1
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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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Thomas A, Upadhyaya K, Bejan D, Adoff H, Cohen MS, Schultz C. A genetically encoded sensor for real-time monitoring of poly-ADP-ribosylation dynamics in-vitro and in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598597. [PMID: 38915511 PMCID: PMC11195289 DOI: 10.1101/2024.06.11.598597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
ADP-ribosylation, the transfer of ADP-ribose (ADPr) from nico-tinamide adenine dinucleotide (NAD+) groups to proteins, is a conserved post-translational modification (PTM) that occurs most prominently in response to DNA damage. ADP-ribosylation is a dynamic PTM regulated by writers (PARPs), erasers (ADPr hy-drolases), and readers (ADPR binders). PARP1 is the primary DNA damage-response writer responsible for adding a polymer of ADPR to proteins (PARylation). Real-time monitoring of PARP1-mediated PARylation, especially in live cells, is critical for under-standing the spatial and temporal regulation of this unique PTM. Here, we describe a genetically encoded FRET probe (pARS) for semi-quantitative monitoring of PARylation dynamics. pARS feature a PAR-binding WWE domain flanked with turquoise and Venus. With a ratiometric readout and excellent signal-to-noise characteristics, we show that pARS can monitor PARP1-dependent PARylation temporally and spatially in real-time. pARS provided unique insights into PARP1-mediated PARylation kinetics in vitro and high-sensitivity detection of PARylation in live cells, even under mild DNA damage. We also show that pARS can be used to determine the potency of PARP inhibitors in vitro and, for the first time, in live cells in response to DNA damage. The robustness and ease of use of pARS make it an important tool for the PARP field.
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3
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Lyons SN, Cambronne XA. A chemical solution for FRET(ful) pairs. Nat Chem Biol 2023; 19:1048-1049. [PMID: 37567947 DOI: 10.1038/s41589-023-01403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Affiliation(s)
- Scott N Lyons
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Xiaolu A Cambronne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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4
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Design and construction of chimeric linker library with controllable flexibilities for precision protein engineering. Methods Enzymol 2020; 647:23-49. [PMID: 33482990 DOI: 10.1016/bs.mie.2020.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Linkers play essential roles in the engineering of fusion proteins, and have been extensively demonstrated to affect protein properties such as expression level, solubility, and biological functions. For linker design and optimization, one of the key factors is the flexibility or rigidity of linkers, which describes the tendency of a linker to maintain a stable conformation when expressed, and can directly contribute to the physical distance between domains of a fusion protein. In this chapter, we discuss the design and engineering of linkers in fusion proteins, and describe a library-based method for optimization of linker flexibility. This approach is based on chimeric linkers, which are composed of both flexible and rigid (helix-forming) linker motifs. We demonstrate that the chimeric linker library capable of controlling the flexibility in a wide range can fill the gap between flexible and rigid linkers by molecular dynamics simulation and fluorescence resonance energy transfer experiments, as well as its applications in fusion protein optimization.
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5
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Abdelbaki A, Akman HB, Poteau M, Grant R, Gavet O, Guarguaglini G, Lindon C. AURKA destruction is decoupled from its activity at mitotic exit but is essential to suppress interphase activity. J Cell Sci 2020; 133:jcs243071. [PMID: 32393600 PMCID: PMC7328152 DOI: 10.1242/jcs.243071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/19/2020] [Indexed: 12/22/2022] Open
Abstract
Activity of AURKA is controlled through multiple mechanisms including phosphorylation, ubiquitin-mediated degradation and allosteric interaction with TPX2. Activity peaks at mitosis, before AURKA is degraded during and after mitotic exit in a process strictly dependent on the APC/C coactivator FZR1. We used FZR1 knockout cells (FZR1KO) and a novel FRET-based AURKA biosensor to investigate how AURKA activity is regulated in the absence of destruction. We found that AURKA activity in FZR1KO cells dropped at mitotic exit as rapidly as in parental cells, despite absence of AURKA destruction. Unexpectedly, TPX2 was degraded normally in FZR1KO cells. Overexpression of an N-terminal TPX2 fragment sufficient for AURKA binding, but that is not degraded at mitotic exit, caused delay in AURKA inactivation. We conclude that inactivation of AURKA at mitotic exit is determined not by AURKA degradation but by degradation of TPX2 and therefore is dependent on CDC20 rather than FZR1. The biosensor revealed that FZR1 instead suppresses AURKA activity in interphase and is critically required for assembly of the interphase mitochondrial network after mitosis.This article has an associated First Person interview with the first authors of the paper.
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Affiliation(s)
- Ahmed Abdelbaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - H Begum Akman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Marion Poteau
- Institut Gustave Roussy, UMR9019 - CNRS, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Rhys Grant
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Olivier Gavet
- Institut Gustave Roussy, UMR9019 - CNRS, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Roma, Italy
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
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6
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Kriplani N, Duncan RR, Leslie NR. SWAP70 undergoes dynamic conformational regulation at the leading edge of migrating cells. FEBS Lett 2019; 593:395-405. [PMID: 30636036 DOI: 10.1002/1873-3468.13326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 12/23/2018] [Indexed: 01/01/2023]
Abstract
Rearrangements of the actin cytoskeleton are regulated in part by dynamic localised activation and inactivation of Rho family small GTPases. SWAP70 binds to and activates the small GTPase RAC1 as well as binding to filamentous actin and PIP3 . We have developed an encoded biosensor, which uses Forster resonance energy transfer to reveal conformational changes in SWAP70 in live cells. SWAP70 adopts a distinct conformation at the plasma membrane, which in migrating glioma cells is enriched at the leading edge but does not always associate with its PIP3 -dependent translocation to the membrane. This supports a role for SWAP70 in positive feedback activation of RAC1 at sites of filamentous actin, PIP3 and active RAC1.
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Affiliation(s)
- Nisha Kriplani
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Rory R Duncan
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
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7
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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: 302] [Impact Index Per Article: 50.3] [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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8
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Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U, Aulehla A. Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development. Dev Cell 2017; 40:331-341.e4. [PMID: 28245920 PMCID: PMC5337618 DOI: 10.1016/j.devcel.2017.01.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 12/01/2016] [Accepted: 01/27/2017] [Indexed: 12/27/2022]
Abstract
How metabolism is rewired during embryonic development is still largely unknown, as it remains a major technical challenge to resolve metabolic activities or metabolite levels with spatiotemporal resolution. Here, we investigated metabolic changes during development of organogenesis-stage mouse embryos, focusing on the presomitic mesoderm (PSM). We measured glycolytic labeling kinetics from 13C-glucose tracing experiments and detected elevated glycolysis in the posterior, more undifferentiated PSM. We found evidence that the spatial metabolic differences are functionally relevant during PSM development. To enable real-time quantification of a glycolytic metabolite with spatiotemporal resolution, we generated a pyruvate FRET-sensor reporter mouse line. We revealed dynamic changes in cytosolic pyruvate levels as cells transit toward a more anterior PSM state. Combined, our approach identifies a gradient of glycolytic activity across the PSM, and we provide evidence that these spatiotemporal metabolic changes are intrinsically linked to PSM development and differentiation. Identification of glycolytic activity gradient in mouse presomitic mesoderm Development of a pyruvate FRET-reporter mouse model Real-time imaging reveals pyruvate gradient dynamics Metabolic state is linked to presomitic mesoderm cell differentiation
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Affiliation(s)
- Vinay Bulusu
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Nicole Prior
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marteinn T Snaebjornsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Katharina F Sonnen
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jana Kress
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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9
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Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
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Affiliation(s)
- Martin Pelosse
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Cécile Cottet-Rousselle
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Alexei Grichine
- Inserm, U1055 and U1209, Grenoble, France.,Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | | | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France. .,Inserm, U1055 and U1209, Grenoble, France.
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10
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Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmüller U, Schultz C. High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells. Cell Chem Biol 2016; 23:1550-1559. [PMID: 27939899 PMCID: PMC5193178 DOI: 10.1016/j.chembiol.2016.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 01/06/2023]
Abstract
Essential characteristics of cellular signaling networks include a complex interconnected architecture and temporal dynamics of protein activity. The latter can be monitored by Förster resonance energy transfer (FRET) biosensors at a single-live-cell level with high temporal resolution. However, these experiments are typically limited to the use of a couple of FRET biosensors. Here, we describe a FRET-based multi-parameter imaging platform (FMIP) that allows simultaneous high-throughput monitoring of multiple signaling pathways. We apply FMIP to monitor the crosstalk between epidermal growth factor receptor (EGFR) and insulin-like growth factor-1 receptor signaling, signaling perturbations caused by pathophysiologically relevant EGFR mutations, and the effects of a clinically important MEK inhibitor (selumetinib) on the EGFR network. We expect that in the future the platform will be applied to develop comprehensive models of signaling networks and will help to investigate the mechanism of action as well as side effects of therapeutic treatments.
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Affiliation(s)
- Dmitry Kuchenov
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Vibor Laketa
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Florian Salopiata
- Division of Systems Biology of Signal Transduction, Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany; Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97201, USA.
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11
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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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12
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Ohta Y, Kamagata T, Mukai A, Takada S, Nagai T, Horikawa K. Nontrivial Effect of the Color-Exchange of a Donor/Acceptor Pair in the Engineering of Förster Resonance Energy Transfer (FRET)-Based Indicators. ACS Chem Biol 2016; 11:1816-22. [PMID: 27232891 DOI: 10.1021/acschembio.6b00221] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded indicators driven by the Förster resonance energy transfer (FRET) mechanism are reliable tools for live imaging. While the properties of FRET-based indicators have been improved over the years, they often suffer from a poor dynamic range due to the lack of comprehensive understanding about how to apply an appropriate strategy to optimize the FRET parameters. One of the most successful optimizations is the incorporation of circularly permuted fluorescent proteins (cpFPs). To better understand the effects of this strategy, we systematically investigated the properties of the indicators by utilizing a set of FRET backbones consisting of native or one of the most effective cp variants (cp173FPs) with considerations of their order. As a result, the ordering of donor and acceptor FPs, which has been ignored in previous studies, was found to significantly affect the dynamic range of indicators. By utilizing these backbones, we succeeded in improving a cGMP indicator with 3.6-fold increased dynamic range and in generating an ultrasensitive cAMP indicator capable of environmental imaging, demonstrating the practical importance of the ordering of donors and acceptors in the engineering of FRET-based indicators.
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Affiliation(s)
- Yusaku Ohta
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
| | - Takanori Kamagata
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
- Okazaki
Institute for Integrative Bioscience and National Institute for Basic
Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Asuka Mukai
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
| | - Shinji Takada
- Okazaki
Institute for Integrative Bioscience and National Institute for Basic
Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Takeharu Nagai
- The
Institute of Scientific and Industrial Research, Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuki Horikawa
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
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13
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Gheghiani L, Gavet O. Spatiotemporal Investigation of Phosphorylation Events During Cell Cycle Progression. Methods Mol Biol 2016; 1342:157-71. [PMID: 26254922 DOI: 10.1007/978-1-4939-2957-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Polo-like kinase 1 (Plk1) is an essential kinase for mitotic commitment and progression through mitosis. In contrast to its well characterized roles during mitosis, the precise molecular events controlled by Plk1 during G2/M progression and their spatiotemporal regulation are still poorly elucidated. We recently investigated Plk1-dependent regulation of Cdc25C phosphatase, an activator of the master mitotic driver Cyclin B1-Cdk1. To this end, we generated a genetically encoded FRET (Förster Resonance Energy Transfer)-based Cdc25C phosphorylation biosensor to observe Cdc25 spatiotemporal phosphorylation during cell cycle progression in live single cell assays. Because this approach proved to be powerful, we provide here guidelines for the development of biosensors for any phosphorylation site of interest.
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Affiliation(s)
- Lilia Gheghiani
- Sorbonne Universités, UPMC Paris VI, UFR927, 75005, Paris, France
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14
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Large Scale Bacterial Colony Screening of Diversified FRET Biosensors. PLoS One 2015; 10:e0119860. [PMID: 26061878 PMCID: PMC4464885 DOI: 10.1371/journal.pone.0119860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/16/2015] [Indexed: 11/30/2022] Open
Abstract
Biosensors based on Förster Resonance Energy Transfer (FRET) between fluorescent protein mutants have started to revolutionize physiology and biochemistry. However, many types of FRET biosensors show relatively small FRET changes, making measurements with these probes challenging when used under sub-optimal experimental conditions. Thus, a major effort in the field currently lies in designing new optimization strategies for these types of sensors. Here we describe procedures for optimizing FRET changes by large scale screening of mutant biosensor libraries in bacterial colonies. We describe optimization of biosensor expression, permeabilization of bacteria, software tools for analysis, and screening conditions. The procedures reported here may help in improving FRET changes in multiple suitable classes of biosensors.
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15
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Kim TJ, Zheng S, Sun J, Muhamed I, Wu J, Lei L, Kong X, Leckband DE, Wang Y. Dynamic visualization of α-catenin reveals rapid, reversible conformation switching between tension states. Curr Biol 2015; 25:218-224. [PMID: 25544608 PMCID: PMC4302114 DOI: 10.1016/j.cub.2014.11.017] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 12/13/2022]
Abstract
The cytosolic protein α-catenin is a postulated force transducer at cadherin complexes. The demonstration of force activation, identification of consequent downstream events in live cells, and development of tools to study these dynamic processes in living cells are central to elucidating the role of α-catenin in cellular mechanics and tissue function. Here we demonstrate that α-catenin is a force-activatable mechanotransducer at cell-cell junctions by using an engineered α-catenin conformation sensor based on fluorescence resonance energy transfer (FRET). This sensor reconstitutes α-catenin-dependent functions in α-catenin-depleted cells and recapitulates the behavior of the endogenous protein. Dynamic imaging of cells expressing the sensor demonstrated that α-catenin undergoes immediate, reversible conformation switching in direct response to different mechanical perturbations of cadherin adhesions. Combined magnetic twisting cytometry with dynamic FRET imaging revealed rapid, local conformation switching upon the mechanical stimulation of specific cadherin bonds. At acutely stretched cell-cell junctions, the immediate, reversible conformation change further reveals that α-catenin behaves like an elastic spring in series with cadherin and actin. The force-dependent recruitment of vinculin—a principal α-catenin effector—to junctions requires the vinculin binding site of the α-catenin sensor. In cells, the relative rates of force-dependent α-catenin conformation switching and vinculin recruitment reveal that α-catenin activation and vinculin recruitment occur sequentially, rather than in a concerted process, with vinculin accumulation being significantly slower. This engineered α-catenin sensor revealed that α-catenin is a reversible, stretch-activatable sensor that mechanically links cadherin complexes and actin and is an indispensable player in cadherin-specific mechanotransduction at intercellular junctions.
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Affiliation(s)
- Tae-Jin Kim
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shuai Zheng
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jie Sun
- Department of Integrative and Molecular Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ismaeel Muhamed
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun Wu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lei Lei
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xinyu Kong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Deborah E Leckband
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Yingxiao Wang
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Integrative and Molecular Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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16
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Peroza EA, Boumezbeur AH, Zamboni N. Rapid, randomized development of genetically encoded FRET sensors for small molecules. Analyst 2015; 140:4540-8. [DOI: 10.1039/c5an00707k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A generally applicable protocol for random and yet efficient construction of genetically encoded FRET sensors for small molecules was established.
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17
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Lindenburg L, Merkx M. Engineering genetically encoded FRET sensors. SENSORS 2014; 14:11691-713. [PMID: 24991940 PMCID: PMC4168480 DOI: 10.3390/s140711691] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/24/2014] [Accepted: 06/26/2014] [Indexed: 01/15/2023]
Abstract
Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening.
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Affiliation(s)
- Laurens Lindenburg
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600MB, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600MB, The Netherlands.
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18
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Waadt R, Hitomi K, Nishimura N, Hitomi C, Adams SR, Getzoff ED, Schroeder JI. FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis. eLife 2014; 3:e01739. [PMID: 24737861 PMCID: PMC3985518 DOI: 10.7554/elife.01739] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abscisic acid (ABA) is a plant hormone that regulates plant growth and development and mediates abiotic stress responses. Direct cellular monitoring of dynamic ABA concentration changes in response to environmental cues is essential for understanding ABA action. We have developed ABAleons: ABA-specific optogenetic reporters that instantaneously convert the phytohormone-triggered interaction of ABA receptors with PP2C-type phosphatases to send a fluorescence resonance energy transfer (FRET) signal in response to ABA. We report the design, engineering and use of ABAleons with ABA affinities in the range of 100–600 nM to map ABA concentration changes in plant tissues with spatial and temporal resolution. High ABAleon expression can partially repress Arabidopsis ABA responses. ABAleons report ABA concentration differences in distinct cell types, ABA concentration increases in response to low humidity and NaCl in guard cells and to NaCl and osmotic stress in roots and ABA transport from the hypocotyl to the shoot and root. DOI:http://dx.doi.org/10.7554/eLife.01739.001 Plants are able to respond to detrimental changes in their environment—when, for example, water becomes scarce or the soil becomes too salty—in ways that minimize stress and damage caused by these changes. Hormones are chemicals that trigger the plant’s response under these circumstances. Abscisic acid is the hormone that regulates how plants respond to drought and salt stress and that controls the plant growth in these conditions. In the past, it was possible to measure the average level of this hormone in a given tissue, but not the level in individual cells in a living plant. Moreover, it was difficult to follow directly how abscisic acid moved between the plant cells, tissues or organs. Now, Waadt et al. (and independently Jones et al.) have developed tools that can measure the levels of abscisic acid within individual cells in living plants and in real time. The plants were genetically engineered to produce sensor proteins with two properties: they can bind to abscisic acid in a reversible manner, and they contain two ‘tags’ that fluoresce at different wavelengths. Shining light onto the plant at a specific wavelength that is only absorbed by one of the tags actually causes both of the tags on the sensor proteins to fluoresce. However, the sensors fluoresce more at one wavelength when they are bound to abscisic acid, and more at the other wavelength when they are not bound to abscisic acid. Hence, measuring the ratio of these two wavelengths in the light that is given off by the sensor proteins can be used as a measure of the concentration of abscisic acid in a plant cell. Waadt et al. developed sensor proteins called ‘ABAleons’, and used one of these to analyze the uptake, distribution and movement of abscisic acid in different tissues in the model plant Arabidopsis thaliana. Changes in the level of abscisic acid could be detected at the level of an individual plant cell, and over time scales of fractions of seconds to hours. ABAleons also revealed that the concentration of abscisic acid in guard cells—specialized cells that help stop the loss of water vapor from a leaf—increases when humidity levels are low, or when salt levels are high. Low water levels, or high salt levels, also slowly increased the concentration of abscisic acid in the roots of the plant. Furthermore, Waadt et al. saw that abscisic acid moved long distances from the base of the stem up into the shoot, and down to the root. Waadt et al. also report that the ABAleons made plants less responsive to abscisic acid, possibly because binding to the ABAleons reduced the amount of abscisic acid that was available to perform its role as a hormone. The next challenge is to engineer ABAleons that minimize this unwanted side effect, and then go on to use ABAleons to study environmental conditions and proteins involved in plant hormone responses. DOI:http://dx.doi.org/10.7554/eLife.01739.002
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Affiliation(s)
- Rainer Waadt
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, United States
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19
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Rational design of FRET sensor proteins based on mutually exclusive domain interactions. Biochem Soc Trans 2014; 41:1201-5. [PMID: 24059509 DOI: 10.1042/bst20130128] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins that switch between distinct conformational states are ideal to monitor and control molecular processes within the complexity of biological systems. Inspired by the modular architecture of natural signalling proteins, our group explores generic design strategies for the construction of FRET-based sensor proteins and other protein switches. In the present article, I show that designing FRET sensors based on mutually exclusive domain interactions provides a robust method to engineer sensors with predictable properties and an inherently large change in emission ratio. The modularity of this approach should make it easily transferable to other applications of protein switches in fields ranging from synthetic biology, optogenetics and molecular diagnostics.
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20
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Hamers D, van Voorst Vader L, Borst JW, Goedhart J. Development of FRET biosensors for mammalian and plant systems. PROTOPLASMA 2014; 251:333-347. [PMID: 24337770 DOI: 10.1007/s00709-013-0590-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Förster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic processes in living cells. The development of these FRET biosensors requires careful selection of fluorophores, substrates and recognition domains. In this review, we will discuss recent developments, strategies to create and optimise FRET biosensors and applications of FRET-based biosensors for use in the two major eukaryotic kingdoms and elaborate on different methods for FRET detection.
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Affiliation(s)
- Danny Hamers
- Laboratory of Biochemistry and Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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21
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Oldach L, Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. ACTA ACUST UNITED AC 2014; 21:186-97. [PMID: 24485761 DOI: 10.1016/j.chembiol.2013.12.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
Fluorescence-based, genetically encodable biosensors are widely used tools for real-time analysis of biological processes. Over the last few decades, the number of available genetically encodable biosensors and the types of processes they can monitor have increased rapidly. Here, we aim to introduce the reader to general principles and practices in biosensor development and highlight ways in which biosensors can be used to illuminate outstanding questions of biological function. Specifically, we focus on sensors developed for monitoring kinase activity and use them to illustrate some common considerations for biosensor design. We describe several uses to which kinase and second-messenger biosensors have been put, and conclude with considerations for the use of biosensors once they are developed. Overall, as fluorescence-based biosensors continue to diversify and improve, we expect them to continue to be widely used as reliable and fruitful tools for gaining deeper insights into cellular and organismal function.
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Affiliation(s)
- Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Department of Oncology, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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22
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Hu HY, Gehrig S, Reither G, Subramanian D, Mall MA, Plettenburg O, Schultz C. FRET-based and other fluorescent proteinase probes. Biotechnol J 2014; 9:266-81. [PMID: 24464820 DOI: 10.1002/biot.201300201] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 10/25/2013] [Accepted: 12/24/2013] [Indexed: 12/28/2022]
Abstract
The continuous detection of enzyme activities and their application in medical diagnostics is one of the challenges in the translational sciences. Proteinases represent one of the largest groups of enzymes in the human genome and many diseases are based on malfunctions of proteolytic activity. Fluorescent sensors may shed light on regular and irregular proteinase activity in vitro and in vivo and provide a deeper insight into the function of these enzymes and their role in pathophysiological processes. The focus of this review is on Förster resonance energy transfer (FRET)-based proteinase sensors and reporters because these probes are most likely to provide quantitative data. The medical relevance of proteinases are discussed using lung diseases as a prominent example. Probe design and probe targeting are described and fluorescent probe development for disease-relevant proteinases, including matrix-metalloproteinases, cathepsins, caspases, and other selected proteinases, is reviewed.
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Affiliation(s)
- Hai-Yu Hu
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Heidelberg, Germany; Sanofi Deutschland GmbH, Diabetes Division, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
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23
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Gheghiani L, Gavet O. Deciphering the spatio-temporal regulation of entry and progression through mitosis. Biotechnol J 2014; 9:213-23. [DOI: 10.1002/biot.201300194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/19/2013] [Accepted: 12/03/2013] [Indexed: 11/07/2022]
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24
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Belal ASF, Sell BR, Hoi H, Davidson MW, Campbell RE. Optimization of a genetically encoded biosensor for cyclin B1-cyclin dependent kinase 1. ACTA ACUST UNITED AC 2014; 10:191-5. [DOI: 10.1039/c3mb70402e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Ueda Y, Kwok S, Hayashi Y. Application of FRET probes in the analysis of neuronal plasticity. Front Neural Circuits 2013; 7:163. [PMID: 24133415 PMCID: PMC3794420 DOI: 10.3389/fncir.2013.00163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/23/2013] [Indexed: 12/12/2022] Open
Abstract
Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since green fluorescent protein (GFP) was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET), which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM) allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo.
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26
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Affiliation(s)
- Kees Jalink
- Department of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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27
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Zhang C, Wei ZH, Ye BC. Imaging and tracing of intracellular metabolites utilizing genetically encoded fluorescent biosensors. Biotechnol J 2013; 8:1280-91. [DOI: 10.1002/biot.201300001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 12/11/2022]
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28
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Stein F, Kress M, Reither S, Piljić A, Schultz C. FluoQ: a tool for rapid analysis of multiparameter fluorescence imaging data applied to oscillatory events. ACS Chem Biol 2013; 8:1862-8. [PMID: 23882997 DOI: 10.1021/cb4003442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The number of fluorescent sensors and their use in living cells has significantly increased in the past years. Yet, the analysis of data from single cells or cell populations usually remains a very time-consuming enterprise. Here, we introduce FluoQ, a new macro for the image analysis software ImageJ, which enables fast analysis of multiparameter time-lapse fluorescence microscopy data with minimal manual input. FluoQ provides statistical analysis of all measured parameters and delivers the results in multiple graphic and numeric displays. We demonstrate the power of FluoQ by applying the macro to data analysis in the development and optimization of novel FRET reporters for monitoring the performance of calcium/calmodulin-binding inositol trisphosphate kinases A and B (ITPKA and ITPKB) in HeLa cells. We find that conformational changes in the ITPKA-based sensor follow receptor-mediated calcium oscillations. This indicates that ITPKA contributes to the regulation of intracellular calcium transients by limiting inositol trisphosphate levels.
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Affiliation(s)
- Frank Stein
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Manuel Kress
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Sabine Reither
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Alen Piljić
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
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29
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Fritz RD, Letzelter M, Reimann A, Martin K, Fusco L, Ritsma L, Ponsioen B, Fluri E, Schulte-Merker S, van Rheenen J, Pertz O. A versatile toolkit to produce sensitive FRET biosensors to visualize signaling in time and space. Sci Signal 2013; 6:rs12. [PMID: 23882122 DOI: 10.1126/scisignal.2004135] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Genetically encoded, ratiometric biosensors based on fluorescence resonance energy transfer (FRET) are powerful tools to study the spatiotemporal dynamics of cell signaling. However, many biosensors lack sensitivity. We present a biosensor library that contains circularly permutated mutants for both the donor and acceptor fluorophores, which alter the orientation of the dipoles and thus better accommodate structural constraints imposed by different signaling molecules while maintaining FRET efficiency. Our strategy improved the brightness and dynamic range of preexisting RhoA and extracellular signal-regulated protein kinase (ERK) biosensors. Using the improved RhoA biosensor, we found micrometer-sized zones of RhoA activity at the tip of F-actin bundles in growth cone filopodia during neurite extension, whereas RhoA was globally activated throughout collapsing growth cones. RhoA was also activated in filopodia and protruding membranes at the leading edge of motile fibroblasts. Using the improved ERK biosensor, we simultaneously measured ERK activation dynamics in multiple cells using low-magnification microscopy and performed in vivo FRET imaging in zebrafish. Thus, we provide a construction toolkit consisting of a vector set, which enables facile generation of sensitive biosensors.
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Affiliation(s)
- Rafael D Fritz
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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30
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Piatkevich KD, Subach FV, Verkhusha VV. Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals. Chem Soc Rev 2013; 42:3441-52. [PMID: 23361376 PMCID: PMC3618476 DOI: 10.1039/c3cs35458j] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Near-infrared light is favourable for imaging in mammalian tissues due to low absorbance of hemoglobin, melanin, and water. Therefore, fluorescent proteins, biosensors and optogenetic constructs for optimal imaging, optical readout and light manipulation in mammals should have fluorescence and action spectra within the near-infrared window. Interestingly, natural Bacterial Phytochrome Photoreceptors (BphPs) utilize the low molecular weight biliverdin, found in most mammalian tissues, as a photoreactive chromophore. Due to their near-infrared absorbance BphPs are preferred templates for designing optical molecular tools for applications in mammals. Moreover, BphPs spectrally complement existing genetically-encoded probes. Several BphPs were already developed into the near-infrared fluorescent variants. Based on the analysis of the photochemistry and structure of BphPs we suggest a variety of possible BphP-based fluorescent proteins, biosensors, and optogenetic tools. Putative design strategies and experimental considerations for such probes are discussed.
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Affiliation(s)
- Kiryl D. Piatkevich
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
| | - Fedor V. Subach
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
| | - Vladislav V. Verkhusha
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
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31
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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32
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De Meulenaere E, Nguyen Bich N, de Wergifosse M, Van Hecke K, Van Meervelt L, Vanderleyden J, Champagne B, Clays K. Improving the second-order nonlinear optical response of fluorescent proteins: the symmetry argument. J Am Chem Soc 2013; 135:4061-9. [PMID: 23406416 DOI: 10.1021/ja400098b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have successfully designed and expressed a new fluorescent protein with improved second-order nonlinear optical properties. It is the first time that a fluorescent protein has been rationally altered for this particular characteristic. On the basis of the specific noncentrosymmetry requirements for second-order nonlinear optical effects, we had hypothesized that the surprisingly low first hyperpolarizability (β) of the enhanced yellow fluorescent protein (eYFP) could be explained by centrosymmetric stacking of the chromophoric Tyr66 and the neighboring Tyr203 residue. The inversion center was removed by mutating Tyr203 into Phe203, with minor changes in the linear optical properties and even an improved fluorescence quantum yield. Structure determination by X-ray crystallography as well as linear optical characterization corroborate a correct folding and maturation. Measurement of β by means of hyper-Rayleigh scattering (HRS) as well as their analysis using quantum chemistry calculations validate our hypothesis. This observation can eventually lead to improved red fluorescent proteins for even better performance. On the basis of the specific function (second-harmonic generation), the color of its emission, and in analogy with the "fruit" names, we propose SHardonnay as the name for this Tyr203Phe mutant of eYFP.
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Affiliation(s)
- Evelien De Meulenaere
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, BE-3001 Leuven, Belgium
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33
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Dedecker P, De Schryver FC, Hofkens J. Fluorescent Proteins: Shine on, You Crazy Diamond. J Am Chem Soc 2013; 135:2387-402. [DOI: 10.1021/ja309768d] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Peter Dedecker
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Frans C. De Schryver
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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34
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From FRET Imaging to Practical Methodology for Kinase Activity Sensing in Living Cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:145-216. [DOI: 10.1016/b978-0-12-386932-6.00005-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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Nhu Ngoc Van T, Morris MC. Fluorescent Sensors of Protein Kinases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:217-74. [DOI: 10.1016/b978-0-12-386932-6.00006-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Socher E, Imperiali B. FRET-capture: a sensitive method for the detection of dynamic protein interactions. Chembiochem 2012; 14:53-7. [PMID: 23239458 DOI: 10.1002/cbic.201200700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 01/14/2023]
Abstract
Caught in the act: The FRET-Capture approach exploits a bound solvatochromic fluorophore, 4-N,N-dimethylamino-1,8-naphthalimide, as a FRET donor in both inter- and intramolecular energy transfer. A unique feature of this method is the additional level of signal selectivity as the FRET signal is only turned on when the donor is specifically bound to the protein of interest, eliminating high background and false positive signals.
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Affiliation(s)
- Elke Socher
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Park JG, Qin Y, Galati DF, Palmer AE. New sensors for quantitative measurement of mitochondrial Zn(2+). ACS Chem Biol 2012; 7:1636-40. [PMID: 22850482 DOI: 10.1021/cb300171p] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc (Zn(2+)) homeostasis plays a vital role in cell function, and the dysregulation of intracellular Zn(2+) is associated with mitochondrial dysfunction. Few tools exist to quantitatively monitor the buffered, free Zn(2+) concentration in mitochondria of living cells ([Zn(2+)](mito)). We have validated three high dynamic range, ratiometric, genetically encoded, fluorescent Zn(2+) sensors that we have successfully used to precisely measure and monitor [Zn(2+)](mito) in several cell types. Using one of these sensors, called mito-ZapCY1, we report observations that free Zn(2+) is buffered at concentrations about 3 orders of magnitude lower in mitochondria than in the cytosol and that HeLa cells expressing mito-ZapCY1 have an average [Zn(2+)](mito) of 0.14 pM, which differs significantly from other cell types. These optimized mitochondrial Zn(2+) sensors could improve our understanding of the relationship between Zn(2+) homeostasis and mitochondrial function.
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Affiliation(s)
- J. Genevieve Park
- Department of Chemistry
and Biochemistry and BioFrontiers Institute and ‡Department of Molecular, Cellular,
and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yan Qin
- Department of Chemistry
and Biochemistry and BioFrontiers Institute and ‡Department of Molecular, Cellular,
and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Domenico F. Galati
- Department of Chemistry
and Biochemistry and BioFrontiers Institute and ‡Department of Molecular, Cellular,
and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Amy E. Palmer
- Department of Chemistry
and Biochemistry and BioFrontiers Institute and ‡Department of Molecular, Cellular,
and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Schifferer M, Griesbeck O. A Dynamic FRET Reporter of Gene Expression Improved by Functional Screening. J Am Chem Soc 2012; 134:15185-8. [DOI: 10.1021/ja3055673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Martina Schifferer
- Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, 82152
Martinsried, Germany
| | - Oliver Griesbeck
- Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, 82152
Martinsried, Germany
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Mertens HDT, Piljić A, Schultz C, Svergun DI. Conformational analysis of a genetically encoded FRET biosensor by SAXS. Biophys J 2012; 102:2866-75. [PMID: 22735537 DOI: 10.1016/j.bpj.2012.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/09/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022] Open
Abstract
Genetically encoded FRET (Foerster resonance energy transfer) sensors are exciting tools in modern cell biology. Changes in the conformation of a sensor lead to an altered emission ratio and provide the means to determine both temporal and spatial changes in target molecules, as well as the activity of enzymes. FRET sensors are widely used to follow phosphorylation events and to monitor the effects of elevated calcium levels. Here, we report for the first time, to our knowledge, on the analysis of the conformational changes involved in sensor function at low resolution using a combination of in vitro and in cellulo FRET measurements and small-angle scattering of x rays (SAXS). The large and dynamic structural rearrangements involved in the modification of the calcium- and phosphorylation-sensitive probe CYNEX4 are comprehensively characterized. It is demonstrated that the synergistic use of SAXS and FRET methods allows one to resolve the ambiguities arising due to the rotation of the sensor molecules and the flexibility of the probe.
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Affiliation(s)
- Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany
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Thompson AD, Makley LN, McMenimen K, Gestwicki JE. The three cornerstones of chemical biology: innovative probes, new discoveries, and enabling tools. ACS Chem Biol 2012; 7:791-6. [PMID: 22594530 DOI: 10.1021/cb3001827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea D. Thompson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leah N. Makley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kathryn McMenimen
- Department of Chemistry, Mt. Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Jason E. Gestwicki
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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Looger LL, Griesbeck O. Genetically encoded neural activity indicators. Curr Opin Neurobiol 2012; 22:18-23. [DOI: 10.1016/j.conb.2011.10.024] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
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Bruton JD, Cheng AJ, Westerblad H. Methods to Detect Ca2+ in Living Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 740:27-43. [DOI: 10.1007/978-94-007-2888-2_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Rutkowska A, Haering CH, Schultz C. A FlAsH-Based Cross-Linker to Study Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2011; 50:12655-8. [DOI: 10.1002/anie.201106404] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Indexed: 11/11/2022]
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Rutkowska A, Haering CH, Schultz C. FlAsH-basierte Verknüpfungen von Proteinen in lebenden Zellen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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A bacteria colony-based screen for optimal linker combinations in genetically encoded biosensors. BMC Biotechnol 2011; 11:105. [PMID: 22074568 PMCID: PMC3225322 DOI: 10.1186/1472-6750-11-105] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/10/2011] [Indexed: 11/13/2022] Open
Abstract
Background Fluorescent protein (FP)-based biosensors based on the principle of intramolecular Förster resonance energy transfer (FRET) enable the visualization of a variety of biochemical events in living cells. The construction of these biosensors requires the genetic insertion of a judiciously chosen molecular recognition element between two distinct hues of FP. When the molecular recognition element interacts with the analyte of interest and undergoes a conformational change, the ratiometric emission of the construct is altered due to a change in the FRET efficiency. The sensitivity of such biosensors is proportional to the change in ratiometric emission, and so there is a pressing need for methods to maximize the ratiometric change of existing biosensor constructs in order to increase the breadth of their utility. Results To accelerate the development and optimization of improved FRET-based biosensors, we have developed a method for function-based high-throughput screening of biosensor variants in colonies of Escherichia coli. We have demonstrated this technology by undertaking the optimization of a biosensor for detection of methylation of lysine 27 of histone H3 (H3K27). This effort involved the construction and screening of 3 distinct libraries: a domain library that included several engineered binding domains isolated by phage-display; a lower-resolution linker library; and a higher-resolution linker library. Conclusion Application of this library screening methodology led to the identification of an optimized H3K27-trimethylation biosensor that exhibited an emission ratio change (66%) that was 2.3 × improved relative to that of the initially constructed biosensor (29%).
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Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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