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Frei MS, Mehta S, Zhang J. Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. Annu Rev Biophys 2024; 53:275-297. [PMID: 38346245 DOI: 10.1146/annurev-biophys-030722-021359] [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: 02/28/2024]
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.
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Affiliation(s)
- Michelle S Frei
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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2
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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3
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Kim JM, Seong BL, Jung J. Highly chromophoric dual-terminus labeling of an intrinsically disordered native eukaryotic protein of interest at nanoscale. Int J Biol Macromol 2023:125396. [PMID: 37348577 DOI: 10.1016/j.ijbiomac.2023.125396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
Chemical conjugation of purified proteins of interest (POIs) in Escherichia coli cells is effective for high expression but has limitations for highly chromogenic dual labeling of intrinsically disordered native proteins (IDNPs). Our probes can tag IDNPs using chemical conjugation during protein synthesis and folding while preserving biologically active structures in mammalian cells. We fluorescently labeled IDNPs in mammalian cells using pure fluorescent methionine and ATTO 565-biotin at the N-or C-terminus, respectively. The dual-labeled Tat protein was used as a model for IDNPs in HeLa cells and detected using Ni-NTA beads to estimate its highly chromogenic concentration. We also demonstrated highly chromogenic double labeling of genetically encoded fluorescent-Tat expression in eukaryotic cells using a single fluorescent dye pair with Förster resonance energy transfer (FRET) ratio and two-color correlation analysis. This study aims to solve native POI processing and achieve ultra-sensitive protein folding for biological and ecological applications at the nanoscale.
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Affiliation(s)
- Jung Min Kim
- Department of Environmental Science and Ecological Engineering, Ojeong Resilience Institute, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02842, Republic of Korea.
| | - Baik Lin Seong
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jinho Jung
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02842, Republic of Korea
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4
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Davis MJ, Earley S, Li YS, Chien S. Vascular mechanotransduction. Physiol Rev 2023; 103:1247-1421. [PMID: 36603156 PMCID: PMC9942936 DOI: 10.1152/physrev.00053.2021] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 01/07/2023] Open
Abstract
This review aims to survey the current state of mechanotransduction in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs), including their sensing of mechanical stimuli and transduction of mechanical signals that result in the acute functional modulation and longer-term transcriptomic and epigenetic regulation of blood vessels. The mechanosensors discussed include ion channels, plasma membrane-associated structures and receptors, and junction proteins. The mechanosignaling pathways presented include the cytoskeleton, integrins, extracellular matrix, and intracellular signaling molecules. These are followed by discussions on mechanical regulation of transcriptome and epigenetics, relevance of mechanotransduction to health and disease, and interactions between VSMCs and ECs. Throughout this review, we offer suggestions for specific topics that require further understanding. In the closing section on conclusions and perspectives, we summarize what is known and point out the need to treat the vasculature as a system, including not only VSMCs and ECs but also the extracellular matrix and other types of cells such as resident macrophages and pericytes, so that we can fully understand the physiology and pathophysiology of the blood vessel as a whole, thus enhancing the comprehension, diagnosis, treatment, and prevention of vascular diseases.
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Affiliation(s)
- Michael J Davis
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Scott Earley
- Department of Pharmacology, University of Nevada, Reno, Nevada
| | - Yi-Shuan Li
- Department of Bioengineering, University of California, San Diego, California
- Institute of Engineering in Medicine, University of California, San Diego, California
| | - Shu Chien
- Department of Bioengineering, University of California, San Diego, California
- Institute of Engineering in Medicine, University of California, San Diego, California
- Department of Medicine, University of California, San Diego, California
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5
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Van Thillo T, Van Deuren V, Dedecker P. Smart genetically-encoded biosensors for the chemical monitoring of living systems. Chem Commun (Camb) 2023; 59:520-534. [PMID: 36519509 DOI: 10.1039/d2cc05363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.
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Affiliation(s)
- Toon Van Thillo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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6
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dos Santos Rodrigues FH, Delgado GG, Santana da Costa T, Tasic L. Applications of fluorescence spectroscopy in protein conformational changes and intermolecular contacts. BBA ADVANCES 2023; 3:100091. [PMID: 37207090 PMCID: PMC10189374 DOI: 10.1016/j.bbadva.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Emission fluorescence is one of the most versatile and powerful biophysical techniques used in several scientific subjects. It is extensively applied in the studies of proteins, their conformations, and intermolecular contacts, such as in protein-ligand and protein-protein interactions, allowing qualitative, quantitative, and structural data elucidation. This review, aimed to outline some of the most widely used fluorescence techniques in this area, illustrate their applications and display a few examples. At first, the data on the intrinsic fluorescence of proteins is disclosed, mainly on the tryptophan side chain. Predominantly, research to study protein conformational changes, protein interactions, and changes in intensities and shifts of the fluorescence emission maximums were discussed. Fluorescence anisotropy or fluorescence polarization is a measurement of the changing orientation of a molecule in space, concerning the time between the absorption and emission events. Absorption and emission indicate the spatial alignment of the molecule's dipoles relative to the electric vector of the electromagnetic wave of excitation and emitted light, respectively. In other words, if the fluorophore population is excited with vertically polarized light, the emitted light will retain some polarization based on how fast it rotates in solution. Therefore, fluorescence anisotropy can be successfully used in protein-protein interaction investigations. Then, green fluorescent proteins (GFPs), photo-transformable fluorescent proteins (FPs) such as photoswitchable and photoconvertible FPs, and those with Large Stokes Shift (LSS) are disclosed in more detail. FPs are potent tools for the study of biological systems. Their versatility and wide range of colours and properties allow many applications. Finally, the application of fluorescence in life sciences is exposed, especially the application of FPs in fluorescence microscopy techniques with super-resolution that enables precise in vivo photolabeling to monitor the movement and interactions of target proteins.
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Affiliation(s)
| | - Gonzalo Garcia Delgado
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Thyerre Santana da Costa
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
- Corresponding author: Ljubica Tasic: IQ, UNICAMP, Rua Josué de Castro sn, 13083-970 Campinas, SP, Brazil
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7
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Suzuki M, Shindo Y, Yamanaka R, Oka K. Live imaging of apoptotic signaling flow using tunable combinatorial FRET-based bioprobes for cell population analysis of caspase cascades. Sci Rep 2022; 12:21160. [PMID: 36476686 PMCID: PMC9729311 DOI: 10.1038/s41598-022-25286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding cellular signaling flow is required to comprehend living organisms. Various live cell imaging tools have been developed but challenges remain due to complex cross-talk between pathways and response heterogeneities among cells. We have focused on multiplex live cell imaging for statistical analysis to address the difficulties and developed simple multiple fluorescence imaging system to quantify cell signaling at single-cell resolution using Förster Resonance Energy Transfer (FRET)-based chimeric molecular sensors comprised of fluorescent proteins and dyes. The dye-fluorescent protein conjugate is robust for a wide selection of combinations, facilitating rearrangement for coordinating emission profile of molecular sensors to adjust for visualization conditions, target phenomena, and simultaneous use. As the molecular sensor could exhibit highly sensitive in detection for protease activity, we customized molecular sensor of caspase-9 and combine the established sensor for caspase-3 to validate the system by observation of caspase-9 and -3 dynamics simultaneously, key signaling flow of apoptosis. We found cumulative caspase-9 activity rather than reaction rate inversely regulated caspase-3 execution times for apoptotic cell death. Imaging-derived statistics were thus applied to discern the dominating aspects of apoptotic signaling unavailable by common live cell imaging and proteomics protein analysis. Adopted to various visualization targets, the technique can discriminate between rivalling explanations and should help unravel other protease involved signaling pathways.
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Affiliation(s)
- Miho Suzuki
- grid.263023.60000 0001 0703 3735Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570 Japan
| | - Yutaka Shindo
- grid.26091.3c0000 0004 1936 9959Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Kanagawa, 223-0061 Japan
| | - Ryu Yamanaka
- grid.469470.80000 0004 0617 5071Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, 756-0884 Japan
| | - Kotaro Oka
- grid.26091.3c0000 0004 1936 9959Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Kanagawa, 223-0061 Japan ,grid.412019.f0000 0000 9476 5696Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan ,grid.5290.e0000 0004 1936 9975Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
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8
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Pellissier-Tanon A, Chouket R, Zhang R, Lahlou A, Espagne A, Lemarchand A, Croquette V, Jullien L, Le Saux T. Resonances at Fundamental and Harmonic Frequencies for Selective Imaging of Sine-Wave Illuminated Reversibly Photoactivatable Labels. Chemphyschem 2022; 23:e202200295. [PMID: 35976176 PMCID: PMC10087976 DOI: 10.1002/cphc.202200295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/15/2022] [Indexed: 01/04/2023]
Abstract
We introduce HIGHLIGHT as a simple and general strategy to selectively image a reversibly photoactivatable fluorescent label associated with a given kinetics. The label is submitted to sine-wave illumination of large amplitude, which generates oscillations of its concentration and fluorescence at higher harmonic frequencies. For singularizing a label, HIGHLIGHT uses specific frequencies and mean light intensities associated with resonances of the amplitudes of concentration and fluorescence oscillations at harmonic frequencies. Several non-redundant resonant observables are simultaneously retrieved from a single experiment with phase-sensitive detection. HIGHLIGHT is used for selective imaging of four spectrally similar fluorescent proteins that had not been discriminated so far. Moreover, labels out of targeted locations can be discarded in an inhomogeneous spatial profile of illumination. HIGHLIGHT opens roads for simplified optical setups at reduced cost and easier maintenance.
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Affiliation(s)
- Agnès Pellissier-Tanon
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Raja Chouket
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Ruikang Zhang
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Aliénor Lahlou
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France.,Sony Computer Science Laboratories, Paris, France
| | - Agathe Espagne
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Annie Lemarchand
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), 4, Place Jussieu, Case Courrier 121, 75252, Paris Cedex 05, France
| | - Vincent Croquette
- Laboratoire de Physique Statistique, Département de Physique and Département de Biologie, École normale supérieure, PSL Research University, F-, 75005, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Thomas Le Saux
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
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9
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Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
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Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
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10
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Yongabi D, Khorshid M, Losada‐Pérez P, Bakhshi Sichani S, Jooken S, Stilman W, Theßeling F, Martens T, Van Thillo T, Verstrepen K, Dedecker P, Vanden Berghe P, Lettinga MP, Bartic C, Lieberzeit P, Schöning MJ, Thoelen R, Fransen M, Wübbenhorst M, Wagner P. Synchronized, Spontaneous, and Oscillatory Detachment of Eukaryotic Cells: A New Tool for Cell Characterization and Identification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200459. [PMID: 35780480 PMCID: PMC9403630 DOI: 10.1002/advs.202200459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Despite the importance of cell characterization and identification for diagnostic and therapeutic applications, developing fast and label-free methods without (bio)-chemical markers or surface-engineered receptors remains challenging. Here, we exploit the natural cellular response to mild thermal stimuli and propose a label- and receptor-free method for fast and facile cell characterization. Cell suspensions in a dedicated sensor are exposed to a temperature gradient, which stimulates synchronized and spontaneous cell-detachment with sharply defined time-patterns, a phenomenon unknown from literature. These patterns depend on metabolic activity (controlled through temperature, nutrients, and drugs) and provide a library of cell-type-specific indicators, allowing to distinguish several yeast strains as well as cancer cells. Under specific conditions, synchronized glycolytic-type oscillations are observed during detachment of mammalian and yeast-cell ensembles, providing additional cell-specific signatures. These findings suggest potential applications for cell viability analysis and for assessing the collective response of cancer cells to drugs.
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Affiliation(s)
- Derick Yongabi
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Mehran Khorshid
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Patricia Losada‐Pérez
- Faculté des SciencesExperimental Soft Matter and Thermal Physics (EST)Université Libre de BruxellesBoulevard du Triomphe ACC.2BrusselsB‐1050Belgium
| | - Soroush Bakhshi Sichani
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Stijn Jooken
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Wouter Stilman
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Florian Theßeling
- Laboratory for Systems BiologyVIB Center for MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenGaston Geenslaan 1HeverleeB‐3001Belgium
| | - Tobie Martens
- Laboratory for Enteric Neuroscience (LENS)Department of Chronic Diseases Metabolism and AgeingKU LeuvenHerestraat 49LeuvenB‐3000Belgium
| | - Toon Van Thillo
- BiochemistryMolecular and Structural BiologyKU LeuvenCelestijnenlaan 200 GLeuvenB‐3001Belgium
| | - Kevin Verstrepen
- Laboratory for Systems BiologyVIB Center for MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenGaston Geenslaan 1HeverleeB‐3001Belgium
| | - Peter Dedecker
- BiochemistryMolecular and Structural BiologyKU LeuvenCelestijnenlaan 200 GLeuvenB‐3001Belgium
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS)Department of Chronic Diseases Metabolism and AgeingKU LeuvenHerestraat 49LeuvenB‐3000Belgium
| | - Minne Paul Lettinga
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
- Biomacromolecular Systems and Processes (IBI‐4)Research Center Jülich GmbHLeo‐Brandt‐StraßeD‐52425JülichGermany
| | - Carmen Bartic
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Peter Lieberzeit
- Faculty of ChemistryDepartment of Physical ChemistryUniversity of ViennaWähringer, Straße 38ViennaA‐1090Austria
| | - Michael J. Schöning
- Institute of Nano‐ and Biotechnologies INBAachen University of Applied SciencesHeinrich‐Mußmann‐Straße 1D‐52428JülichGermany
| | - Ronald Thoelen
- Institute for Materials ResearchHasselt UniversityWetenschapspark 1DiepenbeekB‐3590Belgium
| | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular CommunicationDepartment of Cellular and Molecular MedicineKU LeuvenHerestraat 49LeuvenB‐3000Belgium
| | - Michael Wübbenhorst
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
| | - Patrick Wagner
- Laboratory for Soft Matter and BiophysicsDepartment of Physics and AstronomyKU LeuvenCelestijnenlaan 200 DLeuvenB‐3001Belgium
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11
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Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification. Nat Commun 2022; 13:1850. [PMID: 35387971 PMCID: PMC8986857 DOI: 10.1038/s41467-022-29508-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled absolute quantification (PEAQ) biosensing, a method that leverages the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop proof-of-concept photochromic variants of the popular GCaMP family of Ca2+ biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also develop intermittent quantification, a technique that combines absolute aquisitions with fast fluorescence acquisitions to deliver fast but fully quantitative measurements. We also show how the photochromism-based measurements can be expanded to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems. Biosensors often report relative rather than absolute values. Here the authors report a method that utilises the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity: photochromism-enabled absolute quantification (PEAQ) biosensing.
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12
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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13
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Li W, Zhou J, Maccaferri N, Krahne R, Wang K, Garoli D. Enhanced Optical Spectroscopy for Multiplexed DNA and Protein-Sequencing with Plasmonic Nanopores: Challenges and Prospects. Anal Chem 2022; 94:503-514. [PMID: 34974704 PMCID: PMC8771637 DOI: 10.1021/acs.analchem.1c04459] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Wang Li
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Juan Zhou
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Nicolò Maccaferri
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg, Luxembourg
- Department
of Physics, Umeå University, Linnaeus väg 20, SE-90736 Umeå, Sweden
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
| | - Kang Wang
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
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14
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Valenta H, Hugelier S, Duwé S, Lo Gerfo G, Müller M, Dedecker P, Vandenberg W. Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation. BIOPHYSICAL REPORTS 2021; 1:100026. [PMID: 36425462 PMCID: PMC9680798 DOI: 10.1016/j.bpr.2021.100026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/17/2021] [Indexed: 12/03/2022]
Abstract
Multicolor fluorescence imaging is an excellent method for the simultaneous visualization of multiple structures, although it is limited by the available spectral window. More labels can be measured by distinguishing these on properties, such as their fluorescence dynamics, but usually these dynamics must be directly resolvable by the instrument. We propose an approach to distinguish emitters over a much broader range of light-induced dynamics by combining fast modulation of the light source with the detection of the time-integrated fluorescence. We demonstrate our method by distinguishing four spectrally overlapping photochromic fluorophores within Escherichia coli bacteria, showing that we can accurately classify all four probes by acquiring just two to four fluorescence images. Our strategy expands the range of probes and processes that can be used for fluorescence multiplexing.
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15
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Floerchinger A, Murphy KJ, Latham SL, Warren SC, McCulloch AT, Lee YK, Stoehr J, Mélénec P, Guaman CS, Metcalf XL, Lee V, Zaratzian A, Da Silva A, Tayao M, Rolo S, Phimmachanh M, Sultani G, McDonald L, Mason SM, Ferrari N, Ooms LM, Johnsson AKE, Spence HJ, Olson MF, Machesky LM, Sansom OJ, Morton JP, Mitchell CA, Samuel MS, Croucher DR, Welch HCE, Blyth K, Caldon CE, Herrmann D, Anderson KI, Timpson P, Nobis M. Optimizing metastatic-cascade-dependent Rac1 targeting in breast cancer: Guidance using optical window intravital FRET imaging. Cell Rep 2021; 36:109689. [PMID: 34525350 DOI: 10.1016/j.celrep.2021.109689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 07/06/2021] [Accepted: 08/18/2021] [Indexed: 01/18/2023] Open
Abstract
Assessing drug response within live native tissue provides increased fidelity with regards to optimizing efficacy while minimizing off-target effects. Here, using longitudinal intravital imaging of a Rac1-Förster resonance energy transfer (FRET) biosensor mouse coupled with in vivo photoswitching to track intratumoral movement, we help guide treatment scheduling in a live breast cancer setting to impair metastatic progression. We uncover altered Rac1 activity at the center versus invasive border of tumors and demonstrate enhanced Rac1 activity of cells in close proximity to live tumor vasculature using optical window imaging. We further reveal that Rac1 inhibition can enhance tumor cell vulnerability to fluid-flow-induced shear stress and therefore improves overall anti-metastatic response to therapy during transit to secondary sites such as the lung. Collectively, this study demonstrates the utility of single-cell intravital imaging in vivo to demonstrate that Rac1 inhibition can reduce tumor progression and metastases in an autochthonous setting to improve overall survival.
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Affiliation(s)
- Alessia Floerchinger
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sharissa L Latham
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sean C Warren
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew T McCulloch
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Young-Kyung Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Janett Stoehr
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Pauline Mélénec
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Cris S Guaman
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Xanthe L Metcalf
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Victoria Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew Da Silva
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael Tayao
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sonia Rolo
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Monica Phimmachanh
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Ghazal Sultani
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Laura McDonald
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Susan M Mason
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Nicola Ferrari
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Lisa M Ooms
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | | | - Heather J Spence
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael F Olson
- Department of Chemistry and Biology, Ryerson University, Toronto ON, M5B 2K3, Canada
| | - Laura M Machesky
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Jennifer P Morton
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, SA Pathology and University of South Australia; and the School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David R Croucher
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Heidi C E Welch
- Signalling Programme, Babraham Institute, Cambridge CB223AT, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - C Elizabeth Caldon
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kurt I Anderson
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Francis Crick Institute, London NW11AT, UK
| | - Paul Timpson
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
| | - Max Nobis
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
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16
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Wang YW, Li MH, Zhang SQ, Fang X, Lin MJ. Photochromic and photocontrolled luminescent rare-earth D–A hybrid crystals based on rigid viologen acceptors. CrystEngComm 2021. [DOI: 10.1039/d1ce00789k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Due to the introduction of a strong electron donor, CoIII(CN)63−, into the structure, the rare-earth donor–acceptor (D–A) hybrid crystal shows enhanced photochromism. The coordinative Eu3+ cation is also beneficial toward improving the luminescence.
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Affiliation(s)
- Yi-Wen Wang
- Key Laboratory of Molecule Synthesis and Function Discovery (Fujian Province University), College of Chemistry, Fuzhou University, Fuzhou, 350116, P.R. China
| | - Meng-Hua Li
- Key Laboratory of Molecule Synthesis and Function Discovery (Fujian Province University), College of Chemistry, Fuzhou University, Fuzhou, 350116, P.R. China
| | - Shu-Quan Zhang
- College of Zhicheng, Fuzhou University, 350002, P.R. China
| | - Xin Fang
- Key Laboratory of Molecule Synthesis and Function Discovery (Fujian Province University), College of Chemistry, Fuzhou University, Fuzhou, 350116, P.R. China
| | - Mei-Jin Lin
- Key Laboratory of Molecule Synthesis and Function Discovery (Fujian Province University), College of Chemistry, Fuzhou University, Fuzhou, 350116, P.R. China
- College of Materials Science and Engineering, Fuzhou University, 350116, China
- Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, Fuzhou University, Fuzhou, Fujian, 350002, China
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