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Pedre B. A guide to genetically-encoded redox biosensors: State of the art and opportunities. Arch Biochem Biophys 2024; 758:110067. [PMID: 38908743 DOI: 10.1016/j.abb.2024.110067] [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: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Genetically-encoded redox biosensors have become invaluable tools for monitoring cellular redox processes with high spatiotemporal resolution, coupling the presence of the redox-active analyte with a change in fluorescence signal that can be easily recorded. This review summarizes the available fluorescence recording methods and presents an in-depth classification of the redox biosensors, organized by the analytes they respond to. In addition to the fluorescent protein-based architectures, this review also describes the recent advances on fluorescent, chemigenetic-based redox biosensors and other emerging chemigenetic strategies. This review examines how these biosensors are designed, the biosensors sensing mechanism, and their practical advantages and disadvantages.
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Affiliation(s)
- Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.
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2
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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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3
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Koveal D. Functional principles of genetically encoded fluorescent biosensors for metabolism and their quantitative use. J Neurochem 2024; 168:496-505. [PMID: 37314388 DOI: 10.1111/jnc.15878] [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: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Genetically encoded fluorescent biosensors provide an attractive means of measuring chemical changes in single cells on fast timescales (milliseconds to seconds). While their most prominent application has been in tracking neural activity and neurotransmitter release, there has been growing interest in developing and deploying new versions of these tools to study brain metabolism. However, the careful use of these tools and the interpretation of the data they provide remain challenging. Many biosensors are subject to interferences that can alter sensor responses within a single cell or between cells, producing ambiguous results. This presents a challenge for quantitation and for our ability to accurately interpret sensor responses. This review describes current methods of sensor quantitation, with a focus on cellular interferences that commonly affect sensor performance, ways to avoid false inferences, and recent advances in sensor optimization to make them more robust.
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Affiliation(s)
- Dorothy Koveal
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia, USA
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4
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Trujillo J, Khan AS, Adhikari DP, Stoneman MR, Chacko JV, Eliceiri KW, Raicu V. Implementation of FRET Spectrometry Using Temporally Resolved Fluorescence: A Feasibility Study. Int J Mol Sci 2024; 25:4706. [PMID: 38731924 PMCID: PMC11083457 DOI: 10.3390/ijms25094706] [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: 03/30/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Förster resonance energy transfer (FRET) spectrometry is a method for determining the quaternary structure of protein oligomers from distributions of FRET efficiencies that are drawn from pixels of fluorescence images of cells expressing the proteins of interest. FRET spectrometry protocols currently rely on obtaining spectrally resolved fluorescence data from intensity-based experiments. Another imaging method, fluorescence lifetime imaging microscopy (FLIM), is a widely used alternative to compute FRET efficiencies for each pixel in an image from the reduction of the fluorescence lifetime of the donors caused by FRET. In FLIM studies of oligomers with different proportions of donors and acceptors, the donor lifetimes may be obtained by fitting the temporally resolved fluorescence decay data with a predetermined number of exponential decay curves. However, this requires knowledge of the number and the relative arrangement of the fluorescent proteins in the sample, which is precisely the goal of FRET spectrometry, thus creating a conundrum that has prevented users of FLIM instruments from performing FRET spectrometry. Here, we describe an attempt to implement FRET spectrometry on temporally resolved fluorescence microscopes by using an integration-based method of computing the FRET efficiency from fluorescence decay curves. This method, which we dubbed time-integrated FRET (or tiFRET), was tested on oligomeric fluorescent protein constructs expressed in the cytoplasm of living cells. The present results show that tiFRET is a promising way of implementing FRET spectrometry and suggest potential instrument adjustments for increasing accuracy and resolution in this kind of study.
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Affiliation(s)
- Justin Trujillo
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Aliyah S. Khan
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Dhruba P. Adhikari
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Michael R. Stoneman
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Jenu V. Chacko
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
| | - Kevin W. Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
- Departments of Biomedical Engineering and Medical Physics, University of Wisconsin-Madison, Madison, WI 53705, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Valerica Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
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5
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Joron K, Viegas JO, Haas-Neill L, Bier S, Drori P, Dvir S, Lim PSL, Rauscher S, Meshorer E, Lerner E. Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation. Nat Commun 2023; 14:4885. [PMID: 37573411 PMCID: PMC10423231 DOI: 10.1038/s41467-023-40647-6] [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: 01/19/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.
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Affiliation(s)
- Khalil Joron
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Juliane Oliveira Viegas
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Liam Haas-Neill
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Sariel Bier
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Shani Dvir
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Patrick Siang Lin Lim
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
- Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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6
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Chang H, Bennett AM, Cameron WD, Floro E, Au A, McFaul CM, Yip CM, Rocheleau JV. Targeting Apollo-NADP + to Image NADPH Generation in Pancreatic Beta-Cell Organelles. ACS Sens 2022; 7:3308-3317. [PMID: 36269889 PMCID: PMC9706804 DOI: 10.1021/acssensors.2c01174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NADPH/NADP+ redox state supports numerous reactions related to cell growth and survival; yet the full impact is difficult to appreciate due to organelle compartmentalization of NADPH and NADP+. To study glucose-stimulated NADPH production in pancreatic beta-cell organelles, we targeted the Apollo-NADP+ sensor by first selecting the most pH-stable version of the single-color sensor. We subsequently targeted mTurquoise2-Apollo-NADP+ to various organelles and confirmed activity in the cytoplasm, mitochondrial matrix, nucleus, and peroxisome. Finally, we measured the glucose- and glutamine-stimulated NADPH responses by single- and dual-color imaging of the targeted sensors. Overall, we developed multiple organelle-targeted Apollo-NADP+ sensors to reveal the prominent role of beta-cell mitochondria in determining NADPH production in the cytoplasm, nucleus, and peroxisome.
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Affiliation(s)
- Huntley
H. Chang
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Alex M. Bennett
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - William D. Cameron
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Eric Floro
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Aaron Au
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. McFaul
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. Yip
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Jonathan V. Rocheleau
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada,Department
of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada,Banting
and Best Diabetes Centre, University of
Toronto, Toronto, Ontario M5G 2C4, Canada,
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7
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De CK, Ghosh A, Mandal PK. Hydrophobicity-Dependent Heterogeneous Nanoaggregates and Fluorescence Dynamics in Room-Temperature Ionic Liquids. J Phys Chem B 2022; 126:1551-1557. [PMID: 35166544 DOI: 10.1021/acs.jpcb.1c08598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The hydrophobicity of room-temperature ionic liquids (RTILs) has been shown to have a very significant effect on the optical and structural properties of and in RTILs. The average excited state lifetime of neat RTILs has been shown to be increasing with increasing hydrophobicity of the RTILs. By employing pico-nanosecond-based fluorescence anisotropy decay, the volume of the nanoaggregates in neat RTILs have been calculated. The volume of these nanoaggregates have been shown to be decreasing with increase in hydrophobicity of the RTILs. Thus, hydrophobicity has been shown to have an important role, i.e., hydrophobicity can be used as a handle to tune the properties of RTILs as designer solvents. Moreover, the excited-state lifetime of red-emitting fluorophores, i.e., whose fluorescence emission is not perturbed by the inherent emission of RTILs, has been shown to increase with the increasing hydrophobicity of the RTILs. Highly hydrophobic RTILs have been shown to exhibit positive deviation and highly hydrophilic RTIL has been shown to exhibit negative deviation from the linear correlation between average solvation time (τs) versus viscosity/temperature (η/T).
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8
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Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022; 9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."
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Affiliation(s)
- Panagiotis Chandris
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
| | | | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
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9
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Al-Fahad D, Al-Harbi B, Abbas Y, Al-Yaseen F. A Comparative Study to Visualize PtdIns(4,5) P2 and PtdIns(3,4,5) P3 in MDA-MB-231 Breast Cancer Cell Line. Rep Biochem Mol Biol 2022; 10:518-526. [PMID: 35291610 PMCID: PMC8903368 DOI: 10.52547/rbmb.10.4.518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 09/19/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5) P3) and Phosphatidylinositol 4,5-trisphosphate (PtdIns(4,5) P2] form an insignificant amount of phospholipids but play important roles in controlling membrane-bound signalling. Little attention has been given to visualize and monitor changes or differences in the local generation of PtdIns(4,5) P2 and PtdIns(3,4,5) P3 in the cell membranes of MDA-MB-231 breast cancer cell lines. METHODS PLCδ1-PH-GFP and Btk-PH-GFP were used as biosensors to detected PtdIns(4,5) P2 and PtdIns(3,4,5)P3 respectively. These biosensors and antibodies were transfected, immuostained and then visualized by confocal microscopy on different cell surfaces. RESULTS Our results showed that PLCδ1-PH-GFP/mCherry was localized at the cell membrane, while Btk-PH-GFP/mCherry was sometimes localized at the cell membrane but there was also a large amount of fluorescence present in the cytosol and nucleus. Our results also showed that the cells that expressed low levels of Btk-PH-GFP the fluorescence was predominantly localised to the cell membrane. While the cells that expressed high levels of Btk-PH-GFP the fluorescence was localization in the cytosol and cell membrane. Our results demonstrated that both anti-PtdIns(4,5)P2 and anti-PtdIns(3,4,5)P3 antibodies were localized everywhere in cell. CONCLUSION Our results suggest that PLCδ1-PH-GFP and Btk-PH-GFP/mCherry have more specificity, reliability, suitability and accuracy than antibodies in binding with and detecting PtdIns(4,5)P2 and PtdIns(3,4,5)P3 and in studying the molecular dynamics of phospholipids in live and fixed cells.
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Affiliation(s)
- Dhurgham Al-Fahad
- Department of Pathological Analysis, College of Science, University of Thi-Qar, Thi-Qar 64001, Iraq.
| | - Bandar Al-Harbi
- Department of clinical laboratory, College of Applied Medical Science, University of Hail, Hail 81411, Saudia Arabia.
| | - Yahya Abbas
- Department of Biology, College of Science, University of Thi-Qar, Thi-Qar 64001, Iraq.
| | - Firas Al-Yaseen
- Department of Clinical Biochemistry, College of Pharmacy, University of Thi-Qar, Thi-Qar 64001, Iraq.
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10
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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11
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Laskaratou D, Fernández GS, Coucke Q, Fron E, Rocha S, Hofkens J, Hendrix J, Mizuno H. Quantification of FRET-induced angular displacement by monitoring sensitized acceptor anisotropy using a dim fluorescent donor. Nat Commun 2021; 12:2541. [PMID: 33953187 PMCID: PMC8099864 DOI: 10.1038/s41467-021-22816-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023] Open
Abstract
Förster resonance energy transfer (FRET) between fluorescent proteins has become a common platform for designing genetically encoded biosensors. For live cell imaging, the acceptor-to-donor intensity ratio is most commonly used to readout FRET efficiency, which largely depends on the proximity between donor and acceptor. Here, we introduce an anisotropy-based mode of FRET detection (FADED: FRET-induced Angular Displacement Evaluation via Dim donor), which probes for relative orientation rather than proximity alteration. A key element in this technique is suppression of donor bleed-through, which allows measuring purer sensitized acceptor anisotropy. This is achieved by developing Geuda Sapphire, a low-quantum-yield FRET-competent fluorescent protein donor. As a proof of principle, Ca2+ sensors were designed using calmodulin as a sensing domain, showing sigmoidal dose response to Ca2+. By monitoring the anisotropy, a Ca2+ rise in living HeLa cells is observed upon histamine challenging. We conclude that FADED provides a method for quantifying the angular displacement via FRET.
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Affiliation(s)
- Danai Laskaratou
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | | | - Quinten Coucke
- Chem & Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Eduard Fron
- Chem & Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
- KU Leuven Core Facility for Advanced Spectroscopy, KU Leuven, Heverlee, Belgium
| | - Susana Rocha
- Chem & Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Johan Hofkens
- Chem & Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Jelle Hendrix
- Chem & Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Diepenbeek, Belgium
| | - Hideaki Mizuno
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium.
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12
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Aplin CP, Miller RC, Kay TM, Heikal AA, Boersma AJ, Sheets ED. Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy. Biophys J 2021; 120:1417-1430. [PMID: 33582140 DOI: 10.1016/j.bpj.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022] Open
Abstract
Eukaryotic cells exploit dynamic and compartmentalized ionic strength to impact a myriad of biological functions such as enzyme activities, protein-protein interactions, and catalytic functions. Herein, we investigated the fluorescence depolarization dynamics of recently developed ionic strength biosensors (mCerulean3-linker-mCitrine) in Hofmeister salt (KCl, NaCl, NaI, and Na2SO4) solutions. The mCerulean3-mCitrine acts as a Förster resonance energy transfer (FRET) pair, tethered together by two oppositely charged α-helices in the linker region. We developed a time-resolved fluorescence depolarization anisotropy approach for FRET analyses, in which the donor (mCerulean3) is excited by 425-nm laser pulses, followed by fluorescence depolarization analysis of the acceptor (mCitrine) in KE (lysine-glutamate), arginine-aspartate, and arginine-glutamate ionic strength sensors with variable amino acid sequences. Similar experiments were carried out on the cleaved sensors as well as an E6G2 construct, which has neutral α-helices in the linker region, as a control. Our results show distinct dynamics of the intact and cleaved sensors. Importantly, the FRET efficiency decreases and the donor-acceptor distance increases as the environmental ionic strength increases. Our chemical equilibrium analyses of the collapsed-to-stretched conformational state transition of KE reveal that the corresponding equilibrium constant and standard Gibbs free energy changes are ionic strength dependent. We also tested the existing theoretical models for FRET analyses using steady-state anisotropy, which reveal that the angle between the dipole moments of the donor and acceptor in the KE sensor are sensitive to the ionic strength. These results help establish the time-resolved depolarization dynamics of these genetically encoded donor-acceptor pairs as a quantitative means for FRET analysis, which complement traditional methods such as time-resolved fluorescence for future in vivo studies.
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Affiliation(s)
- Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, Minnesota
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany.
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
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13
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Keyes J, Mehta S, Zhang J. Strategies for Multiplexed Biosensor Imaging to Study Intracellular Signaling Networks. Methods Mol Biol 2021; 2350:1-20. [PMID: 34331275 PMCID: PMC8580745 DOI: 10.1007/978-1-0716-1593-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Signal transduction processes are a necessary component of multicellular life, and their dysregulation is the basis for a host of syndromes and diseases. Thus, it is imperative that we discover the complex details of how signal transduction processes result in specific cellular outcomes. One of the primary mechanisms of regulation over signaling pathways is through spatiotemporal control. However, traditional methods are limited in their ability to reveal such details. To overcome these limitations, researchers have developed a variety of genetically encodable, fluorescent protein-based biosensors to study these dynamic processes in real time in living cells. Due to the complexities and interconnectedness of signaling pathways, it is thus desirable to use multiple biosensors in individual cells to better elucidate the relationships between signaling pathways. However, multiplexed imaging with such biosensors has been historically difficult. Nevertheless, recent developments in designs and multiplexing strategies have led to vast improvements in our capabilities. In this review, we provide perspectives on the recently developed biosensor designs and multiplexing strategies that are available for multiplexed imaging of signal transduction pathways.
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Affiliation(s)
- Jeremiah Keyes
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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14
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Time-Resolved Fluorescence Anisotropy and Molecular Dynamics Analysis of a Novel GFP Homo-FRET Dimer. Biophys J 2020; 120:254-269. [PMID: 33345902 PMCID: PMC7840444 DOI: 10.1016/j.bpj.2020.11.2275] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/06/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Förster resonance energy transfer (FRET) is a powerful tool to investigate the interaction between proteins in living cells. Fluorescence proteins, such as the green fluorescent protein (GFP) and its derivatives, are coexpressed in cells linked to proteins of interest. Time-resolved fluorescence anisotropy is a popular tool to study homo-FRET of fluorescent proteins as an indicator of dimerization, in which its signature consists of a very short component at the beginning of the anisotropy decay. In this work, we present an approach to study GFP homo-FRET via a combination of time-resolved fluorescence anisotropy, the stretched exponential decay model, and molecular dynamics simulations. We characterize a new, to our knowledge, FRET standard formed by two enhanced GFPs (eGFPs) and a flexible linker of 15 aminoacids (eGFP15eGFP) with this protocol, which is validated by using an eGFP monomer as a reference. An excellent agreement is found between the FRET efficiency calculated from the fit of the eGFP15eGFP fluorescence anisotropy decays with a stretched exponential decay model (〈EFRETexp〉 = 0.25 ± 0.05) and those calculated from the molecular dynamics simulations (〈EFRETMD〉 = 0.18 ± 0.14). The relative dipole orientation between the GFPs is best described by the orientation factors 〈κ2〉 = 0.17 ± 0.16 and 〈|κ|〉 = 0.35 ± 0.20, contextualized within a static framework in which the linker hinders the free rotation of the fluorophores and excludes certain configurations. The combination of time- and polarization-resolved fluorescence spectroscopy with molecular dynamics simulations is shown to be a powerful tool for the study and interpretation of homo-FRET.
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15
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Liput DJ, Nguyen TA, Augustin SM, Lee JO, Vogel SS. A Guide to Fluorescence Lifetime Microscopy and Förster's Resonance Energy Transfer in Neuroscience. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e108. [PMID: 33232577 PMCID: PMC8274369 DOI: 10.1002/cpns.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorescence lifetime microscopy (FLIM) and Förster's resonance energy transfer (FRET) are advanced optical tools that neuroscientists can employ to interrogate the structure and function of complex biological systems in vitro and in vivo using light. In neurobiology they are primarily used to study protein-protein interactions, to study conformational changes in protein complexes, and to monitor genetically encoded FRET-based biosensors. These methods are ideally suited to optically monitor changes in neurons that are triggered optogenetically. Utilization of this technique by neuroscientists has been limited, since a broad understanding of FLIM and FRET requires familiarity with the interactions of light and matter on a quantum mechanical level, and because the ultra-fast instrumentation used to measure fluorescent lifetimes and resonance energy transfer are more at home in a physics lab than in a biology lab. In this overview, we aim to help neuroscientists overcome these obstacles and thus feel more comfortable with the FLIM-FRET method. Our goal is to aid researchers in the neuroscience community to achieve a better understanding of the fundamentals of FLIM-FRET and encourage them to fully leverage its powerful ability as a research tool. Published 2020. U.S. Government.
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Affiliation(s)
- Daniel J. Liput
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Tuan A. Nguyen
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Shana M. Augustin
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Jeong Oen Lee
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Steven S. Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Corresponding author:
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16
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Abstract
Peroxiredoxins are most central to the cellular adaptation against oxidative stress. They act as oxidant scavengers, stress sensors, transmitters of signals, and chaperones, and they possess a unique quaternary switch that is intimately related to these functions. However, so far it has not been possible to monitor peroxiredoxin structural changes in the intact cellular environment. This study presents genetically encoded probes, based on homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization, that allow following these quaternary changes in real time, in living cells. We envisage that these probes can be used to address a broad range of questions related to the function of peroxiredoxins. Peroxiredoxins are central to cellular redox homeostasis and signaling. They serve as peroxide scavengers, sensors, signal transducers, and chaperones, depending on conditions and context. Typical 2-Cys peroxiredoxins are known to switch between different oligomeric states, depending on redox state, pH, posttranslational modifications, and other factors. Quaternary states and their changes are closely connected to peroxiredoxin activity and function but so far have been studied, almost exclusively, outside the context of the living cell. Here we introduce the use of homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization to monitor dynamic changes in peroxiredoxin quaternary structure inside the crowded environment of living cells. Using the approach, we confirm peroxide- and thioredoxin-related quaternary transitions to take place in cellulo and observe that the relationship between dimer–decamer transitions and intersubunit disulfide bond formation is more complex than previously thought. Furthermore, we demonstrate the use of the approach to compare different peroxiredoxin isoforms and to identify mutations and small molecules affecting the oligomeric state inside cells. Mutagenesis experiments reveal that the dimer–decamer equilibrium is delicately balanced and can be shifted by single-atom structural changes. We show how to use this insight to improve the design of peroxiredoxin-based redox biosensors.
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17
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Heckmeier PJ, Agam G, Teese MG, Hoyer M, Stehle R, Lamb DC, Langosch D. Determining the Stoichiometry of Small Protein Oligomers Using Steady-State Fluorescence Anisotropy. Biophys J 2020; 119:99-114. [PMID: 32553128 DOI: 10.1016/j.bpj.2020.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 11/19/2022] Open
Abstract
A large fraction of soluble and membrane-bound proteins exists as non-covalent dimers, trimers, and higher-order oligomers. The experimental determination of the oligomeric state or stoichiometry of proteins remains a nontrivial challenge. In one approach, the protein of interest is genetically fused to green fluorescent protein (GFP). If a fusion protein assembles into a non-covalent oligomeric complex, exciting their GFP moiety with polarized fluorescent light elicits homotypic Förster resonance energy transfer (homo-FRET), in which the emitted radiation is partially depolarized. Fluorescence depolarization is associated with a decrease in fluorescence anisotropy that can be exploited to calculate the oligomeric state. In a classical approach, several parameters obtained through time-resolved and steady-state anisotropy measurements are required for determining the stoichiometry of the oligomers. Here, we examined novel approaches in which time-resolved measurements of reference proteins provide the parameters that can be used to interpret the less expensive steady-state anisotropy data of candidates. In one approach, we find that using average homo-FRET rates (kFRET), average fluorescence lifetimes (τ), and average anisotropies of those fluorophores that are indirectly excited by homo-FRET (rET) do not compromise the accuracy of calculated stoichiometries. In the other approach, fractional photobleaching of reference oligomers provides a novel parameter a whose dependence on stoichiometry allows one to quantitatively interpret the increase of fluorescence anisotropy seen after photobleaching the candidates. These methods can at least reliably distinguish monomers from dimers and trimers.
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Affiliation(s)
- Philipp J Heckmeier
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Ganesh Agam
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Mark G Teese
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Maria Hoyer
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM), Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany.
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18
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19
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Silori Y, De AK. Controlling balance between homo-FRET and hetero-FRET within hetero-chromophoric systems by tuning nature of solvent. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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20
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Li CC, Li Y, Zhang Y, Zhang CY. Single-molecule fluorescence resonance energy transfer and its biomedical applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115753] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Gupta N, Renugopalakrishnan V, Liepmann D, Paulmurugan R, Malhotra BD. Cell-based biosensors: Recent trends, challenges and future perspectives. Biosens Bioelectron 2019; 141:111435. [PMID: 31238280 DOI: 10.1016/j.bios.2019.111435] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022]
Abstract
Existing at the interface of biology and electronics, living cells have been in use as biorecognition elements (bioreceptors) in biosensors since the early 1970s. They are an interesting choice of bioreceptors as they allow flexibility in determining the sensing strategy, are cheaper than purified enzymes and antibodies and make the fabrication relatively simple and cost-effective. And with advances in the field of synthetic biology, microfluidics and lithography, many exciting developments have been made in the design of cell-based biosensors in the last about five years. 3D cell culture systems integrated with electrodes are now providing new insights into disease pathogenesis and physiology, while cardiomyocyte-integrated microelectrode array (MEA) technology is set to be standardized for the assessment of drug-induced cardiac toxicity. From cell microarrays for high-throughput applications to plasmonic devices for anti-microbial susceptibility testing and advent of microbial fuel cell biosensors, cell-based biosensors have evolved from being mere tools for detection of specific analytes to multi-parametric devices for real time monitoring and assessment. However, despite these advancements, challenges such as regeneration and storage life, heterogeneity in cell populations, high interference and high costs due to accessory instrumentation need to be addressed before the full potential of cell-based biosensors can be realized at a larger scale. This review summarizes results of the studies that have been conducted in the last five years toward the fabrication of cell-based biosensors for different applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.
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Affiliation(s)
- Niharika Gupta
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi 110042, India
| | | | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Cellular Pathway Imaging Laboratory, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, CA, 94304, USA
| | - Bansi D Malhotra
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi 110042, India.
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22
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Silori Y, De AK. Tuning effect of local environment to control mechanism of fluorescence depolarization: Rotational diffusion and resonance energy transfer within homo-aggregates of xanthenes. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Dlugosz P, Tresky R, Nimpf J. Differential Action of Reelin on Oligomerization of ApoER2 and VLDL Receptor in HEK293 Cells Assessed by Time-Resolved Anisotropy and Fluorescence Lifetime Imaging Microscopy. Front Mol Neurosci 2019; 12:53. [PMID: 30873003 PMCID: PMC6403468 DOI: 10.3389/fnmol.2019.00053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/12/2019] [Indexed: 01/12/2023] Open
Abstract
The canonical Reelin signaling cascade regulates correct neuronal layering during embryonic brain development. Details of this pathway are still not fully understood since the participating components are highly variable and create a complex mixture of interacting molecules. Reelin is proteolytically processed resulting in five different fragments some of which carrying the binding site for two different but highly homologous receptors, apolipoprotein E receptor 2 (ApoER2) and very low density lipoprotein receptor (VLDLR). The receptors are expressed in different variants in different areas of the developing brain. Binding of Reelin and its central fragment to the receptors results in phosphorylation of the intracellular adapter disabled-1 (Dab1) in neurons. Here, we studied the changes of the arrangement of the receptors upon Reelin binding and its central fragment at the molecular level in human embryonic kidney 293 (HEK293) cells by time-resolved anisotropy and fluorescence lifetime imaging microscopy (FLIM). In the off-state of the pathway ApoER2 and VLDLR form homo or hetero-di/oligomers. Upon binding of full length Reelin ApoER2 and VLDLR homo-oligomers are rearranged to higher order receptor clusters which leads to Dab1 phosphorylation. When the central fragment of Reelin binds to the receptors the cluster size of homo-oligomers is not affected and Dab1 is not phosphorylated. Hetero-oligomerization, however, can be induced, but does not lead to Dab1 phosphorylation. Cells expressing only ApoER2 or VLDLR change their shape when stimulated with the central fragment. Cells expressing ApoER2 produce filopodia/lamellipodia and cell size increases, whereas VLDLR-expressing cells decrease in size. These findings demonstrate that the primary event in the canonical Reelin pathway is the rearrangement of preformed receptor homo-oligomers to higher order clusters. In addition the possibility of yet another signaling mechanism which is mediated by the central Reelin fragment independent of Dab1 phosphorylation became apparent.
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Affiliation(s)
- Paula Dlugosz
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University Vienna, Vienna, Austria
| | - Roland Tresky
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University Vienna, Vienna, Austria
| | - Johannes Nimpf
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University Vienna, Vienna, Austria
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Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Crowding Effects on Energy-Transfer Efficiencies of Hetero-FRET Probes As Measured Using Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2019; 123:379-393. [PMID: 30571116 DOI: 10.1021/acs.jpcb.8b09829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Macromolecular crowding is prevalent in all living cells due to the presence of large biomolecules and organelles. Cellular crowding is heterogeneous and is known to influence biomolecular transport, biochemical reactions, and protein folding. Emerging evidence suggests that some cell pathologies may be correlated with compartmentalized crowding. As a result, there is a need for robust biosensors that are sensitive to crowding as well as quantitative, noninvasive fluorescence methods that are compatible with living cells studies. Here, we have developed a model that describes the rotational dynamics of hetero-Förster resonance energy transfer (FRET) biosensors as a means to determine the energy-transfer efficiency and donor-acceptor distance. The model was tested on wavelength-dependent time-resolved fluorescence anisotropy of hetero-FRET probes (mCerulean3-linker-mCitrine) with variable linkers in both crowded (Ficoll-70) and viscous (glycerol) solutions at room temperature. Our results indicate that the energy-transfer efficiencies of these FRET probes increase as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor compact structures with enhanced energy-transfer efficiencies and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the extended conformation of these FRET probes is more favorable in viscous, homogeneous environments with a reduced energy-transfer efficiency compared to those in pure buffer, which we attribute to reduced structural fluctuations of the mCerulean3-mCitrine FRET pair in the glycerol-enriched buffer. Our results represent an important step toward the application of quantitative and noninvasive time-resolved fluorescence anisotropy of hetero-FRET probes to investigate compartmentalized macromolecular crowding and protein-protein interactions in living cells as well as in controlled environments.
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Affiliation(s)
- Hannah J Leopold
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ryan Leighton
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Arnold J Boersma
- DW1-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
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25
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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26
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Kostyuk AI, Panova AS, Bilan DS, Belousov VV. Redox biosensors in a context of multiparameter imaging. Free Radic Biol Med 2018; 128:23-39. [PMID: 29630928 DOI: 10.1016/j.freeradbiomed.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
A wide variety of genetically encoded fluorescent biosensors are available to date. Some of them have already contributed significantly to our understanding of biological processes occurring at cellular and organismal levels. Using such an approach, outstanding success has been achieved in the field of redox biology. The probes allowed researchers to observe, for the first time, the dynamics of important redox parameters in vivo during embryogenesis, aging, the inflammatory response, the pathogenesis of various diseases, and many other processes. Given the differences in the readout and spectra of the probes, they can be used in multiparameter imaging in which several processes are monitored simultaneously in the cell. Intracellular processes form an extensive network of interactions. For example, redox changes are often accompanied by changes in many other biochemical reactions related to cellular metabolism and signaling. Therefore, multiparameter imaging can provide important information concerning the temporal and spatial relationship of various signaling and metabolic processes. In this review, we will describe the main types of genetically encoded biosensors, the most frequently used readout, and their use in multiplexed imaging mode.
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Affiliation(s)
- Alexander I Kostyuk
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anastasiya S Panova
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Institute for Cardiovascular Physiology, Georg August University Göttingen, Göttingen D-37073, Germany.
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27
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Snell NE, Rao VP, Seckinger KM, Liang J, Leser J, Mancini AE, Rizzo MA. Homotransfer of FRET Reporters for Live Cell Imaging. BIOSENSORS-BASEL 2018; 8:bios8040089. [PMID: 30314323 PMCID: PMC6316388 DOI: 10.3390/bios8040089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
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Affiliation(s)
- Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Vishnu P Rao
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Kendra M Seckinger
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Junyi Liang
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Jenna Leser
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Allison E Mancini
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
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28
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Co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy. Redox Biol 2018; 19:210-217. [PMID: 30176560 PMCID: PMC6120609 DOI: 10.1016/j.redox.2018.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
In order to overcome intercellular variability and thereby effectively assess signal propagation in biological networks it is imperative to simultaneously quantify multiple biological observables in single living cells. While fluorescent biosensors have been the tool of choice to monitor the dynamics of protein interaction and enzymatic activity, co-measuring more than two of them has proven challenging. In this work, we designed three spectrally separated anisotropy-based Förster Resonant Energy Transfer (FRET) biosensors to overcome this difficulty. We demonstrate this principle by monitoring the activation of extrinsic, intrinsic and effector caspases upon apoptotic stimulus. Together with modelling and simulations we show that time of maximum activity for each caspase can be derived from the anisotropy of the corresponding biosensor. Such measurements correlate relative activation times and refine existing models of biological signalling networks, providing valuable insight into signal propagation.
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29
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Ross BL, Tenner B, Markwardt ML, Zviman A, Shi G, Kerr JP, Snell NE, McFarland JJ, Mauban JR, Ward CW, Rizzo MA, Zhang J. Single-color, ratiometric biosensors for detecting signaling activities in live cells. eLife 2018; 7:e35458. [PMID: 29968564 PMCID: PMC6037473 DOI: 10.7554/elife.35458] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 11/22/2022] Open
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of signal transduction by enabling the real-time tracking of signaling activities in live cells. Investigating the interaction between signaling networks has become increasingly important to understanding complex cellular phenomena, necessitating an update of the biosensor toolkit to allow monitoring and perturbing multiple activities simultaneously in the same cell. We therefore developed a new class of fluorescent biosensors based on homo-FRET, deemed FLuorescence Anisotropy REporters (FLAREs), which combine the multiplexing ability of single-color sensors with a quantitative, ratiometric readout. Using an array of color variants, we were able to demonstrate multiplexed imaging of three activity reporters simultaneously in the same cell. We further demonstrate the compatibility of FLAREs for use with optogenetic tools as well as intravital two-photon imaging.
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Affiliation(s)
- Brian L Ross
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreUnited States
| | - Brian Tenner
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Michele L Markwardt
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Adam Zviman
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Guoli Shi
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jaclyn P Kerr
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Nicole E Snell
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | | | - Joseph R Mauban
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Christopher W Ward
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Megan A Rizzo
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jin Zhang
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of Pharmacology and Molecular SciencesJohns Hopkins University School of MedicineBaltimoreUnited States
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30
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Abstract
Fluorescence lifetime (FLT) is a robust intrinsic property and material constant of fluorescent matter. Measuring this important physical indicator has evolved from a laboratory curiosity to a powerful and established technique for a variety of applications in drug discovery, medical diagnostics and basic biological research. This distinct trend was mainly driven by improved and meanwhile affordable laser and detection instrumentation on the one hand, and the development of suitable FLT probes and biological assays on the other. In this process two essential working approaches emerged. The first one is primarily focused on high throughput applications employing biochemical in vitro assays with no requirement for high spatial resolution. The second even more dynamic trend is the significant expansion of assay methods combining highly time and spatially resolved fluorescence data by fluorescence lifetime imaging. The latter approach is currently pursued to enable not only the investigation of immortal tumor cell lines, but also specific tissues or even organs in living animals. This review tries to give an actual overview about the current status of FLT based bioassays and the wide range of application opportunities in biomedical and life science areas. In addition, future trends of FLT technologies will be discussed.
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Affiliation(s)
- Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, D-64295 Darmstadt, Germany
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31
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Lagarto J, Hares JD, Dunsby C, French PMW. Development of Low-Cost Instrumentation for Single Point Autofluorescence Lifetime Measurements. J Fluoresc 2017; 27:1643-1654. [PMID: 28540652 PMCID: PMC5583312 DOI: 10.1007/s10895-017-2101-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 01/25/2023]
Abstract
Autofluorescence lifetime measurements, which can provide label-free readouts in biological tissues, contrasting e.g. different types and states of tissue matrix components and different cellular metabolites, may have significant clinical potential for diagnosis and to provide surgical guidance. However, the cost of the instrumentation typically used currently presents a barrier to wider implementation. We describe a low-cost single point time-resolved autofluorescence instrument, exploiting modulated laser diodes for excitation and FPGA-based circuitry for detection, together with a custom constant fraction discriminator. Its temporal accuracy is compared against a "gold-standard" instrument incorporating commercial TCSPC circuitry by resolving the fluorescence decays of reference fluorophores presenting single and double exponential decay profiles. To illustrate the potential to read out intrinsic contrast in tissue, we present preliminary measurements of autofluorescence lifetime measurements of biological tissues ex vivo. We believe that the lower cost of this instrument could enhance the potential of autofluorescence lifetime metrology for clinical deployment and commercial development.
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Affiliation(s)
- João Lagarto
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK.
| | - Jonathan D Hares
- Kentech Instruments Ltd., Howbery Park, Wallingford, OX10 8BD, UK
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK
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32
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Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. J Phys Chem B 2017; 121:5688-5698. [DOI: 10.1021/acs.jpcb.7b01306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Megan Currie
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Hannah Leopold
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jacob Schwarz
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Erin D. Sheets
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Ahmed A. Heikal
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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33
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Abstract
Förster resonance energy transfer (FRET) is a powerful tool for the visualization of molecular signaling events such as protein activities and interactions in cells. In its different implementations, FRET microscopy has been mainly used for monitoring single events. Recently, there has been a trend of extending FRET imaging towards the simultaneous detection of multiple events and interactions. The concomitant increase in experimental complexity requires a deeper understanding of the biophysical background of FRET. The presence of multiple acceptors for one donor affects the well-known formalism for FRET between two molecules, increasing distance sensitivity through mechanisms that have become known as the ‘antenna’ and ‘surplus’ effect. We will discuss the nature of these effects and present the imaging methods that have been used to unravel the combined transfer rates in the multi-protein interactions of multiplexed FRET experiments. Multiplexing strategies are becoming invaluable analytical tools for the elucidation of biological complexes and for the visualization of decision points in cellular signaling networks in physiological and pathological conditions.
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34
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Abstract
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.
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Affiliation(s)
- Lynn Sanford
- University of Colorado Boulder, Boulder, CO, United States
| | - Amy Palmer
- University of Colorado Boulder, Boulder, CO, United States.
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35
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Jozawa H, Kabir MG, Zako T, Maeda M, Chiba K, Kuroda Y. Amorphous protein aggregation monitored using fluorescence self-quenching. FEBS Lett 2016; 590:3501-3509. [DOI: 10.1002/1873-3468.12439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/31/2016] [Accepted: 09/18/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroki Jozawa
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
| | - Md. Golam Kabir
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
| | - Tamotsu Zako
- Bioengineering Laboratory; RIKEN Institute; Wako Japan
| | - Mizuo Maeda
- Bioengineering Laboratory; RIKEN Institute; Wako Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-Organic Chemistry; Tokyo University of Agriculture and Technology; Fuchu Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
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36
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Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
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Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
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37
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Margineanu A, Chan JJ, Kelly DJ, Warren SC, Flatters D, Kumar S, Katan M, Dunsby CW, French PMW. Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM). Sci Rep 2016; 6:28186. [PMID: 27339025 PMCID: PMC4919659 DOI: 10.1038/srep28186] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/19/2016] [Indexed: 11/09/2022] Open
Abstract
We present a high content multiwell plate cell-based assay approach to quantify protein interactions directly in cells using Förster resonance energy transfer (FRET) read out by automated fluorescence lifetime imaging (FLIM). Automated FLIM is implemented using wide-field time-gated detection, typically requiring only 10 s per field of view (FOV). Averaging over biological, thermal and shot noise with 100's to 1000's of FOV enables unbiased quantitative analysis with high statistical power. Plotting average donor lifetime vs. acceptor/donor intensity ratio clearly identifies protein interactions and fitting to double exponential donor decay models provides estimates of interacting population fractions that, with calibrated donor and acceptor fluorescence intensities, can yield dissociation constants. We demonstrate the application to identify binding partners of MST1 kinase and estimate interaction strength among the members of the RASSF protein family, which have important roles in apoptosis via the Hippo signalling pathway. KD values broadly agree with published biochemical measurements.
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Affiliation(s)
- Anca Margineanu
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Jia Jia Chan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Douglas J. Kelly
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Sean C. Warren
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Delphine Flatters
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques in silico, Inserm UMR-S 973, 35 rue Helene Brion, 75013 Paris, France
| | - Sunil Kumar
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Matilda Katan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Christopher W. Dunsby
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Paul M. W. French
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
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38
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Multiplexed imaging of intracellular protein networks. Cytometry A 2016; 89:761-75. [DOI: 10.1002/cyto.a.22876] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022]
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39
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Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening. ACTA ACUST UNITED AC 2016; 21:535-47. [DOI: 10.1177/1087057116634007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/31/2016] [Indexed: 11/16/2022]
Abstract
Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)–activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.
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Affiliation(s)
- Jaimee Doucette
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Ziyan Zhao
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Rory J. Geyer
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Melanie M. Barra
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut at Storrs, Storrs, CT
| | - Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
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40
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Apollo-NADP(+): a spectrally tunable family of genetically encoded sensors for NADP(+). Nat Methods 2016; 13:352-8. [PMID: 26878383 DOI: 10.1038/nmeth.3764] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/08/2016] [Indexed: 02/03/2023]
Abstract
NADPH-dependent antioxidant pathways have a critical role in scavenging hydrogen peroxide (H2O2) produced by oxidative phosphorylation. Inadequate scavenging results in H2O2 accumulation and can cause disease. To measure NADPH/NADP(+) redox states, we explored genetically encoded sensors based on steady-state fluorescence anisotropy due to FRET (fluorescence resonance energy transfer) between homologous fluorescent proteins (homoFRET); we refer to these sensors as Apollo sensors. We created an Apollo sensor for NADP(+) (Apollo-NADP(+)) that exploits NADP(+)-dependent homodimerization of enzymatically inactive glucose-6-phosphate dehydrogenase (G6PD). This sensor is reversible, responsive to glucose-stimulated metabolism and spectrally tunable for compatibility with many other sensors. We used Apollo-NADP(+) to study beta cells responding to oxidative stress and demonstrated that NADPH is significantly depleted before H2O2 accumulation by imaging a Cerulean-tagged version of Apollo-NADP(+) with the H2O2 sensor HyPer.
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