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Valenta H, Bierbuesse F, Vitale R, Ruckebusch C, Vandenberg W, Dedecker P. Per-pixel unmixing of spectrally overlapping fluorophores using intra-exposure excitation modulation. Talanta 2024; 269:125397. [PMID: 38048682 DOI: 10.1016/j.talanta.2023.125397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/06/2023]
Abstract
Multilabel fluorescence imaging is essential for the visualization of complex systems, though a major challenge is the limited width of the useable spectral window. Here, we present a new method, exNEEMO, that enables per-pixel quantification of spectrally-overlapping fluorophores based on their light-induced dynamics, in a way that is compatible with a very broad range of timescales over which these dynamics may occur. Our approach makes use of intra-exposure modulation of the excitation light to distinguish the different emitters given their reference responses to this modulation. We use the approach to simultaneously image four green photochromic fluorescent proteins at the full spatial resolution of the imaging.
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2
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Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B. Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306272. [PMID: 38146132 PMCID: PMC10933604 DOI: 10.1002/advs.202306272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Photoconvertible fluorescent proteins (PCFP) are important cellular markers in advanced imaging modalities such as photoactivatable localization microscopy (PALM). However, their complex photophysical and photochemical behavior hampers applications such as quantitative and single-particle-tracking PALM. This work employs multidimensional NMR combined with ensemble fluorescence measurements to show that the popular mEos4b in its Green state populates two conformations (A and B), differing in side-chain protonation of the conserved residues E212 and H62, altering the hydrogen-bond network in the chromophore pocket. The interconversion (protonation/deprotonation) between these two states, which occurs on the minutes time scale in the dark, becomes strongly accelerated in the presence of UV light, leading to a population shift. This work shows that the reversible photoswitching and Green-to-Red photoconversion properties differ between the A and B states. The chromophore in the A-state photoswitches more efficiently and is proposed to be more prone to photoconversion, while the B-state shows a higher level of photobleaching. Altogether, this data highlights the central role of conformational heterogeneity in fluorescent protein photochemistry.
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Affiliation(s)
- Arijit Maity
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Jip Wulffelé
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Isabel Ayala
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Adrien Favier
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Virgile Adam
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Dominique Bourgeois
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Bernhard Brutscher
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
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3
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Qian Y, Celiker OT, Wang Z, Guner-Ataman B, Boyden ES. Temporally multiplexed imaging of dynamic signaling networks in living cells. Cell 2023; 186:5656-5672.e21. [PMID: 38029746 PMCID: PMC10843875 DOI: 10.1016/j.cell.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/30/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Molecular signals interact in networks to mediate biological processes. To analyze these networks, it would be useful to image many signals at once, in the same living cell, using standard microscopes and genetically encoded fluorescent reporters. Here, we report temporally multiplexed imaging (TMI), which uses genetically encoded fluorescent proteins with different clocklike properties-such as reversibly photoswitchable fluorescent proteins with different switching kinetics-to represent different cellular signals. We linearly decompose a brief (few-second-long) trace of the fluorescence fluctuations, at each point in a cell, into a weighted sum of the traces exhibited by each fluorophore expressed in the cell. The weights then represent the signal amplitudes. We use TMI to analyze relationships between different kinase activities in individual cells, as well as between different cell-cycle signals, pointing toward broad utility throughout biology in the analysis of signal transduction cascades in living systems.
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Affiliation(s)
- Yong Qian
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA
| | - Orhan T Celiker
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 01239, USA
| | - Zeguan Wang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Media Arts and Sciences, MIT, Cambridge, MA 01239, USA
| | - Burcu Guner-Ataman
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Media Arts and Sciences, MIT, Cambridge, MA 01239, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 01239, USA; Department of Biological Engineering, MIT, Cambridge, MA 01239, USA; Koch Institute, MIT, Cambridge, MA 01239, USA; Howard Hughes Medical Institute, Cambridge, MA 01239, USA; Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics at MIT, Cambridge, MA 01239, USA.
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4
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Lahlou A, Tehrani HS, Coghill I, Shpinov Y, Mandal M, Plamont MA, Aujard I, Niu Y, Nedbal L, Lazár D, Mahou P, Supatto W, Beaurepaire E, Eisenmann I, Desprat N, Croquette V, Jeanneret R, Le Saux T, Jullien L. Fluorescence to measure light intensity. Nat Methods 2023; 20:1930-1938. [PMID: 37996751 PMCID: PMC10703675 DOI: 10.1038/s41592-023-02063-y] [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: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
Despite the need for quantitative measurements of light intensity across many scientific disciplines, existing technologies for measuring light dose at the sample of a fluorescence microscope cannot simultaneously retrieve light intensity along with spatial distribution over a wide range of wavelengths and intensities. To address this limitation, we developed two rapid and straightforward protocols that use organic dyes and fluorescent proteins as actinometers. The first protocol relies on molecular systems whose fluorescence intensity decays and/or rises in a monoexponential fashion when constant light is applied. The second protocol relies on a broad-absorbing photochemically inert fluorophore to back-calculate the light intensity from one wavelength to another. As a demonstration of their use, the protocols are applied to quantitatively characterize the spatial distribution of light of various fluorescence imaging systems, and to calibrate illumination of commercially available instruments and light sources.
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Affiliation(s)
- Aliénor Lahlou
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
- Sony Computer Science Laboratories, Paris, France.
| | - Hessam Sepasi Tehrani
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Ian Coghill
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuriy Shpinov
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Mrinal Mandal
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Isabelle Aujard
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuxi Niu
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Ladislav Nedbal
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Dusan Lazár
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Isabelle Eisenmann
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Nicolas Desprat
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Vincent Croquette
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Raphaël Jeanneret
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Thomas Le Saux
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
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Li J, Ma X, Wang Y, Cheng Y, Qin Y, Zhai J, Xie X. Proton-Coupled Photochromic Hemithioindigo: Toward Photoactivated Chemical Sensing and Imaging. Anal Chem 2023; 95:11664-11671. [PMID: 37495553 PMCID: PMC10414032 DOI: 10.1021/acs.analchem.3c01504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
We report photoswitchable fluorescent hemithioindigos (HTIs) where the metastable E isomers were stabilized by the proton-bridged intramolecular hydrogen bond. Titration experiments and computational analysis indicated that the E isomers were much more basic than the Z isomers, which enabled photoactivated colorimetric and fluorescent pH response in solvents and polypropylene films. The HTIs exhibited reversibly switchable fluorescence with the Z isomers being the most fluorescent. Moreover, the HTIs were lysosomotropic and the kinetic fluorescence evolution during photoswitching was able to differentiate subcellular compartments with different pH. The combination of photoenhanced basicity, switchable fluorescence, and proton-coupled photochromism lay the groundwork for a broad range of chemical and biological applications.
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Affiliation(s)
- Jing Li
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Xueqing Ma
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Yifu Wang
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Yu Cheng
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Yuemin Qin
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Jingying Zhai
- Academy
for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaojiang Xie
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
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6
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Pellissier-Tanon A, Chouket R, Zhang R, Lahlou A, Espagne A, Lemarchand A, Croquette V, Jullien L, Le Saux T. Resonances at Fundamental and Harmonic Frequencies for Selective Imaging of Sine-Wave Illuminated Reversibly Photoactivatable Labels. Chemphyschem 2022; 23:e202200295. [PMID: 35976176 PMCID: PMC10087976 DOI: 10.1002/cphc.202200295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/15/2022] [Indexed: 01/04/2023]
Abstract
We introduce HIGHLIGHT as a simple and general strategy to selectively image a reversibly photoactivatable fluorescent label associated with a given kinetics. The label is submitted to sine-wave illumination of large amplitude, which generates oscillations of its concentration and fluorescence at higher harmonic frequencies. For singularizing a label, HIGHLIGHT uses specific frequencies and mean light intensities associated with resonances of the amplitudes of concentration and fluorescence oscillations at harmonic frequencies. Several non-redundant resonant observables are simultaneously retrieved from a single experiment with phase-sensitive detection. HIGHLIGHT is used for selective imaging of four spectrally similar fluorescent proteins that had not been discriminated so far. Moreover, labels out of targeted locations can be discarded in an inhomogeneous spatial profile of illumination. HIGHLIGHT opens roads for simplified optical setups at reduced cost and easier maintenance.
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Affiliation(s)
- Agnès Pellissier-Tanon
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Raja Chouket
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Ruikang Zhang
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Aliénor Lahlou
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France.,Sony Computer Science Laboratories, Paris, France
| | - Agathe Espagne
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Annie Lemarchand
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), 4, Place Jussieu, Case Courrier 121, 75252, Paris Cedex 05, France
| | - Vincent Croquette
- Laboratoire de Physique Statistique, Département de Physique and Département de Biologie, École normale supérieure, PSL Research University, F-, 75005, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Thomas Le Saux
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
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7
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Nath SS. Thermodynamic Consistency and Kinetic Mechanism of a Complex Reaction Pathway by Analysis of Its Constituent Cyclic Networks. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c02906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Sarang S. Nath
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800Lyngby, Denmark
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8
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Nath SS, Nielsen LK, Villadsen J. Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuits. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Nath SS. Evaluation of thermodynamic consistency of kinetic parameters in cyclic enzyme-catalyzed reaction networks. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Pellissier-Tanon A, Adelizzi B, Jullien L, Le Saux T, Lemarchand A. Correlation of fluorescence evolution for quantitative analysis of labels and sensors. Anal Chim Acta 2022; 1225:340180. [DOI: 10.1016/j.aca.2022.340180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/09/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022]
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