1
|
You S, Xu J, Guo Y, Guo X, Zhang Y, Zhang N, Sun G, Sun Y. E3 ubiquitin ligase WWP2 as a promising therapeutic target for diverse human diseases. Mol Aspects Med 2024; 96:101257. [PMID: 38430667 DOI: 10.1016/j.mam.2024.101257] [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: 11/04/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
Mammalian E3 ubiquitin ligases have emerged in recent years as critical regulators of cellular homeostasis due to their roles in targeting substrate proteins for ubiquitination and triggering subsequent downstream signals. In this review, we describe the multiple roles of WWP2, an E3 ubiquitin ligase with unique and important functions in regulating a wide range of biological processes, including DNA repair, gene expression, signal transduction, and cell-fate decisions. As such, WWP2 has evolved to play a key role in normal physiology and diseases, such as tumorigenesis, skeletal development and diseases, immune regulation, cardiovascular disease, and others. We attempt to provide an overview of the biochemical, physiological, and pathophysiological roles of WWP2, as well as open questions for future research, particularly in the context of putative therapeutic opportunities.
Collapse
Affiliation(s)
- Shilong You
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jiaqi Xu
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yushan Guo
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaofan Guo
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ying Zhang
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China.
| | - Naijin Zhang
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China; NHC Key Laboratory of Advanced Reproductive Medicine and Fertility, National Health Commission, China Medical University, Shenyang, Liaoning, China.
| | - Guozhe Sun
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Yingxian Sun
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China.
| |
Collapse
|
2
|
Van Stappen C, Dai H, Jose A, Tian S, Solomon EI, Lu Y. Primary and Secondary Coordination Sphere Effects on the Structure and Function of S-Nitrosylating Azurin. J Am Chem Soc 2023; 145:20610-20623. [PMID: 37696009 PMCID: PMC10539042 DOI: 10.1021/jacs.3c07399] [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: 09/13/2023]
Abstract
Much progress has been made in understanding the roles of the secondary coordination sphere (SCS) in tuning redox potentials of metalloproteins. In contrast, the impact of SCS on reactivity is much less understood. A primary example is how copper proteins can promote S-nitrosylation (SNO), which is one of the most important dynamic post-translational modifications, and is crucial in regulating nitric oxide storage and transportation. Specifically, the factors that instill CuII with S-nitrosylating capabilities and modulate activity are not well understood. To address this issue, we investigated the influence of the primary and secondary coordination sphere on CuII-catalyzed S-nitrosylation by developing a series of azurin variants with varying catalytic capabilities. We have employed a multidimensional approach involving electronic absorption, S and Cu K-edge XAS, EPR, and resonance Raman spectroscopies together with QM/MM computational analysis to examine the relationships between structure and molecular mechanism in this reaction. Our findings have revealed that kinetic competency is correlated with three balancing factors, namely Cu-S bond strength, Cu spin localization, and relative S(ps) vs S(pp) contributions to the ground state. Together, these results support a reaction pathway that proceeds through the attack of the Cu-S bond rather than electrophilic addition to CuII or radical attack of SCys. The insights gained from this work provide not only a deeper understanding of SNO in biology but also a basis for designing artificial and tunable SNO enzymes to regulate NO and prevent diseases due to SNO dysregulation.
Collapse
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
| | - Huiguang Dai
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Anex Jose
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Shiliang Tian
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| |
Collapse
|
3
|
Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
Collapse
Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
| |
Collapse
|
4
|
Aspatwar A, Tolvanen MEE, Barker H, Syrjänen L, Valanne S, Purmonen S, Waheed A, Sly WS, Parkkila S. Carbonic Anhydrases in Metazoan Model Organisms: Molecules, Mechanisms, and Physiology. Physiol Rev 2022; 102:1327-1383. [PMID: 35166161 DOI: 10.1152/physrev.00018.2021] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During the past three decades, mice, zebrafish, fruit flies, and Caenorhabditis elegans have been the primary model organisms used for the study of various biological phenomena. These models have also been adopted and developed to investigate the physiological roles of carbonic anhydrases (CAs) and carbonic anhydrase-related proteins (CARPs). These proteins belong to eight CA families and are identified by Greek letters: α, β, γ, δ, ζ, η, θ, and ι. Studies using model organisms have focused on two CA families, α-CAs and β-CAs, which are expressed in both prokaryotic and eukaryotic organisms with species-specific distribution patterns and unique functions. This review covers the biological roles of CAs and CARPs in light of investigations performed in model organisms. Functional studies demonstrate that CAs are not only linked to the regulation of pH homeostasis, the classical role of CAs but also contribute to a plethora of previously undescribed functions.
Collapse
Affiliation(s)
- Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Harlan Barker
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd and TAYS Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Leo Syrjänen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Otorhinolaryngology, Tampere University Hospital, Tampere, Finland
| | - Susanna Valanne
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Purmonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Abdul Waheed
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research Center, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - William S Sly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research Center, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd and TAYS Cancer Centre, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
5
|
Kolbert Z, Lindermayr C. Computational prediction of NO-dependent posttranslational modifications in plants: Current status and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:851-861. [PMID: 34536898 DOI: 10.1016/j.plaphy.2021.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 05/11/2023]
Abstract
The perception and transduction of nitric oxide (NO) signal is achieved by NO-dependent posttranslational modifications (PTMs) among which S-nitrosation and tyrosine nitration has biological significance. In plants, 100-1000 S-nitrosated and tyrosine nitrated proteins have been identified so far by mass spectrometry. The determination of NO-modified protein targets/amino acid residues is often methodologically challenging. In the past decade, the growing demand for the knowledge of S-nitrosated or tyrosine nitrated sites has motivated the introduction of bioinformatics tools. For predicting S-nitrosation seven computational tools have been developed (GPS-SNO, SNOSite, iSNO-PseACC, iSNO-AAPAir, PSNO, PreSNO, RecSNO). Four predictors have been developed for indicating tyrosine nitration sites (GPS-YNO2, iNitro-Tyr, PredNTS, iNitroY-Deep), and one tool (DeepNitro) predicts both NO-dependent PTMs. The advantage of these computational tools is the fast provision of large amount of information. In this review, the available software tools have been tested on plant proteins in which S-nitrosated or tyrosine nitrated sites have been experimentally identified. The predictors showed distinct performance and there were differences from the experimental results partly due to the fact that the three-dimensional protein structure is not taken into account by the computational tools. Nevertheless, the predictors excellently establish experiments, and it is suggested to apply all available tools on target proteins and compare their results. In the future, computational prediction must be developed further to improve the precision with which S-nitrosation/tyrosine nitration-sites are identified.
Collapse
Affiliation(s)
- Zsuzsanna Kolbert
- Department of Plant Biology, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary.
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764, Oberschleißheim, München, Germany.
| |
Collapse
|
6
|
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: 37] [Impact Index Per Article: 12.3] [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.
Collapse
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.
| |
Collapse
|
7
|
Dafe EA, Rahimi N, Javadian N, Dejban P, Komeili M, Modabberi S, Ghasemi M, Dehpour AR. Effect of Lenalidomide on Pentylenetetrazole-Induced Clonic Seizure Threshold in Mice: A Role for N-Methyl-D-Aspartic Acid Receptor/Nitric Oxide Pathway. J Epilepsy Res 2021; 11:6-13. [PMID: 34395218 PMCID: PMC8357552 DOI: 10.14581/jer.21002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background and Purpose Accumulating evidence suggest that lenalidomide, a structural analog of thalidomide, has neuro-modulatory and neuroprotective properties. In the present study, we investigated effects of acute administration of lenalidomide on clonic seizure threshold in mice induced by pentylenetetrazole (PTZ) and possible role of N-methyl-D-aspartic acid receptor (NMDAR) and nitric oxide (NO) pathway. Methods We have utilized a clonic model of seizure in NMRI mice induced by PTZ to evaluate the potential effect of lenalidomide on seizure threshold. Different doses of lenalidomide (5, 10, 20, and 50 mg/kg, intraperitoneal [i.p.]) were administered 1 hour before PTZ. To evaluate probable role of NMDAR/NO signaling, the non-selective NO synthase inhibitor L-NG-nitroarginine methyl ester (L-NAME; 10 mg/kg, i.p.), neuronal NOS (nNOS) inhibitor 7-nitroindazole (7-NI; 30 mg/kg, i.p.), selective inducible NOS inhibitor aminoguanidine (AG; 100 mg/kg, i.p.), selective NMDAR antagonist MK-801 (0.01 mg/kg, i.p.), and selective NMDAR agonist D-serine (30 mg/kg, i.p.) were injected 15 minutes before lenalidomide. Results Lenalidomide at 10 and 20 mg/kg significantly elevated the PTZ-induced seizure thresholds. Interestingly, L-NAME (10 mg/kg, i.p), 7-NI (30 mg/kg, i.p), and AG (100 mg/kg, i.p) reversed the anticonvulsive effect of lenalidomide (10 mg/kg). Moreover, treatment with the NMDAR agonist D-serine (30 mg/kg, i.p.) did not alter the anticonvulsive properties of lenalidomide (10 mg/kg, i.p). However, the NMDAR antagonist MK-801 (0.01 mg/kg, i.p) significantly reversed the anticonvulsive effects of lenalidomide (10 mg/kg). Conclusions Our study demonstrated a role for the NMDAR/NO pathway in the anticonvulsive effects of lenalidomide on the PTZ-induced clonic seizures in mice.
Collapse
Affiliation(s)
- Elaheh Asgari Dafe
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| | - Nastaran Rahimi
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| | - Nina Javadian
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Dejban
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, NY, USA
| | - Monika Komeili
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Modabberi
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Ghasemi
- Department of Neurology, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Ahmad Reza Dehpour
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
8
|
Di Fiore A, Supuran CT, Scaloni A, De Simone G. Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. J Enzyme Inhib Med Chem 2021; 35:1450-1461. [PMID: 32648529 PMCID: PMC7470082 DOI: 10.1080/14756366.2020.1781846] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human carbonic anhydrases (CAs) have become a well-recognized target for the design of inhibitors and activators with biomedical applications. Accordingly, an enormous amount of literature is available on their biochemical, functional and structural aspects. Nevertheless post-translational modifications (PTMs) occurring on these enzymes and their functional implications have been poorly investigated so far. To fill this gap, in this review we have analysed all PTMs occurring on human CAs, as deriving from the search in dedicated databases, showing a widespread occurrence of modification events in this enzyme family. By combining these data with sequence alignments, inspection of 3 D structures and available literature, we have summarised the possible functional implications of these PTMs. Although in some cases a clear correlation between a specific PTM and the CA function has been highlighted, many modification events still deserve further dedicated studies.
Collapse
Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-National Research Council, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Sesto Fiorentino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
| | | |
Collapse
|
9
|
Chatterji A, Sengupta R. Cellular S-denitrosylases: Potential role and interplay of Thioredoxin, TRP14, and Glutaredoxin systems in thiol-dependent protein denitrosylation. Int J Biochem Cell Biol 2021; 131:105904. [DOI: 10.1016/j.biocel.2020.105904] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
|
10
|
Nakamura T, Oh CK, Liao L, Zhang X, Lopez KM, Gibbs D, Deal AK, Scott HR, Spencer B, Masliah E, Rissman RA, Yates JR, Lipton SA. Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 2020; 371:science.aaw0843. [PMID: 33273062 DOI: 10.1126/science.aaw0843] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Here we describe mechanistically distinct enzymes (a kinase, a guanosine triphosphatase, and a ubiquitin protein hydrolase) that function in disparate biochemical pathways and can also act in concert to mediate a series of redox reactions. Each enzyme manifests a second, noncanonical function-transnitrosylation-that triggers a pathological biochemical cascade in mouse models and in humans with Alzheimer's disease (AD). The resulting series of transnitrosylation reactions contributes to synapse loss, the major pathological correlate to cognitive decline in AD. We conclude that enzymes with distinct primary reaction mechanisms can form a completely separate network for aberrant transnitrosylation. This network operates in the postreproductive period, so natural selection against such abnormal activity may be decreased.
Collapse
Affiliation(s)
- Tomohiro Nakamura
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA. .,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Chang-Ki Oh
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Lujian Liao
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xu Zhang
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Kevin M Lopez
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Daniel Gibbs
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Amanda K Deal
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry R Scott
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Brian Spencer
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA.,VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - John R Yates
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stuart A Lipton
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA. .,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA.,Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| |
Collapse
|
11
|
RNF11 at the Crossroads of Protein Ubiquitination. Biomolecules 2020; 10:biom10111538. [PMID: 33187263 PMCID: PMC7697665 DOI: 10.3390/biom10111538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/18/2022] Open
Abstract
RNF11 (Ring Finger Protein 11) is a 154 amino-acid long protein that contains a RING-H2 domain, whose sequence has remained substantially unchanged throughout vertebrate evolution. RNF11 has drawn attention as a modulator of protein degradation by HECT E3 ligases. Indeed, the large number of substrates that are regulated by HECT ligases, such as ITCH, SMURF1/2, WWP1/2, and NEDD4, and their role in turning off the signaling by ubiquitin-mediated degradation, candidates RNF11 as the master regulator of a plethora of signaling pathways. Starting from the analysis of the primary sequence motifs and from the list of RNF11 protein partners, we summarize the evidence implicating RNF11 as an important player in modulating ubiquitin-regulated processes that are involved in transforming growth factor beta (TGF-β), nuclear factor-κB (NF-κB), and Epidermal Growth Factor (EGF) signaling pathways. This connection appears to be particularly significant, since RNF11 is overexpressed in several tumors, even though its role as tumor growth inhibitor or promoter is still controversial. The review highlights the different facets and peculiarities of this unconventional small RING-E3 ligase and its implication in tumorigenesis, invasion, neuroinflammation, and cancer metastasis.
Collapse
|
12
|
Zhang Y, Deng Y, Yang X, Xue H, Lang Y. The Relationship Between Protein S-Nitrosylation and Human Diseases: A Review. Neurochem Res 2020; 45:2815-2827. [PMID: 32984933 DOI: 10.1007/s11064-020-03136-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 09/19/2020] [Indexed: 01/12/2023]
Abstract
S-nitrosylation (SNO) is a covalent post-translational oxidative modification. The reaction is the nitroso group (-NO) to a reactive cysteine thiol within a protein to form the SNO. In recent years, a variety of proteins in human body have been found to undergo thiol nitrosylation under specific conditions. Protein SNO, which is closely related to cardiovascular disease, Parkinson's syndrome, Alzheimer's disease and tumors, plays an important role in regulatory mechanism of protein function in both physiological and pathological pathways, such as in cellular homeostasis and metabolism. This review discusses possible molecular mechanisms protein SNO modification, such as the role of NO in vivo and the formation mechanism of SNO, with particular emphasis on mechanisms utilized by SNO to cause certain diseases of human. Importantly, the effect of SNO on diseases is multifaceted and multi-channel, and its critical value in vivo is not well defined. Intracellular redox environment is also a key factor affecting its level. Therefore, we should pay more attention to the equilibrium relationship between SNO and denitrosylation pathway in the future researches. These findings provide theoretical support for the improvement or treatment of diseases from the point of view of SNO.
Collapse
Affiliation(s)
- Yadi Zhang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Yuzhen Deng
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Xiaoxi Yang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Hongmei Xue
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Yumiao Lang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China. .,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China.
| |
Collapse
|
13
|
Morgan ET, Skubic C, Lee CM, Cokan KB, Rozman D. Regulation of cytochrome P450 enzyme activity and expression by nitric oxide in the context of inflammatory disease. Drug Metab Rev 2020; 52:455-471. [PMID: 32898444 DOI: 10.1080/03602532.2020.1817061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many hepatic cytochrome P450 enzymes and their associated drug metabolizing activities are down-regulated in disease states, and much of this has been associated with inflammatory cytokines and their signaling pathways. One such pathway is the induction of inducible nitric oxide synthase (NOS2) and generation of nitric oxide (NO) in many tissues and cells including the liver and hepatocytes. Experiments in the 1990s demonstrated that NO could bind to and inhibit P450 enzymes, and suggested that inhibition of NOS could attenuate, and NO generation could mimic, the down-regulation by inflammatory stimuli of not only P450 catalytic activities but also of mRNA expression and protein levels of certain P450 enzymes. This review will summarize and examine the evidence that NO functionally inhibits and down-regulates P450 enzymes in vivo and in vitro, with a particular focus on the mechanisms by which these effects are achieved.
Collapse
Affiliation(s)
- Edward T Morgan
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Cene Skubic
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Choon-Myung Lee
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Kaja Blagotinšek Cokan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
14
|
Mattioni A, Boldt K, Auciello G, Komada M, Rappoport JZ, Ueffing M, Castagnoli L, Cesareni G, Santonico E. Ring Finger Protein 11 acts on ligand-activated EGFR via the direct interaction with the UIM region of ANKRD13 protein family. FEBS J 2020; 287:3526-3550. [PMID: 31985874 DOI: 10.1111/febs.15226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/13/2019] [Accepted: 01/22/2020] [Indexed: 01/07/2023]
Abstract
RING finger protein 11 (RNF11) is an evolutionary conserved Really Interesting New Gene E3 ligase that is overexpressed in several human tumours. Although several reports have highlighted its involvement in crucial cellular processes, the mechanistic details underlying its function are still poorly understood. Utilizing stable isotope labelling by amino acids in culture (SILAC)-based proteomics analysis, we identified 51 proteins that co-immunoprecipitate with wild-type RNF11 and/or with its catalytically inactive mutant. We focused our attention on the interaction of RNF11 with Ankyrin repeat domain-containing protein 13 (ANKRD13)s family. Members of the ANKRD13 family contain ubiquitin-interacting motifs (UIM) that recognize the Lys-63-linked ubiquitin (Ub) chains appended to Epidermal growth factor receptor (EGFR) soon after ligand binding. We show that ANKRD13A, ANKRD13B and ANKRD13D form a complex with RNF11 in vivo and that the UIMs are required for complex formation. However, at odds with the conventional UIM binding mode, Ub modification of RNF11 is not required for the interaction with ANKRD13 proteins. We also show that the interaction between ANKRD13A and RNF11 is modulated by the EGF stimulus and that a complex formed by ANKRD13A, RNF11 and activated EGFR is transiently assembled in the early phases of receptor endocytosis. Moreover, loss of function of the E3 ligases Itchy E3 ubiquitin-protein ligase (ITCH) or RNF11, respectively, abrogates or increases the ubiquitination of endogenous ANKRD13A, affecting its ability to bind activated EGFR. We propose a model whereby the ANKRD13 proteins act as molecular scaffolds that promote the transient formation of a complex between the activated EGFR and the E3 ligases ITCH and RNF11. By regulating the ubiquitination status of ANKRD13A and consequently its endocytic adaptor function, RNF11 promotes sorting of the activated EGFR for lysosomal degradation.
Collapse
Affiliation(s)
- Anna Mattioni
- Department of Biology, University of Rome Tor Vergata, Italy
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | - Giulio Auciello
- Istituto di Ricerche di Biologia Molecolare (IRBM), Pomezia, Italy
| | - Masayuki Komada
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | | | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Italy
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Italy
| |
Collapse
|
15
|
Nakamura T, Lipton SA. Nitric Oxide-Dependent Protein Post-Translational Modifications Impair Mitochondrial Function and Metabolism to Contribute to Neurodegenerative Diseases. Antioxid Redox Signal 2020; 32:817-833. [PMID: 31657228 PMCID: PMC7074890 DOI: 10.1089/ars.2019.7916] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Significance: Most brains affected by neurodegenerative diseases manifest mitochondrial dysfunction as well as elevated production of reactive oxygen species and reactive nitrogen species (RNS), contributing to synapse loss and neuronal injury. Recent Advances: Excessive production of RNS triggers nitric oxide (NO)-mediated post-translational modifications of proteins, such as S-nitrosylation of cysteine residues and nitration of tyrosine residues. Proteins thus affected impair mitochondrial metabolism, mitochondrial dynamics, and mitophagy in the nervous system. Critical Issues: Identification and better characterization of underlying molecular mechanisms for NO-mediated mitochondrial dysfunction will provide important insights into the pathogenesis of neurodegenerative disorders. In this review, we highlight recent discoveries concerning S-nitrosylation of the tricarboxylic acid cycle enzymes, mitochondrial fission GTPase dynamin-related protein 1, and mitophagy-related proteins Parkin and phosphatase and tensin homolog-induced putative kinase protein 1. We delineate signaling cascades affected by pathologically S-nitrosylated proteins that diminish mitochondrial function in neurodegenerative diseases. Future Directions: Further elucidation of the pathological events resulting from aberrant S-nitrosothiol or nitrotyrosine formation may lead to new therapeutic approaches to ameliorate neurodegenerative disorders.
Collapse
Affiliation(s)
- Tomohiro Nakamura
- Departments of Molecular Medicine and Neuroscience, Neuroscience Translational Center, The Scripps Research Institute, La Jolla, California
- Address correspondence to: Dr. Tomohiro Nakamura, Departments of Molecular Medicine and Neuroscience, Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037
| | - Stuart A. Lipton
- Departments of Molecular Medicine and Neuroscience, Neuroscience Translational Center, The Scripps Research Institute, La Jolla, California
- Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, California
- Dr. Stuart A. Lipton, Departments of Molecular Medicine and Neuroscience, Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037
| |
Collapse
|
16
|
Stomberski CT, Hess DT, Stamler JS. Protein S-Nitrosylation: Determinants of Specificity and Enzymatic Regulation of S-Nitrosothiol-Based Signaling. Antioxid Redox Signal 2019; 30:1331-1351. [PMID: 29130312 PMCID: PMC6391618 DOI: 10.1089/ars.2017.7403] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Protein S-nitrosylation, the oxidative modification of cysteine by nitric oxide (NO) to form protein S-nitrosothiols (SNOs), mediates redox-based signaling that conveys, in large part, the ubiquitous influence of NO on cellular function. S-nitrosylation regulates protein activity, stability, localization, and protein-protein interactions across myriad physiological processes, and aberrant S-nitrosylation is associated with diverse pathophysiologies. Recent Advances: It is recently recognized that S-nitrosylation endows S-nitroso-protein (SNO-proteins) with S-nitrosylase activity, that is, the potential to trans-S-nitrosylate additional proteins, thereby propagating SNO-based signals, analogous to kinase-mediated signaling cascades. In addition, it is increasingly appreciated that cellular S-nitrosylation is governed by dynamically coupled equilibria between SNO-proteins and low-molecular-weight SNOs, which are controlled by a growing set of enzymatic denitrosylases comprising two main classes (high and low molecular weight). S-nitrosylases and denitrosylases, which together control steady-state SNO levels, may be identified with distinct physiology and pathophysiology ranging from cardiovascular and respiratory disorders to neurodegeneration and cancer. CRITICAL ISSUES The target specificity of protein S-nitrosylation and the stability and reactivity of protein SNOs are determined substantially by enzymatic machinery comprising highly conserved transnitrosylases and denitrosylases. Understanding the differential functionality of SNO-regulatory enzymes is essential, and is amenable to genetic and pharmacological analyses, read out as perturbation of specific equilibria within the SNO circuitry. FUTURE DIRECTIONS The emerging picture of NO biology entails equilibria among potentially thousands of different SNOs, governed by denitrosylases and nitrosylases. Thus, to elucidate the operation and consequences of S-nitrosylation in cellular contexts, studies should consider the roles of SNO-proteins as both targets and transducers of S-nitrosylation, functioning according to enzymatically governed equilibria.
Collapse
Affiliation(s)
- Colin T Stomberski
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio
| | - Douglas T Hess
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Jonathan S Stamler
- 2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio.,4 Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| |
Collapse
|
17
|
Xu X, Qiu H, Shi F, Wang Z, Wang X, Jin L, Chi L, Zhang Q. The protein S-nitrosylation of splicing and translational machinery in vascular endothelial cells is susceptible to oxidative stress induced by oxidized low-density lipoprotein. J Proteomics 2019; 195:11-22. [PMID: 30630120 DOI: 10.1016/j.jprot.2019.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/18/2018] [Accepted: 01/05/2019] [Indexed: 12/24/2022]
Abstract
Oxidized low-density lipoprotein (ox-LDL) can impair endothelial function and lead to the atherosclerosis development. Protein S-nitrosylation is sensitive to cellular redox state and acts as a crucial regulator and executor of nitric oxide (NO) signaling pathways. Aberrant S-nitrosylation contributes to the pathogenesis of cardiovascular and cerebrovascular diseases. However, the effect of ox-LDL on S-nitrosylation and its significance for endothelial dysfunction have not been studied at proteome level. Herein, the combined quantitative analysis of proteome and S-nitrosoproteome was performed using an integrated biotin switch and iTRAQ labeling approach in EA.hy926 cell line derived from human umbilical vein endothelial cell (HUVEC) treated with ox-LDL. A total of 2204 S-nitrosylated (SNO) peptides of 1318 SNO-proteins were quantified. Notably, 352 SNO-peptides of 262 SNO-proteins were significantly regulated after excluding S-nitrosylation changes caused by protein expression alterations. Many of them belonged to mRNA splicing, ribosomal structure and translational regulatory proteins, covering the entire translation process. The results indicated that S-nitrosylation of the splicing and translational machinery in vascular endothelial cells was susceptible to ox-LDL. Abnormal protein S-nitrosylation may be one pivotal mechanism underlying endothelial dysfunction induced by ox-LDL. This study potentially enriches the present understanding of pro-atherogenic effect of ox-LDL from the perspective of S-nitrosylation. SIGNIFICANCE: The role of ox-LDL in endothelial dysfunction and atherosclerosis development has been recognized from the aspect of impaired NO production. However, its effect on S-nitrosylation, which is directly related to NO signaling pathway, still remains largely unexplored. Our work initially provided a systematic characterization of S-nitrosoproteome in ox-LDL-treated endothelial cells after ruling out the changes of S-nitrosylation modification caused by protein expression alone. MS-based approach coupled with iTRAQ technique indicated 262 SNO-proteins were significantly regulated. Functional enrichment and interaction network analysis revealed that proteins involved in mRNA splicing and translational machinery were susceptible to abnormal S-nitrosylation under ox-LDL treatment. This achievement suggested one potential mechanism underlying endothelial dysfunction induced by ox-LDL from the perspective of S-nitrosoproteome.
Collapse
Affiliation(s)
- Xiaohui Xu
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Hongyan Qiu
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Feng Shi
- Scientific Research Division, Shandong Institute for Food and Drug Control, Jinan, Shandong 250101, China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Provincial Hospital affiliated with Shandong University, Jinan, Shandong 250021, China
| | - Xiaowei Wang
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Lan Jin
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Lianli Chi
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China.
| | - Qunye Zhang
- National Glycoengineering Research Center, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China.
| |
Collapse
|
18
|
Feng Y, Chen CS, Ho J, Pearce D, Hu S, Wang B, Desai P, Kim KS, Zhu H. High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology). Anal Chem 2018; 90:10958-10966. [PMID: 30106562 DOI: 10.1021/acs.analchem.8b02513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial meningitis in neonates and infants is an acute lethal disease and occurs in response to microbial exploitation of the blood-brain barrier (BBB), resulting in the intracranial inflammation. Several pathogens, such as Escherichia coli ( E. coli), can cause this devastating disease; however, the underlying molecular mechanisms by which these pathogens exploit the BBB remain incompletely understood. To identify important players on both the pathogen and host sides that govern the E. coli-BBB cell interactions, we took advantage of the E. coli and human proteome microarrays (i.e., HuProt) as an unbiased, proteome-wide tool for identification of important players on both sides. Using the E. coli proteome microarrays, we developed a unique high throughput chip-based cell probing assay to probe with fluorescent live human brain microvascular endothelial cells (HBMEC, which constitute the BBB). We identified several transmembrane proteins, which effectively bound to live HBMEC. We focused on YojI protein for further study. By probing the HuProt arrays with YojI, interferon-alpha receptor (IFNAR2) was identified as one of its binding proteins. The importance of YojI and IFNAR2 involved in E. coli-HBMEC interactions was characterized using the YojI knockout bacteria and IFNAR2-knock down HBMEC and further confirmed by E. coli binding assay in HBMEC. This study represents a new paradigm (dual-microarray technology) that enables rapid, unbiased discovery of both pathogen and host players that are involved in pathogen-host interactions for human infectious diseases in a high throughput manner.
Collapse
Affiliation(s)
- Yingzhu Feng
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management , Tainan City 701 , Taiwan.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Biomedical Science and Engineering , National Central University , Taoyuan City 32001 , Taiwan
| | - Jessica Ho
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Donna Pearce
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Shaohui Hu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Bochu Wang
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China
| | - Prashant Desai
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21231 , United States
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| |
Collapse
|
19
|
Meng S, Chanda P, Thandavarayan RA, Cooke JP. Transflammation: How Innate Immune Activation and Free Radicals Drive Nuclear Reprogramming. Antioxid Redox Signal 2018; 29:205-218. [PMID: 29634341 PMCID: PMC6003401 DOI: 10.1089/ars.2017.7364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Yamanaka and colleagues galvanized the field of stem cell biology and regenerative medicine by their generation of induced pluripotent stem cells. Evidence is emerging that activation of innate immune signaling is critical for efficient reprogramming to pluripotency and for the nuclear reprogramming occurring in transdifferentiation. Recent Advances: We have shown that innate immune signaling triggers a global change in the expression of epigenetic modifiers to enhance DNA accessibility. In this state of epigenetic plasticity, overexpression of lineage determination factors, and/or environmental cues and paracrine factors, can induce pluripotency, or can direct transdifferentiation to another somatic cell lineage. Accumulating evidence reveals that innate immune activation triggers the generation of reactive oxygen species and reactive nitrogen species, and that these free radicals are required for nuclear reprogramming to pluripotency or for transdifferentiation. CRITICAL ISSUES We have discovered a limb of innate immune signaling that regulates DNA accessibility, in part, by the action of free radicals to induce post-translational modification of epigenetic modifiers. FUTURE DIRECTIONS It is of scientific interest and clinical relevance to understand the mechanisms by which free radicals influence epigenetic plasticity, and how these mechanisms may be therapeutically modulated. Antioxid. Redox Signal. 00, 000-000.
Collapse
Affiliation(s)
- Shu Meng
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute , Houston, Texas
| | - Palas Chanda
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute , Houston, Texas
| | - Rajarajan A Thandavarayan
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute , Houston, Texas
| | - John P Cooke
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute , Houston, Texas
| |
Collapse
|
20
|
Nitric Oxide and Mitochondrial Function in Neurological Diseases. Neuroscience 2018; 376:48-71. [DOI: 10.1016/j.neuroscience.2018.02.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/20/2018] [Accepted: 02/09/2018] [Indexed: 12/17/2022]
|
21
|
Ibáñez-Vea M, Huang H, Martínez de Morentin X, Pérez E, Gato M, Zuazo M, Arasanz H, Fernández-Irigoyen J, Santamaría E, Fernandez-Hinojal G, Larsen MR, Escors D, Kochan G. Characterization of Macrophage Endogenous S-Nitrosoproteome Using a Cysteine-Specific Phosphonate Adaptable Tag in Combination with TiO 2 Chromatography. J Proteome Res 2018; 17:1172-1182. [PMID: 29338241 DOI: 10.1021/acs.jproteome.7b00812] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein S-nitrosylation is a cysteine post-translational modification mediated by nitric oxide. An increasing number of studies highlight S-nitrosylation as an important regulator of signaling involved in numerous cellular processes. Despite the significant progress in the development of redox proteomic methods, identification and quantification of endogeneous S-nitrosylation using high-throughput mass-spectrometry-based methods is a technical challenge because this modification is highly labile. To overcome this drawback, most methods induce S-nitrosylation chemically in proteins using nitrosylating compounds before analysis, with the risk of introducing nonphysiological S-nitrosylation. Here we present a novel method to efficiently identify endogenous S-nitrosopeptides in the macrophage total proteome. Our approach is based on the labeling of S-nitrosopeptides reduced by ascorbate with a cysteine specific phosphonate adaptable tag (CysPAT), followed by titanium dioxide (TiO2) chromatography enrichment prior to nLC-MS/MS analysis. To test our procedure, we performed a large-scale analysis of this low-abundant modification in a murine macrophage cell line. We identified 569 endogeneous S-nitrosylated proteins compared with 795 following exogenous chemically induced S-nitrosylation. Importantly, we discovered 579 novel S-nitrosylation sites. The large number of identified endogenous S-nitrosylated peptides allowed the definition of two S-nitrosylation consensus sites, highlighting protein translation and redox processes as key S-nitrosylation targets in macrophages.
Collapse
Affiliation(s)
- María Ibáñez-Vea
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Honggang Huang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK 5230 Odense M, Denmark
| | - Xabier Martínez de Morentin
- Bioinformatics Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Estela Pérez
- Proteored - ISCIII, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Maria Gato
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Miren Zuazo
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Hugo Arasanz
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Joaquin Fernández-Irigoyen
- Proteored - ISCIII, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Proteored - ISCIII, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Gonzalo Fernandez-Hinojal
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK 5230 Odense M, Denmark
| | - David Escors
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain.,Division of Infection and Immunity, Rayne Institute, University College London , 5 University Street, WC1E 6JF London, United Kingdom
| | - Grazyna Kochan
- Immunomodulation Group, Navarrabiomed Biomedical Research Center, Navarra Institute for Health Research (IdiSNA) , Irunlarrea 3, 31008 Pamplona, Spain
| |
Collapse
|
22
|
Peroxisomes and Cellular Oxidant/Antioxidant Balance: Protein Redox Modifications and Impact on Inter-organelle Communication. Subcell Biochem 2018; 89:435-461. [PMID: 30378035 DOI: 10.1007/978-981-13-2233-4_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disturbances in cellular redox balance have been associated with pro-aging mechanisms and increased risk for various chronic disease states. Multiple lines of evidence indicate that peroxisomes are central players in cellular redox metabolism. Nevertheless, the potential role of this organelle as intracellular redox signaling platform has been largely overlooked for a long time. Fortunately, this situation is now changing. This review provides a snapshot of the current progress in the field, with an emphasis on the situation in mammals. We first briefly introduce the basics of redox biology and how reactive oxygen and nitrogen species can drive cellular signaling events. Next, we discuss current evidence linking peroxisome (dys)function to redox signaling, both in health and disease. We also highlight what is currently known about the downstream targets of peroxisome-derived oxidants. In addition, we present an extensive list of proteins that are involved in peroxisome functioning and have been identified as being responsive to oxidative stress in large scale redox proteomics studies. Finally, we address how changes in peroxisomal redox state may impact on functional mechanisms underlying inter-organelle communication. Gaining more insight into these mechanisms is key to our understanding of how peroxisomes are embedded in cellular signaling networks implicated in aging and diseases such as cancer, diabetes, and neurodegenerative disorders.
Collapse
|
23
|
Transflammation: Innate immune signaling in nuclear reprogramming. Adv Drug Deliv Rev 2017; 120:133-141. [PMID: 28916494 DOI: 10.1016/j.addr.2017.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 12/23/2022]
Abstract
Induction of pluripotency in somatic cells by retroviral overexpression of four transcription factors has revolutionized the field of stem cell biology and regenerative medicine. The efficient induction of pluripotency requires the activation of innate immune signaling in a process termed "transflammation" (Lee et al., 2012). Specifically, the stimulation of pattern recognition receptors (PRRs) causes global alterations in the expression and activity of epigenetic modifiers to favor an open chromatin configuration. Activation of toll-like receptors (TLR) or RIG-1-like receptors (RLR) (Sayed et al. 2017) trigger signaling cascades that result in NFκB or IRF-3 mediated changes in epigenetic plasticity that facilitate reprogramming. Another form of nuclear reprogramming is so-called direct reprogramming or transdifferentiation of one somatic cell to another lineage. We have shown that transdifferentiation of human fibroblasts to endothelial cells also involves transflammation (Sayed et al., 2015). Recently, we also identified reactive oxygen species (ROS) (Zhou et al. 2016) and reactive nitrogen species (RNS) (Meng et al., 2016) as mediators of innate immune signaling in nuclear reprogramming. Innate immune signaling plays a key role in nuclear reprogramming by regulating DNA accessibility (Fig. 1). Here, we review recent progress of innate immunity signaling in nuclear reprogramming and epigenetic plasticity.
Collapse
|
24
|
Endothelial NO Synthase-Dependent S-Nitrosylation of β-Catenin Prevents Its Association with TCF4 and Inhibits Proliferation of Endothelial Cells Stimulated by Wnt3a. Mol Cell Biol 2017; 37:MCB.00089-17. [PMID: 28320874 DOI: 10.1128/mcb.00089-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/14/2017] [Indexed: 11/20/2022] Open
Abstract
Nitric oxide (NO) produced by endothelial NO synthase (eNOS) modulates many functions in endothelial cells. S-nitrosylation (SNO) of cysteine residues on β-catenin by eNOS-derived NO has been shown to influence intercellular contacts between endothelial cells. However, the implication of SNO in the regulation of β-catenin transcriptional activity is ill defined. Here, we report that NO inhibits the transcriptional activity of β-catenin and endothelial cell proliferation induced by activation of Wnt/β-catenin signaling. Interestingly, induction by Wnt3a of β-catenin target genes, such as the axin2 gene, is repressed in an eNOS-dependent manner by vascular endothelial growth factor (VEGF). We identified Cys466 of β-catenin as a target for SNO by eNOS-derived NO and as the critical residue for the repressive effects of NO on β-catenin transcriptional activity. Furthermore, we observed that Cys466 of β-catenin, located at the binding interface of the β-catenin-TCF4 transcriptional complex, is essential for disruption of this complex by NO. Importantly, Cys466 of β-catenin is necessary for the inhibitory effects of NO on Wnt3a-stimulated proliferation of endothelial cells. Thus, our data define the mechanism responsible for the repressive effects of NO on the transcriptional activity of β-catenin and link eNOS-derived NO to the modulation by VEGF of Wnt/β-catenin-induced endothelial cell proliferation.
Collapse
|
25
|
Cox E, Hwang W, Uzoma I, Hu J, Guzzo CM, Jeong J, Matunis MJ, Qian J, Zhu H, Blackshaw S. Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex. Mol Cell Proteomics 2017; 16:812-823. [PMID: 28254775 PMCID: PMC5417823 DOI: 10.1074/mcp.m116.063719] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/14/2017] [Indexed: 12/23/2022] Open
Abstract
SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo We then demonstrated a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo By demonstrating a key role for SUMOylation in regulating the INO80 chromatin remodeling complex, this work illustrates the power of bioinformatics analysis of large data sets in predicting novel biological phenomena.
Collapse
Affiliation(s)
- Eric Cox
- From the ‡Biochemistry, Cellular and Molecular Biology Graduate Program
- §Solomon H. Snyder Department of Neuroscience
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Ijeoma Uzoma
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Catherine M Guzzo
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Junseop Jeong
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Michael J Matunis
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Heng Zhu
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Seth Blackshaw
- §Solomon H. Snyder Department of Neuroscience,
- ‡‡Center for High-Throughput Biology
- §§Institute for Cell Engineering
- ¶¶Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
26
|
Yang Z, Hou Y, Hao T, Rho HS, Wan J, Luan Y, Gao X, Yao J, Pan A, Xie Z, Qian J, Liao W, Zhu H, Zhou X. A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18. Mol Cell Proteomics 2017; 16:469-484. [PMID: 28087594 DOI: 10.1074/mcp.m116.063602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
Toxoplasma kinase ROP18 is a key molecule responsible for the virulence of Toxoplasma gondii; however, the mechanisms by which ROP18 exerts parasite virulence via interaction with host proteins remain limited to a small number of identified substrates. To identify a broader array of ROP18 substrates, we successfully purified bioactive mature ROP18 and used it to probe a human proteome array. Sixty eight new putative host targets were identified. Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. Among these proteins, four candidates, p53, p38, UBE2N, and Smad1, were further validated. We demonstrated that ROP18 targets p53, p38, UBE2N, and Smad1 for degradation. Importantly, we demonstrated that ROP18 phosphorylates Smad1 Ser-187 to trigger its proteasome-dependent degradation. Further functional characterization of the substrates of ROP18 may enhance understanding of the pathogenesis of Toxoplasma infection and provide new therapeutic targets. Similar strategies could be used to identify novel host targets for other microbial kinases functioning at the pathogen-host interface.
Collapse
Affiliation(s)
- Zhaoshou Yang
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yongheng Hou
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Taofang Hao
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Hee-Sool Rho
- the §Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jun Wan
- the ¶Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Yizhao Luan
- the ‖State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.,the **School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Gao
- ‡‡The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; and
| | - Jianping Yao
- §§The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Aihua Pan
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhi Xie
- the ‖State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Jiang Qian
- the ¶Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Wanqin Liao
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| | - Heng Zhu
- the §Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Xingwang Zhou
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| |
Collapse
|
27
|
Pirih N, Kunej T. Toward a Taxonomy for Multi-Omics Science? Terminology Development for Whole Genome Study Approaches by Omics Technology and Hierarchy. ACTA ACUST UNITED AC 2017; 21:1-16. [DOI: 10.1089/omi.2016.0144] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| |
Collapse
|
28
|
Abstract
Thiol groups in protein cysteine residues can be subjected to different oxidative modifications by reactive oxygen/nitrogen species. Reversible cysteine oxidation, including S-nitrosylation, S-sulfenylation, S-glutathionylation, and disulfide formation, modulate multiple biological functions, such as enzyme catalysis, antioxidant, and other signaling pathways. However, the biological relevance of reversible cysteine oxidation is typically underestimated, in part due to the low abundance and high reactivity of some of these modifications, and the lack of methods to enrich and quantify them. To facilitate future research efforts, this chapter describes detailed procedures to target the different modifications using mass spectrometry-based biotin switch assays. By switching the modification of interest to a biotin moiety, these assays leverage the high affinity between biotin and avidin to enrich the modification. The use of stable isotope labeling and a range of selective reducing agents facilitate the quantitation of individual as well as total reversible cysteine oxidation. The biotin switch assay has been widely applied to the quantitative analysis of S-nitrosylation in different disease models and is now also emerging as a valuable research tool for other oxidative cysteine modifications, highlighting its relevance as a versatile, robust strategy for carrying out in-depth studies in redox proteomics.
Collapse
Affiliation(s)
- R Li
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| | - J Kast
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
29
|
Meng S, Zhou G, Gu Q, Chanda PK, Ospino F, Cooke JP. Transdifferentiation Requires iNOS Activation: Role of RING1A S-Nitrosylation. Circ Res 2016; 119:e129-e138. [PMID: 27623813 DOI: 10.1161/circresaha.116.308263] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022]
Abstract
RATIONALE We have previously shown that innate immunity is necessary for transdifferentiation of fibroblasts to endothelial cells. A major signaling molecule involved in innate immunity is inducible nitric oxide synthase (iNOS). Accordingly, we hypothesized that iNOS-generated nitric oxide (NO) might enhance transdifferentiation. OBJECTIVE To elucidate the role of NO in epigenetic plasticity during transdifferentiation. METHODS AND RESULTS We exposed the BJ fibroblasts to transdifferentiation formulation that included endothelial growth factors and innate immune activator polyinosinic:polycytidylic acid to induce endothelial cells. Generation of transdifferentiated endothelial cells was associated with iNOS expression and NO elaboration. In the absence of polyinosinic:polycytidylic acid, or in the presence of antagonists of NFκB (nuclear factor kappa B) or iNOS activity, NO synthesis and induce endothelial cell generation was reduced. Furthermore, genetic knockout (in murine embryonic fibroblasts) or siRNA knockdown (in BJ fibroblasts) of iNOS nearly abolished transdifferentiation, an effect that could be reversed by iNOS overexpression. Notably, polyinosinic:polycytidylic acid induced nuclear localization of iNOS, and its binding to, and nitrosylation of, the epigenetic modifier ring finger protein 1A (RING1A) as assessed by immunostaining, Co-IP, and mass spectrometry. Nitrosylation of RING1A reduced its binding to chromatin and reduced global levels of repressive histone marker H3K27 trimethylation. Overexpression of a mutant form of RING1A (C398A) lacking the nitrosylation site almost abrogated transdifferentiation. CONCLUSIONS Overall, our data indicate that during transdifferentiation, innate immune activation increases iNOS generation of NO to S-nitrosylate RING1A, a key member of the polycomb repressive complex. Nitrosylation of RING1A reduces its binding to chromatin and decreases H3K27 trimethylation level. The release of epigenetic repression by nitrosylation of RING1A is critical for effective transdifferentiation.
Collapse
Affiliation(s)
- Shu Meng
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX
| | - Gang Zhou
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX
| | - Qilin Gu
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX
| | - Palas K Chanda
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX
| | - Frank Ospino
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX
| | - John P Cooke
- From the Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, TX.
| |
Collapse
|
30
|
Atak A, Mukherjee S, Jain R, Gupta S, Singh VA, Gahoi N, K P M, Srivastava S. Protein microarray applications: Autoantibody detection and posttranslational modification. Proteomics 2016; 16:2557-2569. [PMID: 27452627 DOI: 10.1002/pmic.201600104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/09/2016] [Accepted: 07/19/2016] [Indexed: 12/18/2022]
Abstract
The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.
Collapse
Affiliation(s)
- Apurva Atak
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shuvolina Mukherjee
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rekha Jain
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shabarni Gupta
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vedita Anand Singh
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Nikita Gahoi
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Manubhai K P
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
| |
Collapse
|
31
|
Siragusa M, Fleming I. The eNOS signalosome and its link to endothelial dysfunction. Pflugers Arch 2016; 468:1125-1137. [DOI: 10.1007/s00424-016-1839-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 05/10/2016] [Indexed: 12/17/2022]
|
32
|
An overview of innovations and industrial solutions in Protein Microarray Technology. Proteomics 2016; 16:1297-308. [DOI: 10.1002/pmic.201500429] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 01/12/2023]
|
33
|
Induction, Propagation, and Activity of Host Nitric Oxide: Lessons from Leishmania Infection. Trends Parasitol 2015; 31:653-664. [DOI: 10.1016/j.pt.2015.08.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 02/07/2023]
|
34
|
Qu Z, Greenlief CM, Gu Z. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation. J Proteome Res 2015; 15:1-14. [DOI: 10.1021/acs.jproteome.5b00857] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - C. Michael Greenlief
- Department
of Chemistry, University of Missouri College of Arts and Science, Columbia, Missouri 65211, United States
| | - Zezong Gu
- Harry S. Truman Veterans’ Hospital, Columbia, Missouri 65201, United States
| |
Collapse
|
35
|
Differential alkylation-based redox proteomics--Lessons learnt. Redox Biol 2015; 6:240-252. [PMID: 26282677 PMCID: PMC4543216 DOI: 10.1016/j.redox.2015.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023] Open
Abstract
Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms.
Collapse
|
36
|
Bogdan C. Nitric oxide synthase in innate and adaptive immunity: an update. Trends Immunol 2015; 36:161-78. [PMID: 25687683 DOI: 10.1016/j.it.2015.01.003] [Citation(s) in RCA: 552] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 12/22/2022]
Abstract
Thirty years after the discovery of its production by activated macrophages, our appreciation of the diverse roles of nitric oxide (NO) continues to grow. Recent findings have not only expanded our understanding of the mechanisms controlling the expression of NO synthases (NOS) in innate and adaptive immune cells, but have also revealed new functions and modes of action of NO in the control and escape of infectious pathogens, in T and B cell differentiation, and in tumor defense. I discuss these findings, in the context of a comprehensive overview of the various sources and multiple reaction partners of NO, and of the regulation of NOS2 by micromilieu factors, antisense RNAs, and 'unexpected' cytokines.
Collapse
Affiliation(s)
- Christian Bogdan
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie, und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Wasserturmstraße 3/5, 91054 Erlangen, Germany.
| |
Collapse
|
37
|
Lamotte O, Bertoldo JB, Besson-Bard A, Rosnoblet C, Aimé S, Hichami S, Terenzi H, Wendehenne D. Protein S-nitrosylation: specificity and identification strategies in plants. Front Chem 2015; 2:114. [PMID: 25750911 PMCID: PMC4285867 DOI: 10.3389/fchem.2014.00114] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 12/08/2014] [Indexed: 12/23/2022] Open
Abstract
The role of nitric oxide (NO) as a major regulator of plant physiological functions has become increasingly evident. To further improve our understanding of its role, within the last few years plant biologists have begun to embrace the exciting opportunity of investigating protein S-nitrosylation, a major reversible NO-dependent post-translational modification (PTM) targeting specific Cys residues and widely studied in animals. Thanks to the development of dedicated proteomic approaches, in particular the use of the biotin switch technique (BST) combined with mass spectrometry, hundreds of plant protein candidates for S-nitrosylation have been identified. Functional studies focused on specific proteins provided preliminary comprehensive views of how this PTM impacts the structure and function of proteins and, more generally, of how NO might regulate biological plant processes. The aim of this review is to detail the basic principle of protein S-nitrosylation, to provide information on the biochemical and structural features of the S-nitrosylation sites and to describe the proteomic strategies adopted to investigate this PTM in plants. Limits of the current approaches and tomorrow's challenges are also discussed.
Collapse
Affiliation(s)
- Olivier Lamotte
- CNRS, UMR 1347 Agroécologie Dijon, France ; ERL CNRS 6300 Dijon, France
| | - Jean B Bertoldo
- Departamento de Bioquímica Centro de Ciências Biológicas, Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina Florianópolis, Brasil
| | - Angélique Besson-Bard
- ERL CNRS 6300 Dijon, France ; Université de Bourgogne, UMR 1347 Agroécologie Dijon, France
| | - Claire Rosnoblet
- ERL CNRS 6300 Dijon, France ; Université de Bourgogne, UMR 1347 Agroécologie Dijon, France
| | - Sébastien Aimé
- ERL CNRS 6300 Dijon, France ; Institut National de la Recherche Agronomique, UMR 1347 Agroécologie Dijon, France
| | - Siham Hichami
- ERL CNRS 6300 Dijon, France ; Université de Bourgogne, UMR 1347 Agroécologie Dijon, France
| | - Hernán Terenzi
- Departamento de Bioquímica Centro de Ciências Biológicas, Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina Florianópolis, Brasil
| | - David Wendehenne
- ERL CNRS 6300 Dijon, France ; Université de Bourgogne, UMR 1347 Agroécologie Dijon, France
| |
Collapse
|
38
|
Cox E, Uzoma I, Guzzo C, Jeong JS, Matunis M, Blackshaw S, Zhu H. Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray. Methods Mol Biol 2015; 1295:455-463. [PMID: 25820740 PMCID: PMC5882486 DOI: 10.1007/978-1-4939-2550-6_32] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The functional protein microarray is a powerful and versatile systems biology and proteomics tool that allows the rapid activity profiling of thousands of proteins in parallel. We have recently developed a human proteome array, the HuProt array, which includes ~80 % of all the full-length proteins of the human proteome. In one recent application of the HuProt array, we identified numerous SUMO E3 ligase-dependent SUMOylation substrates. For many SUMO E3 ligases, only a small number of substrates have been identified and the target specificities of these ligases therefore remain poorly defined. In this protocol, we outline a method we developed using the HuProt array to screen the human proteome to identify novel SUMO E3 ligase substrates recognized by specific E3 ligases.
Collapse
Affiliation(s)
- Eric Cox
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | | |
Collapse
|
39
|
Zhang Y, Zhang C, Jiang H, Yang P, Lu H. Fishing the PTM proteome with chemical approaches using functional solid phases. Chem Soc Rev 2015; 44:8260-87. [DOI: 10.1039/c4cs00529e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently available chemical approaches for the enrichment and separation of a PTM proteome using functional solid phases were reviewed.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| | - Cheng Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Hucong Jiang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| |
Collapse
|
40
|
Correani V, Francesco LD, Cera I, Mignogna G, Giorgi A, Mazzanti M, Fumagalli L, Fabrizi C, Maras B, Schininà ME. Reversible redox modifications in the microglial proteome challenged by beta amyloid. MOLECULAR BIOSYSTEMS 2015; 11:1584-93. [DOI: 10.1039/c4mb00703d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reversible redox modifications of the microglial proteome contribute to switching of these neuronal sentinel cells toward a neuroinflammatory phenotype.
Collapse
Affiliation(s)
- Virginia Correani
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Laura Di Francesco
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Isabella Cera
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Giuseppina Mignogna
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Michele Mazzanti
- Dipartimento di Bioscienze
- Università degli Studi di Milano
- Milan
- Italy
| | - Lorenzo Fumagalli
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Cinzia Fabrizi
- Dipartimento di Scienze Anatomiche
- Istologiche
- Medico-Legali e dell'Apparato Locomotore
- Sapienza University of Rome
- Rome
| | - Bruno Maras
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - M. Eugenia Schininà
- Dipartimento di Scienze Biochimiche
- Sapienza University of Rome
- 00185 Rome
- Italy
| |
Collapse
|
41
|
Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity. Cell Rep 2014; 9:2317-29. [PMID: 25497094 DOI: 10.1016/j.celrep.2014.11.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/17/2014] [Accepted: 11/17/2014] [Indexed: 12/30/2022] Open
Abstract
Poor understanding of the basic biology of Mycobacterium tuberculosis (MTB), the etiological agent of tuberculosis, hampers development of much-needed drugs, vaccines, and diagnostic tests. Better experimental tools are needed to expedite investigations of this pathogen at the systems level. Here, we present a functional MTB proteome microarray covering most of the proteome and an ORFome library. We demonstrate the broad applicability of the microarray by investigating global protein-protein interactions, small-molecule-protein binding, and serum biomarker discovery, identifying 59 PknG-interacting proteins, 30 bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding proteins, and 14 MTB proteins that together differentiate between tuberculosis (TB) patients with active disease and recovered individuals. Results suggest that the MTB rhamnose pathway is likely regulated by both the serine/threonine kinase PknG and c-di-GMP. This resource has the potential to generate a greater understanding of key biological processes in the pathogenesis of tuberculosis, possibly leading to more effective therapies for the treatment of this ancient disease.
Collapse
|
42
|
Kim YP, Park D, Kim JJ, Choi WJ, Lee SH, Lee SY, Kim S, Chung JM, Jeon J, Lee BD, Shin JH, Lee YI, Cho H, Lee JM, Kang HC. Effective therapeutic approach for head and neck cancer by an engineered minibody targeting the EGFR receptor. PLoS One 2014; 9:e113442. [PMID: 25438047 PMCID: PMC4249956 DOI: 10.1371/journal.pone.0113442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
Cetuximab, a chimeric monoclonal antibody developed for targeting the Epidermal Growth Factor Receptor (EGFR), has been intensively used to treat cancer patients with metastatic colorectal cancer and head and neck cancer. Intact immunoglobulin G (IgG) antibody like cetuximab, however, has some limitations such as high production cost and low penetration rate from vasculature into solid tumor mass due to its large size. In attempt to overcome these limitations, we engineered cetuximab to create single chain variable fragments (scFv-CH3; Minibody) that were expressed in bacterial system. Among three engineered minibodies, we found that MI061 minibody, which is composed of the variable heavy (VH) and light (VL) region joined by an 18-residue peptide linker, displays higher solubility and better extraction properties from bacterial lysate. In addition, we validated that purified MI061 significantly interferes ligand binding to EGFR and blocks EGFR's phosphorylation. By using a protein microarray composed of 16,368 unique human proteins covering around 2,400 plasma membrane associated proteins such as receptors and channels, we also demonstrated that MI061 only recognizes the EGFR but not other proteins as compared with cetuximab. These results indicated that engineered MI061 retains both binding specificity and affinity of cetuximab for EGFR. Although it had relatively short half-life in serum, it was shown to be highly significant anti-tumor effect by inhibiting ERK pathway in A431 xenograft model. Taken together, our present study provides compelling evidence that engineered minibody is more effective and promising agent for in vivo targeting of solid tumors.
Collapse
Affiliation(s)
- Young Pil Kim
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Dongsun Park
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Jae Jin Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Won-Jae Choi
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Sun Hee Lee
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Seo Yun Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Soyeon Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Jee Min Chung
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Jinseon Jeon
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Byoung Dae Lee
- Department of Neuroscience, Kyung Hee University School of Medicine, Seoul, South Korea
| | - Joo-Ho Shin
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon, South Korea
| | - Yun-il Lee
- Well Aging Research Center, Samsung Advanced Institute of Technology (SAIT), Suwon, South Korea
| | - Hyeseong Cho
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
- Department of Biochemistry, Ajou University School of Medicine, Suwon, South Korea
- * E-mail: (HC); (JL); (HCK)
| | - Jeong-Min Lee
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
- * E-mail: (HC); (JL); (HCK)
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
- * E-mail: (HC); (JL); (HCK)
| |
Collapse
|
43
|
Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
Collapse
Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | | |
Collapse
|
44
|
Couvertier SM, Zhou Y, Weerapana E. Chemical-proteomic strategies to investigate cysteine posttranslational modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2315-30. [PMID: 25291386 DOI: 10.1016/j.bbapap.2014.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023]
Abstract
The unique combination of nucleophilicity and redox-sensitivity that is characteristic of cysteine residues results in a variety of posttranslational modifications (PTMs), including oxidation, nitrosation, glutathionylation, prenylation, palmitoylation and Michael adducts with lipid-derived electrophiles (LDEs). These PTMs regulate the activity of diverse protein families by modulating the reactivity of cysteine nucleophiles within active sites of enzymes, and governing protein localization between soluble and membrane-bound forms. Many of these modifications are highly labile, sensitive to small changes in the environment, and dynamic, rendering it difficult to detect these modified species within a complex proteome. Several chemical-proteomic platforms have evolved to study these modifications and enable a better understanding of the diversity of proteins that are regulated by cysteine PTMs. These platforms include: (1) chemical probes to selectively tag PTM-modified cysteines; (2) differential labeling platforms that selectively reveal and tag PTM-modified cysteines; (3) lipid, isoprene and LDE derivatives containing bioorthogonal handles; and (4) cysteine-reactivity profiling to identify PTM-induced decreases in cysteine nucleophilicity. Here, we will provide an overview of these existing chemical-proteomic strategies and their effectiveness at identifying PTM-modified cysteine residues within native biological systems.
Collapse
Affiliation(s)
| | - Yani Zhou
- Boston College, Chestnut Hill, MA 02467, USA
| | | |
Collapse
|
45
|
Jayakumari NR, Reghuvaran AC, Rajendran RS, Pillai VV, Karunakaran J, Sreelatha HV, Gopala S. Are nitric oxide-mediated protein modifications of functional significance in diabetic heart? ye'S, -NO', wh'Y-NO't? Nitric Oxide 2014; 43:35-44. [PMID: 25153035 DOI: 10.1016/j.niox.2014.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/08/2014] [Accepted: 08/14/2014] [Indexed: 12/19/2022]
Abstract
Protein modifications effected by nitric oxide (NO) primarily in conjunction with reactive oxygen species (ROS) include tyrosine nitration, cysteine S-nitrosylation, and glutathionylation. The physiological and pathological relevance of these three modifications is determined by the amino acids on which these modifications occur -cysteine and tyrosine, for instance, ranging from altering structural integrity/catalytic activity of proteins or by altering propensity towards protein degradation. Even though tyrosine nitration is a well-established nitroxidative stress marker, instilled as a footprint of oxygen- and nitrogen-derived oxidants, newer data suggest its wider role in embryonic heart development and substantiate the need to focus on elucidating the underlying mechanisms of reversibility and specificity of tyrosine nitration. S-nitrosylation is a covalent modification in specific cysteine residues of proteins and is suggested as one of the ways in which NO contributes to its ubiquitous signalling. Several sensitive and specific techniques including biotin switch assay and mass spectrometry based analysis make it possible to identify a large number of these modified proteins, and provide a great deal of potential S-nitrosylation sites. The number of studies that have documented nitrated proteins in diabetic heart is relatively much less compared to what has been published in the normal physiology and other cardiac pathologies. Nevertheless, elucidation of nitrated proteome of diabetic heart has revealed the presence of many mitochondrial and cytosolic proteins of functional importance. But, the existence of different models of diabetes and analyses at diverse stages of this disease have impeded scientists from gaining insights that would be essential to understand the cardiac complications during diabetes. This review summarizes NO mediated protein modifications documented in normal and abnormal heart physiology including diabetes.
Collapse
Affiliation(s)
- Nandini Ravikumar Jayakumari
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Anand Chellappan Reghuvaran
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Raji Sasikala Rajendran
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Vivek Velayudhan Pillai
- Department of Cardiovascular and Thoracic Surgery, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Jayakumar Karunakaran
- Department of Cardiovascular and Thoracic Surgery, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Harikrishnan Vijayakumar Sreelatha
- Division of Laboratory Animal Sciences, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695011, India.
| |
Collapse
|
46
|
Importance of NO and its related compounds in enteric nervous system regulation of gut homeostasis and disease susceptibility. Curr Opin Pharmacol 2014; 19:54-60. [PMID: 25108170 DOI: 10.1016/j.coph.2014.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022]
Abstract
Nitric oxide (NO) produced by the enteric nervous system represents an important regulatory mechanism in gut homeostasis. Aberrant NO signaling contributes significantly toward enteric disease by altering gut motility, vascular tone, blood supply, mucosal barrier function, secretions and immunity. Consequently, there is much interest in therapeutically targeting NO production and its bioactive intermediates. This article highlights recent advances in NO signaling and therapeutics as it relates to the gastrointestinal tract and its associated NO producing microbiota. Because of its limited scope, a particular emphasis is placed on S-nitrosylation as the emerging physiologic mechanism for NO signal transduction, and how such signals are modulated by other gaseous transmitters - notably hydrogen disulfide and carbon monoxide - that are produced by the enteric nervous system and share common molecular targets. Recent findings also indicate that druggable regulators of S-nitrosylation, for example S-nitrosoglutathione (GSNO) reductase, provide for a superior pharmacology and finer therapeutic control over classical NO donors, and may be better suited for oral delivery to the gastrointestinal tract.
Collapse
|
47
|
Ben-Lulu S, Ziv T, Admon A, Weisman-Shomer P, Benhar M. A substrate trapping approach identifies proteins regulated by reversible S-nitrosylation. Mol Cell Proteomics 2014; 13:2573-83. [PMID: 24973421 DOI: 10.1074/mcp.m114.038166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protein S-nitrosylation, the nitric oxide-mediated posttranslational modification of cysteine residues, has emerged as an important regulatory mechanism in diverse cellular processes. Yet, knowledge about the S-nitrosoproteome in different cell types and cellular contexts is still limited and many questions remain regarding the precise roles of protein S-nitrosylation and denitrosylation. Here we present a novel strategy to identify reversibly nitrosylated proteins. Our approach is based on nitrosothiol capture and enrichment using a thioredoxin trap mutant, followed by protein identification by mass spectrometry. Employing this approach, we identified more than 400 putative nitroso-proteins in S-nitrosocysteine-treated human monocytes and about 200 nitrosylation substrates in endotoxin and cytokine-stimulated mouse macrophages. The large majority of these represent novel nitrosylation targets and they include many proteins with key functions in cellular homeostasis and signaling. Biochemical and functional experiments in vitro and in cells validated the proteomic results and further suggested a role for thioredoxin in the denitrosylation and activation of inducible nitric oxide synthase and the protein kinase MEK1. Our findings contribute to a better understanding of the macrophage S-nitrosoproteome and the role of thioredoxin-mediated denitrosylation in nitric oxide signaling. The approach described here may prove generally useful for the identification and exploration of nitroso-proteomes under various physiological and pathophysiological conditions.
Collapse
Affiliation(s)
- Shani Ben-Lulu
- From the ‡From the Department of Biochemistry, Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tamar Ziv
- §Smoler Proteomics Center and Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- §Smoler Proteomics Center and Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Pnina Weisman-Shomer
- From the ‡From the Department of Biochemistry, Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Moran Benhar
- From the ‡From the Department of Biochemistry, Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel;
| |
Collapse
|
48
|
Qu Z, Meng F, Bomgarden RD, Viner RI, Li J, Rogers JC, Cheng J, Greenlief CM, Cui J, Lubahn DB, Sun GY, Gu Z. Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagents. J Proteome Res 2014; 13:3200-11. [PMID: 24926564 PMCID: PMC4084841 DOI: 10.1021/pr401179v] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
S-Nitrosylation is a redox-based protein post-translational
modification in response to nitric oxide signaling and is involved
in a wide range of biological processes. Detection and quantification
of protein S-nitrosylation have been challenging
tasks due to instability and low abundance of the modification. Many
studies have used mass spectrometry (MS)-based methods with different
thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed
a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive
iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the
iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides
by anti-TMT resin, and importantly, unambiguous modification site-mapping
and multiplex quantification by liquid chromatography–tandem
MS. Additionally, we significantly improved anti-TMT peptide enrichment
efficiency by competitive elution. Using ISA, we identified a set
of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation
in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic
pathways. ISA proved to be an effective proteomic approach for quantitative
analysis of S-nitrosylation in complex samples and
will facilitate the elucidation of molecular mechanisms of nitrosative
stress in disease.
Collapse
Affiliation(s)
- Zhe Qu
- Department of Pathology and Anatomical Sciences, ‡Department of Biochemistry, and §Center for Translational Neuroscience, University of Missouri School of Medicine , Columbia, Missouri, United States
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Panis C. Unraveling Oxidation-Induced Modifications in Proteins by Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:19-38. [DOI: 10.1016/b978-0-12-800168-4.00002-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|