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Manko H, Burton MG, Mély Y, Godet J. Spectral Phasor Applied to Spectrally-Resolved Single Molecule Localization Microscopy. Chemphyschem 2024; 25:e202400101. [PMID: 38563617 DOI: 10.1002/cphc.202400101] [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: 01/31/2024] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Spectrally-resolved single-molecule localization microscopy (srSMLM) has emerged as a powerful tool for exploring the spectral properties of single emitters in localization microscopy. By simultaneously capturing the spatial positions and spectroscopic signatures of individual fluorescent molecules, srSMLM opens up the possibility of investigating an additional dimension in super-resolution imaging. However, appropriate and dedicated tools are required to fully capitalize on the spectral dimension. Here, we propose the application of the spectral phasor analysis as an effective method for summarizing and analyzing the spectral information obtained from srSMLM experiments. The spectral phasor condenses the complete spectrum of a single emitter into a two-dimensional space, preserving key spectral characteristics for single-molecule spectral exploration. We demonstrate the effectiveness of spectral phasor in efficiently classifying single Nile Red fluorescence emissions from largely overlapping cyanine fluorescence signals in dual-color PAINT experiments. Additionally, we employed spectral phasor with srSMLM to reveal subtle alterations occurring in the membrane of Gram-positive Enterococcus hirae in response to gramicidin exposure, a membrane-perturbing antibiotic treatment. Spectral phasor provides a robust, model-free analytic tool for the detailed analysis of the spectral component of srSMLM, enhancing the capabilities of multi-color spectrally-resolved single-molecule imaging.
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Affiliation(s)
- Hanna Manko
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
| | - Matthew G Burton
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Yves Mély
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
| | - Julien Godet
- Laboratoire iCube, UMR CNRS 7357, Equipe IMAGeS, Université de Strasbourg, Strasbourg, France
- Groupe Méthodes Recherche Clinique, Hôpitaux Universitaires de trasbourg, France
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2
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Manko H, Steffan T, Gasser V, Mély Y, Schalk I, Godet J. PvdL Orchestrates the Assembly of the Nonribosomal Peptide Synthetases Involved in Pyoverdine Biosynthesis in Pseudomonas aeruginosa. Int J Mol Sci 2024; 25:6013. [PMID: 38892200 PMCID: PMC11172790 DOI: 10.3390/ijms25116013] [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: 04/10/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
The pyoverdine siderophore is produced by Pseudomonas aeruginosa to access iron. Its synthesis involves the complex coordination of four nonribosomal peptide synthetases (NRPSs), which are responsible for assembling the pyoverdine peptide backbone. The precise cellular organization of these NRPSs and their mechanisms of interaction remain unclear. Here, we used a combination of several single-molecule microscopy techniques to elucidate the spatial arrangement of NRPSs within pyoverdine-producing cells. Our findings reveal that PvdL differs from the three other NRPSs in terms of localization and mobility patterns. PvdL is predominantly located in the inner membrane, while the others also explore the cytoplasmic compartment. Leveraging the power of multicolor single-molecule localization, we further reveal co-localization between PvdL and the other NRPSs, suggesting a pivotal role for PvdL in orchestrating the intricate biosynthetic pathway. Our observations strongly indicates that PvdL serves as a central orchestrator in the assembly of NRPSs involved in pyoverdine biosynthesis, assuming a critical regulatory function.
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Affiliation(s)
- Hanna Manko
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, 67401 Illkirch, France
| | - Tania Steffan
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, 67401 Illkirch, France
| | | | - Yves Mély
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, 67401 Illkirch, France
- Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France
| | | | - Julien Godet
- Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France
- Groupe Méthodes Recherche Clinique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
- Laboratoire iCube, UMR CNRS 7357, Equipe IMAGeS, Université de Strasbourg, 67000 Strasbourg, France
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3
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Tomishige N, Bin Nasim M, Murate M, Pollet B, Didier P, Godet J, Richert L, Sako Y, Mély Y, Kobayashi T. HIV-1 Gag targeting to the plasma membrane reorganizes sphingomyelin-rich and cholesterol-rich lipid domains. Nat Commun 2023; 14:7353. [PMID: 37990014 PMCID: PMC10663554 DOI: 10.1038/s41467-023-42994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
Although the human immunodeficiency virus type 1 lipid envelope has been reported to be enriched with host cell sphingomyelin and cholesterol, the molecular mechanism of the enrichment is not well understood. Viral Gag protein plays a central role in virus budding. Here, we report the interaction between Gag and host cell lipids using different quantitative and super-resolution microscopy techniques in combination with specific probes that bind endogenous sphingomyelin and cholesterol. Our results indicate that Gag in the inner leaflet of the plasma membrane colocalizes with the outer leaflet sphingomyelin-rich domains and cholesterol-rich domains, enlarges sphingomyelin-rich domains, and strongly restricts the mobility of sphingomyelin-rich domains. Moreover, Gag multimerization induces sphingomyelin-rich and cholesterol-rich lipid domains to be in close proximity in a curvature-dependent manner. Our study suggests that Gag binds, coalesces, and reorganizes pre-existing lipid domains during assembly.
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Affiliation(s)
- Nario Tomishige
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan.
| | - Maaz Bin Nasim
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Motohide Murate
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan
| | - Brigitte Pollet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Julien Godet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
| | - Toshihide Kobayashi
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan.
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Maika JE, Krämer B, Strotmann VI, Wellmer F, Weidtkamp-Peters S, Stahl Y, Simon R. One pattern analysis (OPA) for the quantitative determination of protein interactions in plant cells. PLANT METHODS 2023; 19:73. [PMID: 37501124 PMCID: PMC10375638 DOI: 10.1186/s13007-023-01049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND A commonly used approach to study the interaction of two proteins of interest (POIs) in vivo is measuring Förster Resonance Energy Transfer (FRET). This requires the expression of the two POIs fused to two fluorescent proteins that function as a FRET pair. A precise way to record FRET is Fluorescence Lifetime IMaging (FLIM) which generates quantitative data that, in principle, can be used to resolve both complex structure and protein affinities. However, this potential resolution is often lost in many experimental approaches. Here we introduce a novel tool for FLIM data analysis of multiexponential decaying donor fluorophores, one pattern analysis (OPA), which allows to obtain information about protein affinity and complex arrangement by extracting the relative amplitude of the FRET component and the FRET transfer efficiency from other FRET parameters. RESULTS As a proof of concept for OPA, we used FLIM-FRET, or FLIM-FRET in combination with BiFC to reassess the dimerization and tetramerization properties of known interacting MADS-domain transcription factors in Nicotiana benthamiana leaf cells and Arabidopsis thaliana flowers. Using the OPA tool and by extracting protein BINDING efficiencies from FRET parameters to dissect MADS-domain protein interactions in vivo in transient N. benthamiana experiments, we could show that MADS-domain proteins display similar proximities within dimeric or tetrameric complexes but bind with variable affinities. By combining FLIM with BiFC, we were able to identify SEPALLATA3 as a mediator for tetramerization between the other MADS-domain factors. OPA also revealed that in vivo expression from native promoters at low levels in Arabidopsis flower meristems, makes in situ complex formation of MADS-domain proteins barely detectable. CONCLUSIONS We conclude that MADS-domain protein interactions are transient in situ and may involve additional, so far unknown interaction mediators. We conclude that OPA can be used to separate protein binding from information about proximity and orientation of the interacting proteins in their complexes. Visualization of individual protein interactions within the underlying interaction networks in the native environment is still restrained if expression levels are low and will require continuous improvements in fluorophore labelling, instrumentation set-ups and analysis tools.
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Affiliation(s)
- Jan Eric Maika
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Benedikt Krämer
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | - Vivien I Strotmann
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefanie Weidtkamp-Peters
- Centre for Advanced Imaging, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Rüdiger Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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6
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Walter RJ, Sonnentag SJ, Munoz-Sagredo L, Merkel M, Richert L, Bunert F, Heneka YM, Loustau T, Hodder M, Ridgway RA, Sansom OJ, Mely Y, Rothbauer U, Schmitt M, Orian-Rousseau V. Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop. Cell Death Dis 2022; 13:168. [PMID: 35190527 PMCID: PMC8861016 DOI: 10.1038/s41419-022-04607-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 12/24/2022]
Abstract
Enhancement of Wnt signaling is fundamental for stem cell function during intestinal regeneration. Molecular modules control Wnt activity by regulating signal transduction. CD44 is such a positive regulator and a Wnt target gene. While highly expressed in intestinal crypts and used as a stem cell marker, its role during intestinal homeostasis and regeneration remains unknown. Here we propose a CD44 positive-feedback loop that boosts Wnt signal transduction, thus impacting intestinal regeneration. Excision of Cd44 in Cd44fl/fl;VillinCreERT2 mice reduced Wnt target gene expression in intestinal crypts and affected stem cell functionality in organoids. Although the integrity of the intestinal epithelium was conserved in mice lacking CD44, they were hypersensitive to dextran sulfate sodium, and showed more severe inflammation and delayed regeneration. We localized the molecular function of CD44 at the Wnt signalosome, and identified novel DVL/CD44 and AXIN/CD44 complexes. CD44 thus promotes optimal Wnt signaling during intestinal regeneration.
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Affiliation(s)
- Romina J Walter
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Steffen J Sonnentag
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Leonel Munoz-Sagredo
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Faculty of Medicine, Universidad de Valparaiso, Angamos 655, 2540064, Vina del Mar, Chile
| | - Melanie Merkel
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ludovic Richert
- UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Felix Bunert
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yvonne M Heneka
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Thomas Loustau
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Michael Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Rachel A Ridgway
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Yves Mely
- UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Mark Schmitt
- Institute of Pharmacology, University of Marburg, Karl-von-Frisch-Strasse 2, 35043, Marburg, Germany
| | - Véronique Orian-Rousseau
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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7
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Carlon-Andres I, Malinauskas T, Padilla-Parra S. Structure dynamics of HIV-1 Env trimers on native virions engaged with living T cells. Commun Biol 2021; 4:1228. [PMID: 34707229 PMCID: PMC8551276 DOI: 10.1038/s42003-021-02658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra- and intermolecular mechanics when engaged with live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Förster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env on native virions. Our observations reveal Env dynamics at two levels: transitions between different intramolecular conformations and intermolecular interactions between Env within the viral membrane. Furthermore, we show that three broad neutralizing anti-Env antibodies directed to different epitopes restrict Env intramolecular dynamics and interactions between adjacent Env molecules when engaged with living T cells. Importantly, our results show that Env-Env interactions depend on efficient virus maturation, and that is disrupted upon binding of Env to CD4 or by neutralizing antibodies. Thus, this study illuminates how different intramolecular conformations and distribution of Env molecules mediate HIV-1 Env-T cell interactions in real time and therefore might control immune evasion.
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Affiliation(s)
- Irene Carlon-Andres
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergi Padilla-Parra
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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8
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Wolfbeis OS. Fluorescent chameleon labels for bioconjugation and imaging of proteins, nucleic acids, biogenic amines and surface amino groups. a review. Methods Appl Fluoresc 2021; 9. [PMID: 34340216 DOI: 10.1088/2050-6120/ac1a0a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Chameleon labels (ChLs) possess the unique property of changing (visible) color and fluorescence on binding to amino groups of biomolecules. MostChLs react with primary aliphatic amino groups such as those in lysine or with amino groups artificially introduced into polynucleic acids or saccharides, but someothers also react with secondary amino groups. Under controlled circumstances, the reactions are fairly specific. The review is subdivided into the following sections: (1) An introduction and classification of fluorescent labels; (2) pyrylium labels that undergo shortwave color changes upon labelling, typically from blue to red; (3) polymethine type of labels (that also undergo shortwave color changes, typically from green to blue; (4) various other (less common) chromogenic and fluorogenic systems; (5) hemicyanine labels that undergolongwavecolor changes, typically from yellow to purple; (6) the application of ChLs to labeling of proteins and oligonucleotides; (7) applications to fluorometric assays and sensing; (8) applications to fluorescence imaging of biomolecules; (9) applications in studies on affinity interactions (receptor-ligand binding); (10) applications in surface and interface chemistry; and (11) applications in chromatography, electrophoresis and isotachophoresis of biomolecules.
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Affiliation(s)
- Otto S Wolfbeis
- University of Regensburg, Institute of Analytical Chemistry, Chemo- and Biosensors, 94040 Regensburg, Germany
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9
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Eckenstaler R, Benndorf RA. A Combined Acceptor Photobleaching and Donor Fluorescence Lifetime Imaging Microscopy Approach to Analyze Multi-Protein Interactions in Living Cells. Front Mol Biosci 2021; 8:635548. [PMID: 34055873 PMCID: PMC8160235 DOI: 10.3389/fmolb.2021.635548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Protein-protein interaction studies often provide new insights, i.e., into the formation of protein complexes relevant for structural oligomerization, regulation of enzymatic activity or information transfer within signal transduction pathways. Mostly, biochemical approaches have been used to study such interactions, but their results are limited to observations from lysed cells. A powerful tool for the non-invasive investigation of protein-protein interactions in the context of living cells is the microscopic analysis of Förster Resonance Energy Transfer (FRET) among fluorescent proteins. Normally, FRET is used to monitor the interaction state of two proteins, but in addition, FRET studies have been used to investigate three or more interacting proteins at the same time. Here we describe a fluorescence microscopy-based method which applies a novel 2-step acceptor photobleaching protocol to discriminate between non-interacting, dimeric interacting and trimeric interacting states within a three-fluorophore setup. For this purpose, intensity- and fluorescence lifetime-related FRET effects were analyzed on representative fluorescent dimeric and trimeric FRET-constructs expressed in the cytosol of HEK293 cells. In particular, by combining FLIM- and intensity-based FRET data acquisition and interpretation, our method allows to distinguish trimeric from different types of dimeric (single-, double- or triple-dimeric) protein-protein interactions of three potential interaction partners in the physiological setting of living cells.
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Affiliation(s)
- Robert Eckenstaler
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Ralf A Benndorf
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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10
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Birch DJS, Levitus M, Mély Y. MAF and fluorescence play their part. Methods Appl Fluoresc 2020; 9. [PMID: 33238256 DOI: 10.1088/2050-6120/abce06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Affiliation(s)
- David J S Birch
- The Photophysics Research Group, University of Strathclyde, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow, G4 0NG, United Kingdom
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, PO Box 875601, Tempe AZ, 85287-5601, United States of America
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Cedex, 67401 Illkirch, France
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11
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Ameer-Beg S, Suhling K, Kuimova M. Special issue on fluorescence lifetime imaging (FLIM): from fundamentals to applications. Methods Appl Fluoresc 2020; 8:040401. [PMID: 33021203 DOI: 10.1088/2050-6120/abad19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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In cellulo FRET-FLIM and single molecule tracking reveal the supra-molecular organization of the pyoverdine bio-synthetic enzymes in Pseudomonas aeruginosa. Q Rev Biophys 2020; 53:e1. [PMID: 31915092 DOI: 10.1017/s0033583519000155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The bio-synthesis of pyoverdine (PVD) in Pseudomonas aeruginosa involves multiple enzymatic steps including the action of non-ribosomal peptide synthetases (NRPSs). One hallmark of NRPS is their ability to make usage of non-proteinogenic amino-acids synthesized by co-expressed accessory enzymes. It is generally proposed that different enzymes of a secondary metabolic pathway assemble into large supra-molecular complexes. However, evidence for the assembly of sequential enzymes in the cellular context is sparse. Here, we used in cellulo single-molecule tracking and Förster resonance energy transfer measured by fluorescence lifetime microscopy (FRET-FLIM) to explore the spatial partitioning of the ornithine hydroxylase PvdA and its interactions with NRPS. We found PvdA was mostly diffusing bound to large complexes in the cytoplasm with a small exchangeable trapped fraction. FRET-FLIM clearly showed that PvdA is physically interacting with PvdJ, PvdI, PvdL, and PvdD, the four NRPS involved in the PVD pathway in Pseudomonas aeruginosa PAO1. The binding modes of PvdA were strikingly different according to the NRPS it is interacting with, suggesting that PvdA binding sites have co-evolved with the enzymatic active sites of NRPS. Our data provide evidence for strongly organized multi-enzymatic complexes responsible for the bio-synthesis of PVD and illustrate how binding sites have evolved to finely control the co-localization of sequential enzymes and promote metabolic pathway efficiency.
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