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Besson B, Eun H, Kim S, Windisch MP, Bourhy H, Grailhe R. Optimization of BRET saturation assays for robust and sensitive cytosolic protein-protein interaction studies. Sci Rep 2022; 12:9987. [PMID: 35705637 PMCID: PMC9200754 DOI: 10.1038/s41598-022-12851-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) saturation is a method of studying protein–protein interaction (PPI) upon quantification of the dependence of the BRET signal on the acceptor/donor (A:D) expression ratio. In this study, using the very bright Nluc/YFP BRET pair acquired respectively with microplate reader and automated confocal microscopy, we significantly improved BRET saturation assay by extending A:D expression detection range and normalizing A:D expression with a new BRET-free probe. We next found that upon using variable instead of fixed amount of donor molecules co-expressed with increasing acceptor concentrations, BRET saturation assay robustness can be further improved when studying cytosolic protein, although the relative amounts of dimers (BRETmax) and the relative dimer affinity (BRET50) remain similar. Altogether, we show that our method can be applied to many PPI networks, involving the NF-κB pathway, high-affinity nanobody, rabies virus-host interactions, mTOR complex and JAK/STAT signaling. Altogether our approach paves the way for robust PPI validation and characterization in living cells.
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Affiliation(s)
- Benoit Besson
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea.,Institut Pasteur, Unité Dynamique des Lyssavirus et Adaptation à l'Hôte, 28 rue du docteur Roux, 75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Docteur Roux, 75015, Paris, France
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Seonhee Kim
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Marc P Windisch
- Applied Molecular Virology, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Herve Bourhy
- Institut Pasteur, Unité Dynamique des Lyssavirus et Adaptation à l'Hôte, 28 rue du docteur Roux, 75015, Paris, France
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea.
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2
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Lim J, Petersen M, Bunz M, Simon C, Schindler M. Flow cytometry based-FRET: basics, novel developments and future perspectives. Cell Mol Life Sci 2022; 79:217. [PMID: 35352201 PMCID: PMC8964568 DOI: 10.1007/s00018-022-04232-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022]
Abstract
Förster resonance energy transfer (FRET) is a widespread technology used to analyze and quantify protein interactions in multiple settings. While FRET is traditionally measured by microscopy, flow cytometry based-FRET is becoming popular within the last decade and more commonly used. Flow cytometry based-FRET offers the possibility to assess FRET in a short time-frame in a high number of cells thereby allowing stringent and statistically robust quantification of FRET in multiple samples. Furthermore, established, simple and easy to implement gating strategies facilitate the adaptation of flow cytometry based-FRET measurements to most common flow cytometers. We here summarize the basics of flow cytometry based-FRET, highlight recent novel developments in this field and emphasize on exciting future perspectives.
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Affiliation(s)
- JiaWen Lim
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Maximilian Bunz
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Claudia Simon
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany.
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Park IS, Seo HR, Kim K, Lee H, Shum D, Choi I, Kim J. Identification of inhibitors of Bcl-2 family protein-protein interaction by combining the BRET screening platform with virtual screening. Biochem Biophys Res Commun 2020; 527:709-715. [PMID: 32423828 DOI: 10.1016/j.bbrc.2020.05.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 11/19/2022]
Abstract
Bcl-2 family proteins play key roles in tumor initiation, progression, and resistance to therapy. Therefore, the protein-protein interactions (PPIs) between the pro-survival proteins, B-cell lymphoma (Bcl)-2 and Bcl-xL, and the pro-apoptotic proteins, Bax and Bak, could be attractive therapeutic targets for anti-cancer drug discovery. Here, we found new small molecules, BIP-A1001 and BIP-A2001 that modulated Bak/Bax and Bcl-xL interactions by combining the Nanoluc/YFP-based bioluminescence resonance energy transfer (BRET) assay with structure based virtual screening. In addition, we chose compounds with similar structures to BIP-A1001 and BIP-A2001 and tested their inhibitory effects using the BRET assay as a dose-response function. The results indicated that identifying compounds that inhibit interactions between Bak/Bax and Bcl-xL could be a promising approach to enhance cancer therapy.
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Affiliation(s)
- I-Seul Park
- Screening Discovery Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea
| | - Haeng Ran Seo
- Cancer Biology Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea
| | - Kideok Kim
- Screening Discovery Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea
| | - Inhee Choi
- Medicinal Chemistry, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea.
| | - Jiho Kim
- Screening Discovery Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, South Korea.
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Moreno E, Canet J, Gracia E, Lluís C, Mallol J, Canela EI, Cortés A, Casadó V. Molecular Evidence of Adenosine Deaminase Linking Adenosine A 2A Receptor and CD26 Proteins. Front Pharmacol 2018; 9:106. [PMID: 29497379 PMCID: PMC5818423 DOI: 10.3389/fphar.2018.00106] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/30/2018] [Indexed: 01/05/2023] Open
Abstract
Adenosine is an endogenous purine nucleoside that acts in all living systems as a homeostatic network regulator through many pathways, which are adenosine receptor (AR)-dependent and -independent. From a metabolic point of view, adenosine deaminase (ADA) is an essential protein in the regulation of the total intracellular and extracellular adenosine in a tissue. In addition to its cytosolic localization, ADA is also expressed as an ecto-enzyme on the surface of different cells. Dipeptidyl peptidase IV (CD26) and some ARs act as binding proteins for extracellular ADA in humans. Since CD26 and ARs interact with ADA at opposite sites, we have investigated if ADA can function as a cell-to-cell communication molecule by bridging the anchoring molecules CD26 and A2AR present on the surfaces of the interacting cells. By combining site-directed mutagenesis of ADA amino acids involved in binding to A2AR and a modification of the bioluminescence resonance energy transfer (BRET) technique that allows detection of interactions between two proteins expressed in different cell populations with low steric hindrance (NanoBRET), we show direct evidence of the specific formation of trimeric complexes CD26-ADA-A2AR involving two cells. By dynamic mass redistribution assays and ligand binding experiments, we also demonstrate that A2AR-NanoLuc fusion proteins are functional. The existence of this ternary complex is in good agreement with the hypothesis that ADA could bridge T-cells (expressing CD26) and dendritic cells (expressing A2AR). This is a new metabolic function for ecto-ADA that, being a single chain protein, it has been considered as an example of moonlighting protein, because it performs more than one functional role (as a catalyst, a costimulator, an allosteric modulator and a cell-to-cell connector) without partitioning these functions in different subunits.
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Affiliation(s)
- Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Júlia Canet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Eduard Gracia
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Carme Lluís
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Josefa Mallol
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Enric I. Canela
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Antoni Cortés
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain
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Kim J, Grailhe R. Nanoluciferase signal brightness using furimazine substrates opens bioluminescence resonance energy transfer to widefield microscopy. Cytometry A 2016; 89:742-6. [PMID: 27144967 DOI: 10.1002/cyto.a.22870] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/06/2016] [Accepted: 04/12/2016] [Indexed: 01/21/2023]
Abstract
Fluorescence and bioluminescence resonance energy transfer (FRET, BRET) techniques are powerful tools for studying protein-protein interactions in cellular assays. In contrast to fluorescent proteins, chemiluminescent proteins do not require excitation light, known to trigger autofluorescence, phototoxicity, and photobleaching. Regrettably, low signal intensity of luciferase systems restricts their usage as they require specialized microscopes equipped with ultra low-light imaging cameras. In this study, we report that bioluminescence quantification in living cells using a standard widefield automated microscope dedicated to screening and high content analysis is possible with the newer luciferase systems, Nanoluciferase (Nluc). With such equipment, we showed that robust intramolecular BRET can be measured using a combination of Nluc and yellow fluorescent protein (YFP). Using the human Superoxide Dismutase 1 (SOD1) dimer model, we next validated that intermolecular BRET could be quantified at a single cell level. The enhanced signal brightness of Nluc enabling BRET imaging to widefield microscopy shows strong potential to open up single cell protein-protein interactions studies to a wider audience. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Jiho Kim
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
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Hagen N, Bayer K, Rösch K, Schindler M. The intraviral protein interaction network of hepatitis C virus. Mol Cell Proteomics 2014; 13:1676-89. [PMID: 24797426 DOI: 10.1074/mcp.m113.036301] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) is a global health problem and one of the main reasons for chronic liver diseases such as cirrhosis and hepatocellular carcinoma. The HCV genome is translated into a polyprotein which is proteolytically processed into 10 viral proteins. The interactome of the HCV proteins with the host cell has been worked out; however, it remains unclear how viral proteins interact with each other. We aimed to generate the interaction network of these 10 HCV proteins using a flow-cytometry-based FRET assay established in our laboratory (Banning, C., Votteler, J., Hoffmann, D., Koppensteiner, H., Warmer, M., Reimer, R., Kirchhoff, F., Schubert, U., Hauber, J., and Schindler, M. (2010) A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells. PLoS One 5, e9344). HCV proteins were constructed as fusions with the chromophores CFP and YFP. All HCV fusions were expressed and localized to specific subcellular compartments, indicating that they were functional. FACS-FRET measurements identified a total of 20 interactions; 13 of these were previously described and have now been confirmed in living cells via our method. Among the seven novel protein binding pairs, HCV p7 plays a pivotal role. It binds to the HCV capsid protein Core and the two glycoproteins E1 and E2. These interplays were further demonstrated in the relevant context of Huh7.5 liver cells expressing infectious HCV. Our work demonstrates the feasibility of rapidly generating small interaction networks via FACS-FRET and defines the network of intra-HCV protein interactions. Furthermore, our data support an important role of p7 in HCV assembly.
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Affiliation(s)
- Nicole Hagen
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Karen Bayer
- ¶Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Kathrin Rösch
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Michael Schindler
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; ¶Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany; ‖Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, 72076 Tübingen, Germany
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7
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Kim J, Lee H, Lee JH, Kwon DY, Genovesio A, Fenistein D, Ogier A, Brondani V, Grailhe R. Dimerization, oligomerization, and aggregation of human amyotrophic lateral sclerosis copper/zinc superoxide dismutase 1 protein mutant forms in live cells. J Biol Chem 2014; 289:15094-103. [PMID: 24692554 DOI: 10.1074/jbc.m113.542613] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
More than 100 copper/zinc superoxide dismutase 1 (SOD1) genetic mutations have been characterized. These mutations lead to the death of motor neurons in ALS. In its native form, the SOD1 protein is expressed as a homodimer in the cytosol. In vitro studies have shown that SOD1 mutations impair the dimerization kinetics of the protein, and in vivo studies have shown that SOD1 forms aggregates in patients with familial forms of ALS. In this study, we analyzed WT SOD1 and 9 mutant (mt) forms of the protein by non-invasive fluorescence techniques. Using microscopic techniques such as fluorescence resonance energy transfer, fluorescence complementation, image-based quantification, and fluorescence correlation spectroscopy, we studied SOD1 dimerization, oligomerization, and aggregation. Our results indicate that SOD1 mutations lead to an impairment in SOD1 dimerization and, subsequently, affect protein aggregation. We also show that SOD1 WT and mt proteins can dimerize. However, aggregates are predominantly composed of SOD1 mt proteins.
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Affiliation(s)
- Jiho Kim
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Honggun Lee
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Joo Hyun Lee
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Do-yoon Kwon
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Auguste Genovesio
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Denis Fenistein
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Arnaud Ogier
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Vincent Brondani
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
| | - Regis Grailhe
- From Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-Si, Gyeonggi-Do 463-400, Republic of Korea
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Andreazza AC. Combining redox-proteomics and epigenomics to explain the involvement of oxidative stress in psychiatric disorders. MOLECULAR BIOSYSTEMS 2013; 8:2503-12. [PMID: 22710408 DOI: 10.1039/c2mb25118c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Psychiatric disorders affect approximately 10% of adults in North-America. The complex nature of these illnesses makes the search for their pathophysiology a challenge. However, studies have consistently shown that mitochondrial dysfunction and oxidative stress are common features across major psychiatric disorders, including bipolar disorder and schizophrenia. Nevertheless, little is known about specific targets of oxidation in the brain. The search for redox sensors (protein targets for oxidation) will offer information about which pathways are regulated by oxidation in psychiatric disorders. Additionally, DNA is also a target for oxidative damage and recently, studies have suggested that oxidation of cytosine and guanosine can serve as an epigenetic modulator by decreasing or preventing further DNA methylation. Therefore, this review aims to discuss how we can use redox-proteomics and epigenomics to help explain the role of oxidative damage in major psychiatric disorders, which may ultimately lead to the identification of targets for development of new medications.
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Affiliation(s)
- Ana Cristina Andreazza
- Department of Psychiatry, University of Toronto, Medical Science Building, Room 4204, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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