
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Molecular Insight into the Regulation of Vimentin by Cysteine Modifications and Zinc Binding. Antioxidants (Basel) 2021; 10:antiox10071039. [PMID: 34203497 PMCID: PMC8300659 DOI: 10.3390/antiox10071039] [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: 05/22/2021] [Revised: 06/20/2021] [Accepted: 06/24/2021] [Indexed: 01/11/2023] Open
Abstract
The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.
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42
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Maarifi G, Lagisquet J, Hertel Q, Bonaventure B, Chamontin C, Fuchs K, Moncorgé O, Tauziet M, Mombled M, Papin L, Molès JP, Bodet C, Lévèque N, Gross A, Arhel N, Nisole S, Van de Perre P, Goujon C, Blanchet FP. Alarmin S100A9 restricts retroviral infection by limiting reverse transcription in human dendritic cells. EMBO J 2021; 40:e106540. [PMID: 34121210 DOI: 10.15252/embj.2020106540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
Dendritic cells (DC) subsets, like Langerhans cells (LC), are immune cells involved in pathogen sensing. They express specific antimicrobial cellular factors that are able to restrict infection and limit further pathogen transmission. Here, we identify the alarmin S100A9 as a novel intracellular antiretroviral factor expressed in human monocyte-derived and skin-derived LC. The intracellular expression of S100A9 is decreased upon LC maturation and inversely correlates with enhanced susceptibility to HIV-1 infection of LC. Furthermore, silencing of S100A9 in primary human LC relieves HIV-1 restriction while ectopic expression of S100A9 in various cell lines promotes intrinsic resistance to both HIV-1 and MLV infection by acting on reverse transcription. Mechanistically, the intracellular expression of S100A9 alters viral capsid uncoating and reverse transcription. S100A9 also shows potent inhibitory effect against HIV-1 and MMLV reverse transcriptase (RTase) activity in vitro in a divalent cation-dependent manner. Our findings uncover an unexpected intracellular function of the human alarmin S100A9 in regulating antiretroviral immunity in Langerhans cells.
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Affiliation(s)
- Ghizlane Maarifi
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Justine Lagisquet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Quentin Hertel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Boris Bonaventure
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Célia Chamontin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Kyra Fuchs
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marine Tauziet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Margaux Mombled
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Laure Papin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Charles Bodet
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Nicolas Lévèque
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Antoine Gross
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Nathalie Arhel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
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Lin KH, Wilson GM, Blanco R, Steinert ND, Zhu WG, Coon JJ, Hornberger TA. A deep analysis of the proteomic and phosphoproteomic alterations that occur in skeletal muscle after the onset of immobilization. J Physiol 2021; 599:2887-2906. [PMID: 33873245 PMCID: PMC8353513 DOI: 10.1113/jp281071] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/06/2021] [Indexed: 02/04/2023] Open
Abstract
KEY POINTS A decrease in protein synthesis plays a major role in the loss of muscle mass that occurs in response to immobilization. In mice, immobilization leads to a rapid (within 6 h) and progressive decrease in the rate of protein synthesis and this effect is mediated by a decrease in translational efficiency. Deep proteomic and phosphoproteomic analyses of mouse skeletal muscles revealed that the rapid immobilization-induced decrease in protein synthesis cannot be explained by changes in the abundance or phosphorylation state of proteins that have been implicated in the regulation of translation. ABSTRACT The disuse of skeletal muscle, such as that which occurs during immobilization, can lead to the rapid loss of muscle mass, and a decrease in the rate of protein synthesis plays a major role in this process. Indeed, current dogma contends that the decrease in protein synthesis is mediated by changes in the activity of protein kinases (e.g. mTOR); however, the validity of this model has not been established. Therefore, to address this, we first subjected mice to 6, 24 or 72 h of unilateral immobilization and then used the SUnSET technique to measure changes in the relative rate of protein synthesis. The result of our initial experiments revealed that immobilization leads to a rapid (within 6 h) and progressive decrease in the rate of protein synthesis and that this effect is mediated by a decrease in translational efficiency. We then performed a deep mass spectrometry-based analysis to determine whether this effect could be explained by changes in the expression and/or phosphorylation state of proteins that regulate translation. From this analysis, we were able to quantify 4320 proteins and 15,020 unique phosphorylation sites, and surprisingly, the outcomes revealed that the rapid immobilization-induced decrease in protein synthesis could not be explained by changes in either the abundance, or phosphorylation state, of proteins. The results of our work not only challenge the current dogma in the field, but also provide an expansive resource of information for future studies that are aimed at defining how disuse leads to loss of muscle mass.
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Affiliation(s)
- Kuan-Hung Lin
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
| | - Rocky Blanco
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel D Steinert
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Wenyuan G Zhu
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Troy A Hornberger
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
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Davis JC, Alves TC, Helman A, Chen JC, Kenty JH, Cardone RL, Liu DR, Kibbey RG, Melton DA. Glucose Response by Stem Cell-Derived β Cells In Vitro Is Inhibited by a Bottleneck in Glycolysis. Cell Rep 2021; 31:107623. [PMID: 32402282 PMCID: PMC7433758 DOI: 10.1016/j.celrep.2020.107623] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/30/2020] [Accepted: 04/16/2020] [Indexed: 12/29/2022] Open
Abstract
Stem cell-derived β (SC-β) cells could provide unlimited human β cells toward a curative diabetes treatment. Differentiation of SC-β cells yields transplantable islets that secrete insulin in response to glucose challenges. Following transplantation into mice, SC-β cell function is comparable to human islets, but the magnitude and consistency of response in vitro are less robust than observed in cadaveric islets. Here, we profile metabolism of SC-β cells and islets to quantify their capacity to sense glucose and identify reduced anaplerotic cycling in the mitochondria as the cause of reduced glucose-stimulated insulin secretion in SC-β cells. This activity can be rescued by challenging SC-β cells with intermediate metabolites from the TCA cycle and late but not early glycolysis, downstream of the enzymes glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase. Bypassing this metabolic bottleneck results in a robust, bi-phasic insulin release in vitro that is identical in magnitude to functionally mature human islets. Glucose-stimulated insulin secretion is deficient in stem cell-derived β (SC-β) cells in vitro. Davis et al. use metabolomic analysis to define a glycolytic bottleneck inhibiting glucose metabolism and sensing in SC-β cells. Cell-permeable intermediates bypass this bottleneck, as does transplantation in vivo, producing insulin secretion indistinguishable from human islets.
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Affiliation(s)
- Jeffrey C Davis
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Tiago C Alves
- Department of Internal Medicine (Endocrinology), Yale University, New Haven, CT, USA; Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
| | - Aharon Helman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jennifer H Kenty
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Rebecca L Cardone
- Department of Internal Medicine (Endocrinology), Yale University, New Haven, CT, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard G Kibbey
- Department of Internal Medicine (Endocrinology), Yale University, New Haven, CT, USA; Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
| | - Douglas A Melton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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45
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Helmer RA, Martinez-Zaguilan R, Kaur G, Smith LA, Dufour JM, Chilton BS. Helicase-like transcription factor-deletion from the tumor microenvironment in a cell line-derived xenograft model of colorectal cancer reprogrammed the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis. PLoS One 2021; 16:e0251132. [PMID: 34010296 PMCID: PMC8133447 DOI: 10.1371/journal.pone.0251132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Methylation of the HLTF gene in colorectal cancer (CRC) cells occurs more frequently in men than women. Progressive epigenetic silencing of HLTF in tumor cells is accompanied by negligible expression in the tumor microenvironment (TME). Cell line-derived xenografts (CDX) were established in control (Hltf+/+) and Hltf-deleted male Rag2-/-IL2rg-/- mice by direct orthotopic cell microinjection (OCMI) of HLTF+/+HCT116 Red-FLuc cells into the submucosa of the cecum. Combinatorial induction of IL6 and S100A8/A9 in the Hltf-deleted TME with ICAM-1 and IL8 in the primary tumor activated a positive feedback loop. The proinflammatory niche produced a major shift in CDX metastasis to peritoneal dissemination compared to controls. Inducible nitric oxide (iNOS) gene expression and transactivation of the iNOS-S100A8/A9 signaling complex in Hltf-deleted TME reprogrammed the human S-nitroso-proteome. POTEE, TRIM52 and UN45B were S-nitrosylated on the conserved I/L-X-C-X2-D/E motif indicative of iNOS-S100A8/A9-mediated S-nitrosylation. 2D-DIGE and protein identification by MALDI-TOF/TOF mass spectrometry authenticated S-nitrosylation of 53 individual cysteines in half-site motifs (I/L-X-C or C-X-X-D/E) in CDX tumors. POTEE in CDX tumors is both a general S-nitrosylation target and an iNOS-S100A8/A9 site-specific (Cys638) target in the Hltf-deleted TME. REL is an example of convergence of transcriptomic-S-nitroso-proteomic signaling. The gene is transcriptionally activated in CDX tumors with an Hltf-deleted TME, and REL-SNO (Cys143) was found in primary CDX tumors and all metastatic sites. Primary CDX tumors from Hltf-deleted TME shared 60% of their S-nitroso-proteome with all metastatic sites. Forty percent of SNO-proteins from primary CDX tumors were variably expressed at metastatic sites. Global S-nitrosylation of proteins in pathways related to cytoskeleton and motility was strongly implicated in the metastatic dissemination of CDX tumors. Hltf-deletion from the TME played a major role in the pathogenesis of inflammation and linked protein S-nitrosylation in primary CDX tumors with spatiotemporal continuity in metastatic progression when the tumor cells expressed HLTF.
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Affiliation(s)
- Rebecca A. Helmer
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Lisa A. Smith
- Department of Pathology, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Cancer Center, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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Bago Á, Íñiguez MA, Serrador JM. Nitric Oxide and Electrophilic Cyclopentenone Prostaglandins in Redox signaling, Regulation of Cytoskeleton Dynamics and Intercellular Communication. Front Cell Dev Biol 2021; 9:673973. [PMID: 34026763 PMCID: PMC8137968 DOI: 10.3389/fcell.2021.673973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/01/2021] [Indexed: 12/16/2022] Open
Abstract
Nitric oxide (NO) and electrophilic cyclopentenone prostaglandins (CyPG) are local mediators that modulate cellular response to oxidative stress in different pathophysiological processes. In particular, there is increasing evidence about their functional role during inflammation and immune responses. Although the mechanistic details about their relationship and functional interactions are still far from resolved, NO and CyPG share the ability to promote redox-based post-translational modification (PTM) of proteins that play key roles in cellular homeostasis, signal transduction and transcription. NO-induced S-nitrosylation and S-glutathionylation as well as cyclopentenone-mediated adduct formation, are a few of the main PTMs by which intra- and inter-cellular signaling are regulated. There is a growing body of evidence indicating that actin and actin-binding proteins are susceptible to covalent PTM by these agents. It is well known that the actin cytoskeleton is key for the establishment of interactions among leukocytes, endothelial and muscle cells, enabling cellular activation and migration. In this review we analyze the current knowledge about the actions exerted by NO and CyPG electrophilic lipids on the regulation of actin dynamics and cytoskeleton organization, and discuss some open questions regarding their functional relevance in the regulation of intercellular communication.
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Affiliation(s)
- Ángel Bago
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
| | - Miguel A Íñiguez
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain.,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan M Serrador
- Interactions with the Environment Program, Immune System Development and Function Unit, Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
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47
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Sharma V, Fernando V, Letson J, Walia Y, Zheng X, Fackelman D, Furuta S. S-Nitrosylation in Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms22094600. [PMID: 33925645 PMCID: PMC8124305 DOI: 10.3390/ijms22094600] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
S-nitrosylation is a selective and reversible post-translational modification of protein thiols by nitric oxide (NO), which is a bioactive signaling molecule, to exert a variety of effects. These effects include the modulation of protein conformation, activity, stability, and protein-protein interactions. S-nitrosylation plays a central role in propagating NO signals within a cell, tissue, and tissue microenvironment, as the nitrosyl moiety can rapidly be transferred from one protein to another upon contact. This modification has also been reported to confer either tumor-suppressing or tumor-promoting effects and is portrayed as a process involved in every stage of cancer progression. In particular, S-nitrosylation has recently been found as an essential regulator of the tumor microenvironment (TME), the environment around a tumor governing the disease pathogenesis. This review aims to outline the effects of S-nitrosylation on different resident cells in the TME and the diverse outcomes in a context-dependent manner. Furthermore, we will discuss the therapeutic potentials of modulating S-nitrosylation levels in tumors.
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48
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Laan M, Salumets A, Klein A, Reintamm K, Bichele R, Peterson H, Peterson P. Post-Aire Medullary Thymic Epithelial Cells and Hassall's Corpuscles as Inducers of Tonic Pro-Inflammatory Microenvironment. Front Immunol 2021; 12:635569. [PMID: 33868260 PMCID: PMC8050345 DOI: 10.3389/fimmu.2021.635569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
While there is convincing evidence on the role of Aire-positive medullary thymic epithelial cells (mTEC) in the induction of central tolerance, the nature and function of post-Aire mTECs and Hassall's corpuscles have remained enigmatic. Here we summarize the existing data on these late stages of mTEC differentiation with special focus on their potential to contribute to central tolerance induction by triggering the unique pro-inflammatory microenvironment in the thymus. In order to complement the existing evidence that has been obtained from mouse models, we performed proteomic analysis on microdissected samples from human thymic medullary areas at different differentiation stages. The analysis confirms that at the post-Aire stages, the mTECs lose their nuclei but maintain machinery required for translation and exocytosis and also upregulate proteins specific to keratinocyte differentiation and cornification. In addition, at the late stages of differentiation, the human mTECs display a distinct pro-inflammatory signature, including upregulation of the potent endogenous TLR4 agonist S100A8/S100A9. Collectively, the study suggests a novel mechanism by which the post-Aire mTECs and Hassall's corpuscles contribute to the thymic microenvironment with potential cues on the induction of central tolerance.
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Affiliation(s)
- Martti Laan
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ahto Salumets
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Annabel Klein
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kerli Reintamm
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Rudolf Bichele
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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49
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Exploiting S-nitrosylation for cancer therapy: facts and perspectives. Biochem J 2021; 477:3649-3672. [PMID: 33017470 DOI: 10.1042/bcj20200064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022]
Abstract
S-nitrosylation, the post-translational modification of cysteines by nitric oxide, has been implicated in several cellular processes and tissue homeostasis. As a result, alterations in the mechanisms controlling the levels of S-nitrosylated proteins have been found in pathological states. In the last few years, a role in cancer has been proposed, supported by the evidence that various oncoproteins undergo gain- or loss-of-function modifications upon S-nitrosylation. Here, we aim at providing insight into the current knowledge about the role of S-nitrosylation in different aspects of cancer biology and report the main anticancer strategies based on: (i) reducing S-nitrosylation-mediated oncogenic effects, (ii) boosting S-nitrosylation to stimulate cell death, (iii) exploiting S-nitrosylation through synthetic lethality.
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50
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Li S, Yu K, Wu G, Zhang Q, Wang P, Zheng J, Liu ZX, Wang J, Gao X, Cheng H. pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework. Front Cell Dev Biol 2021; 9:617366. [PMID: 33732693 PMCID: PMC7959776 DOI: 10.3389/fcell.2021.617366] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Thiol groups on cysteines can undergo multiple post-translational modifications (PTMs), acting as a molecular switch to maintain redox homeostasis and regulating a series of cell signaling transductions. Identification of sophistical protein cysteine modifications is crucial for dissecting its underlying regulatory mechanism. Instead of a time-consuming and labor-intensive experimental method, various computational methods have attracted intense research interest due to their convenience and low cost. Here, we developed the first comprehensive deep learning based tool pCysMod for multiple protein cysteine modification prediction, including S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation. Experimentally verified cysteine sites curated from literature and sites collected by other databases and predicting tools were integrated as benchmark dataset. Several protein sequence features were extracted and united into a deep learning model, and the hyperparameters were optimized by particle swarm optimization algorithms. Cross-validations indicated our model showed excellent robustness and outperformed existing tools, which was able to achieve an average AUC of 0.793, 0.807, 0.796, 0.793, and 0.876 for S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation, demonstrating pCysMod was stable and suitable for protein cysteine modification prediction. Besides, we constructed a comprehensive protein cysteine modification prediction web server based on this model to benefit the researches finding the potential modification sites of their interested proteins, which could be accessed at http://pcysmod.omicsbio.info. This work will undoubtedly greatly promote the study of protein cysteine modification and contribute to clarifying the biological regulation mechanisms of cysteine modification within and among the cells.
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Affiliation(s)
- Shihua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Kai Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guandi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jichao Wang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xinjiao Gao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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