51
|
Maryu G, Miura H, Uda Y, Komatsubara AT, Matsuda M, Aoki K. Live-cell Imaging with Genetically Encoded Protein Kinase Activity Reporters. Cell Struct Funct 2018; 43:61-74. [DOI: 10.1247/csf.18003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Gembu Maryu
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences
| | - Haruko Miura
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences
| | - Youichi Uda
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University
| | - Akira T. Komatsubara
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University
- Imaging Platform for Spatio-Temporal Information, Graduate School of Medicine, Kyoto University
| | - Kazuhiro Aoki
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies)
- Imaging Platform for Spatio-Temporal Information, Graduate School of Medicine, Kyoto University
| |
Collapse
|
52
|
Chen B, Su Q, Kong W, Wang Y, Shi P, Wang F. Energy transfer-based biodetection using optical nanomaterials. J Mater Chem B 2018; 6:2924-2944. [DOI: 10.1039/c8tb00614h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review focuses on recent progress in the development of FRET probes and the applications of FRET-based sensing systems.
Collapse
Affiliation(s)
- Bing Chen
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Qianqian Su
- Institute of Nanochemistry and Nanobiology
- Shanghai University
- Shanghai 200444
- China
| | - Wei Kong
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Yuan Wang
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
- China
| | - Peng Shi
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
- China
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
| | - Feng Wang
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| |
Collapse
|
53
|
Bassard JE, Halkier BA. How to prove the existence of metabolons? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:211-227. [PMID: 29755303 PMCID: PMC5932110 DOI: 10.1007/s11101-017-9509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.
Collapse
Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
54
|
SensorFRET: A Standardless Approach to Measuring Pixel-based Spectral Bleed-through and FRET Efficiency using Spectral Imaging. Sci Rep 2017; 7:15609. [PMID: 29142199 PMCID: PMC5688180 DOI: 10.1038/s41598-017-15411-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/25/2017] [Indexed: 12/03/2022] Open
Abstract
Fluorescence microscopy of FRET-based biosensors allow nanoscale interactions to be probed in living cells. This paper describes a novel approach to spectrally resolved fluorescence microscopy, termed sensorFRET, that enables quantitative measurement of FRET efficiency. This approach is an improvement on existing methods (FLIM, sRET, luxFRET, pFRET), as it does not require single fluorophore standards to be measured with every experiment and the acquisition is intensity independent, allowing the laser power to be optimized for varying levels of fluorophore expression. Additionally, it was found that all spectral based methods, including sensorFRET, fail at specific fluorophore-excitation wavelength combinations. These combinations can be determined a priori using sensorFRET, whereas other methods would give no indication of inaccuracies. This method was thoroughly validated and compared to existing methods using simulated spectra, Fluorescein and TAMRA dye mixtures as a zero FRET control, and Cerulean-Venus FRET standards as positive FRET controls. Simulations also provided a means of quantifying the uncertainty in each measurement by relating the fit residual of noisy spectra to the standard deviation of the measured FRET efficiency. As an example application, Teal-Venus force sensitive biosensors integrated into E-cadherin were used to resolve piconewton scale forces along different parts of an individual cell junction.
Collapse
|
55
|
Lagendijk AK, Gomez GA, Baek S, Hesselson D, Hughes WE, Paterson S, Conway DE, Belting HG, Affolter M, Smith KA, Schwartz MA, Yap AS, Hogan BM. Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish. Nat Commun 2017; 8:1402. [PMID: 29123087 PMCID: PMC5680264 DOI: 10.1038/s41467-017-01325-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Forces play diverse roles in vascular development, homeostasis and disease. VE-cadherin at endothelial cell-cell junctions links the contractile acto-myosin cytoskeletons of adjacent cells, serving as a tension-transducer. To explore tensile changes across VE-cadherin in live zebrafish, we tailored an optical biosensor approach, originally established in vitro. We validate localization and function of a VE-cadherin tension sensor (TS) in vivo. Changes in tension across VE-cadherin observed using ratio-metric or lifetime FRET measurements reflect acto-myosin contractility within endothelial cells. Furthermore, we apply the TS to reveal biologically relevant changes in VE-cadherin tension that occur as the dorsal aorta matures and upon genetic and chemical perturbations during embryonic development. Mechanical forces play a crucial role during morphogenesis, but how these are sensed and transduced in vivo is not fully understood. Here the authors apply a FRET tension sensor to live zebrafish and study changes in VE-cadherin tension at endothelial cell-cell junctions during arterial maturation.
Collapse
Affiliation(s)
- Anne Karine Lagendijk
- Institute for Molecular Bioscience, Genomics of Development and Disease division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia.
| | - Guillermo A Gomez
- Institute for Molecular Bioscience, Cell Biology and Molecular Medicine division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia.,Centre for Cancer Biology, SA Pathology and the University of South Australia, Frome Road, Adelaide, 5000, SA, Australia
| | - Sungmin Baek
- Institute for Molecular Bioscience, Genomics of Development and Disease division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia
| | - Daniel Hesselson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, 2010, NSW, Australia
| | - William E Hughes
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, 2010, NSW, Australia
| | - Scott Paterson
- Institute for Molecular Bioscience, Genomics of Development and Disease division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia
| | - Daniel E Conway
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Heinz-Georg Belting
- Biozentrum der Universität Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Markus Affolter
- Biozentrum der Universität Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Kelly A Smith
- Institute for Molecular Bioscience, Genomics of Development and Disease division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia
| | - Martin A Schwartz
- Yale Cardiovascular Research Center and Department of Internal Medicine, Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Alpha S Yap
- Institute for Molecular Bioscience, Cell Biology and Molecular Medicine division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, Genomics of Development and Disease division, The University of Queensland, 306 Carmody Road, St Lucia, 4072, QLD, Australia
| |
Collapse
|
56
|
Camborde L, Jauneau A, Brière C, Deslandes L, Dumas B, Gaulin E. Detection of nucleic acid-protein interactions in plant leaves using fluorescence lifetime imaging microscopy. Nat Protoc 2017; 12:1933-1950. [PMID: 28837131 DOI: 10.1038/nprot.2017.076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA-binding proteins (DNA-BPs) and RNA-binding proteins (RNA-BPs) have critical roles in living cells in all kingdoms of life. Various experimental approaches exist for the study of nucleic acid-protein interactions in vitro and in vivo, but the detection of such interactions at the subcellular level remains challenging. Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM). Proteins of interest (POI) are tagged with a GFP and transiently expressed in plant cells to serve as donor fluorophore. After sample fixation and cell wall permeabilization, leaves are treated with Sytox Orange, a nucleic acid dye that can function as a FRET acceptor. Upon close association of the GFP-tagged POI with Sytox-Orange-stained nucleic acids, a substantial decrease of the GFP lifetime due to FRET between the donor and the acceptor can be monitored. Treatment with RNase before FRET-FLIM measurements allows determination of whether the POI associates with DNA and/or RNA. A step-by-step protocol is provided for sample preparation, data acquisition and analysis. We describe how to calibrate the equipment and include a tutorial explaining the use of the FLIM software. To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis). This protocol allows the detection of protein-nucleic acid interactions in plant cells and can be completed in <2 d.
Collapse
Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, Castanet-Tolosan, France
| | - Christian Brière
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Laurent Deslandes
- LIPM, Université de Toulouse, INRA, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| |
Collapse
|
57
|
Kashima D, Kawade R, Nagamune T, Kawahara M. A Chemically Inducible Helper Module for Detecting Protein–Protein Interactions with Tunable Sensitivity Based on KIPPIS. Anal Chem 2017; 89:4824-4830. [DOI: 10.1021/acs.analchem.6b04063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Daiki Kashima
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Raiji Kawade
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
58
|
Multiplexing PKA and ERK1&2 kinases FRET biosensors in living cells using single excitation wavelength dual colour FLIM. Sci Rep 2017; 7:41026. [PMID: 28106114 PMCID: PMC5247693 DOI: 10.1038/srep41026] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/14/2016] [Indexed: 02/04/2023] Open
Abstract
Monitoring of different signalling enzymes in a single assay using multiplex biosensing provides a multidimensional workspace to elucidate biological processes, signalling pathway crosstalk, and determine precise sequence of events at the single living cell level. In this study, we interrogate the complexity in cAMP/PKA-MAPK/ERK1&2 crosstalk by using multi-parameter biosensing experiments to correlate biochemical activities simultaneously in time and space. Using a single excitation wavelength dual colour FLIM method we are able to detect fluorescence lifetime images of two donors to simultaneously measure PKA and ERK1&2 kinase activities in the same cellular localization by using FRET biosensors. To this end, we excite two FRET donors mTFP1 and LSSmOrange with a 440 nm wavelength and we alleviate spectral bleed-through associated limitations with the very dim-fluorescent acceptor ShadowG for mTFP1 and the red-shifted mKate2 for LSSmOrange. The simultaneous recording of PKA and ERK1&2 kinase activities reveals concomitant EGF-mediated activations of both kinases in HeLa cells. Under these conditions the subsequent Forskolin-induced cAMP release reverses the transient increase of EGF-mediated ERK1&2 kinase activity while reinforcing PKA activation. Here we propose a validated methodology for multiparametric kinase biosensing in living cells using FRET-FLIM.
Collapse
|
59
|
A Guide to Fluorescent Protein FRET Pairs. SENSORS 2016; 16:s16091488. [PMID: 27649177 PMCID: PMC5038762 DOI: 10.3390/s16091488] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022]
Abstract
Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies.
Collapse
|
60
|
Bertolin G, Sizaire F, Herbomel G, Reboutier D, Prigent C, Tramier M. A FRET biosensor reveals spatiotemporal activation and functions of aurora kinase A in living cells. Nat Commun 2016; 7:12674. [PMID: 27624869 PMCID: PMC5027284 DOI: 10.1038/ncomms12674] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/21/2016] [Indexed: 12/20/2022] Open
Abstract
Overexpression of AURKA is a major hallmark of epithelial cancers. It encodes the multifunctional serine/threonine kinase aurora A, which is activated at metaphase and is required for cell cycle progression; assessing its activation in living cells is mandatory for next-generation drug design. We describe here a Förster's resonance energy transfer (FRET) biosensor detecting the conformational changes of aurora kinase A induced by its autophosphorylation on Thr288. The biosensor functionally replaces the endogenous kinase in cells and allows the activation of the kinase to be followed throughout the cell cycle. Inhibiting the catalytic activity of the kinase prevents the conformational changes of the biosensor. Using this approach, we discover that aurora kinase A activates during G1 to regulate the stability of microtubules in cooperation with TPX2 and CEP192. These results demonstrate that the aurora kinase A biosensor is a powerful tool to identify new regulatory pathways controlling aurora kinase A activation.
Collapse
Affiliation(s)
- Giulia Bertolin
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
| | - Florian Sizaire
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
| | - Gaëtan Herbomel
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
| | - David Reboutier
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
- Equipe labéllisée Ligue Contre Le Cancer 2014–2016, Rennes 35043, France
| | - Claude Prigent
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
- Equipe labéllisée Ligue Contre Le Cancer 2014–2016, Rennes 35043, France
| | - Marc Tramier
- CNRS, UMR 6290, Rennes 35043, France
- Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes 35043, France
- Microscopy Rennes Imaging Centre, Biosit, Université de Rennes 1, Rennes 35043, France
| |
Collapse
|
61
|
Finnigan GC, Duvalyan A, Liao EN, Sargsyan A, Thorner J. Detection of protein-protein interactions at the septin collar in Saccharomyces cerevisiae using a tripartite split-GFP system. Mol Biol Cell 2016; 27:2708-25. [PMID: 27385335 PMCID: PMC5007091 DOI: 10.1091/mbc.e16-05-0337] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/30/2016] [Indexed: 01/22/2023] Open
Abstract
A tripartite split-GFP system faithfully reports the order of the subunits in septin hetero-octamers (and thus can serve as a “molecular ruler”), conversely yields little or no false signal even with very highly expressed cytosolic proteins, and detects authentic interactions of other cellular proteins that are bona fide septin-binding proteins. Various methods can provide a readout of the physical interaction between two biomolecules. A recently described tripartite split-GFP system has the potential to report by direct visualization via a fluorescence signal the intimate association of minimally tagged proteins expressed at their endogenous level in their native cellular milieu and can capture transient or weak interactions. Here we document the utility of this tripartite split-GFP system to assess in living cells protein–protein interactions in a dynamic cytoskeletal structure—the septin collar at the yeast bud neck. We show, first, that for septin–septin interactions, this method yields a robust signal whose strength reflects the known spacing between the subunits in septin filaments and thus serves as a “molecular ruler.” Second, the method yields little or no spurious signal even with highly abundant cytosolic proteins readily accessible to the bud neck (including molecular chaperone Hsp82 and glycolytic enzyme Pgk1). Third, using two proteins (Bni5 and Hsl1) that have been shown by other means to bind directly to septins at the bud neck in vivo, we validate that the tripartite split-GFP method yields the same conclusions and further insights about specificity. Finally, we demonstrate the capacity of this approach to uncover additional new information by examining whether three other proteins reported to localize to the bud neck (Nis1, Bud4, and Hof1) are able to interact physically with any of the subunits in the septin collar and, if so, with which ones.
Collapse
Affiliation(s)
- Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Angela Duvalyan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Elizabeth N Liao
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Aspram Sargsyan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| |
Collapse
|
62
|
Zhang Y, Chen Y, Li DDU. Optimizing Laguerre expansion based deconvolution methods for analysing bi-exponential fluorescence lifetime images. OPTICS EXPRESS 2016; 24:13894-905. [PMID: 27410552 DOI: 10.1364/oe.24.013894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fast deconvolution is an essential step to calibrate instrument responses in big fluorescence lifetime imaging microscopy (FLIM) image analysis. This paper examined a computationally effective least squares deconvolution method based on Laguerre expansion (LSD-LE), recently developed for clinical diagnosis applications, and proposed new criteria for selecting Laguerre basis functions (LBFs) without considering the mutual orthonormalities between LBFs. Compared with the previously reported LSD-LE, the improved LSD-LE allows to use a higher laser repetition rate, reducing the acquisition time per measurement. Moreover, we extended it, for the first time, to analyze bi-exponential fluorescence decays for more general FLIM-FRET applications. The proposed method was tested on both synthesized bi-exponential and realistic FLIM data for studying the endocytosis of gold nanorods in Hek293 cells. Compared with the previously reported constrained LSD-LE, it shows promising results.
Collapse
|
63
|
Leng AW, Li D, Chen L, Xia H, Tang Q, Chen B, Gong Q, Gao F, Bi F. Novel Bioluminescent Activatable Reporter for Src Tyrosine Kinase Activity in Living Mice. Theranostics 2016; 6:594-609. [PMID: 26941850 PMCID: PMC4775867 DOI: 10.7150/thno.14306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/27/2016] [Indexed: 02/05/2023] Open
Abstract
Aberrant activation of the Src kinase is implicated in the development of a variety of human malignancies. However, it is almost impossible to monitor Src activity in an in vivo setting with current biochemical techniques. To facilitate the noninvasive investigation of the activity of Src kinase both in vitro and in vivo, we developed a genetically engineered, activatable bioluminescent reporter using split-luciferase complementation. The bioluminescence of this reporter can be used as a surrogate for Src activity in real time. This hybrid luciferase reporter was constructed by sandwiching a Src-dependent conformationally responsive unit (SH2 domain-Srcpep) between the split luciferase fragments. The complementation bioluminescence of this reporter was dependent on the Src activity status. In our study, Src kinase activity in cultured cells and tumor xenografts was monitored quantitatively and dynamically in response to clinical small-molecular kinase inhibitors, dasatinib and saracatinib. This system was also applied for high-throughput screening of Src inhibitors against a kinase inhibitor library in living cells. These results provide unique insights into drug development and pharmacokinetics/phoarmocodynamics of therapeutic drugs targeting Src signaling pathway enabling the optimization of drug administration schedules for maximum benefit. Using both Firefly and Renilla luciferase imaging, we have successfully monitored Src tyrosine kinase activity and Akt serine/threonine kinase activity concurrently in one tumor xenograft. This dual luciferase reporter imaging system will be helpful in exploring the complex signaling networks in vivo. The strategies reported here can also be extended to study and image other important kinases and the cross-talks among them.
Collapse
|
64
|
Chen W, Avezov E, Schlachter SC, Gielen F, Laine RF, Harding HP, Hollfelder F, Ron D, Kaminski CF. A method to quantify FRET stoichiometry with phasor plot analysis and acceptor lifetime ingrowth. Biophys J 2016; 108:999-1002. [PMID: 25762312 PMCID: PMC4375440 DOI: 10.1016/j.bpj.2015.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/23/2014] [Accepted: 01/09/2015] [Indexed: 11/26/2022] Open
Abstract
FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations.
Collapse
Affiliation(s)
- WeiYue Chen
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Edward Avezov
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Simon C Schlachter
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Romain F Laine
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Heather P Harding
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Ron
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
65
|
Hu R, Yap HK, Fung YH, Wang Y, Cheong WL, So LY, Tsang CS, Lee LYS, Lo WKC, Yuan J, Sun N, Leung YC, Yang G, Wong KY. ‘Light up’ protein–protein interaction through bioorthogonal incorporation of a turn-on fluorescent probe into β-lactamase. MOLECULAR BIOSYSTEMS 2016; 12:3544-3549. [DOI: 10.1039/c6mb00566g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aggregation induced emissive compound EPB can detect protein–protein interaction.
Collapse
|
66
|
Chen SJ, Sinsuebphon N, Intes X. Assessment of Gate Width Size on Lifetime-Based Förster Resonance Energy Transfer Parameter Estimation. PHOTONICS 2015; 2:1027-1042. [PMID: 26557647 PMCID: PMC4636205 DOI: 10.3390/photonics2041027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Förster Resonance Energy Transfer (FRET) enables the observation of interactions at the nanoscale level through the use of fluorescence optical imaging techniques. In FRET, fluorescence lifetime imaging can be used to quantify the fluorescence lifetime changes of the donor molecule, which are associated with proximity between acceptor and donor molecules. Among the FRET parameters derived from fluorescence lifetime imaging, the percentage of donor that interacts with the acceptor (in proximity) can be estimated via model-based fitting. However, estimation of the lifetime parameters can be affected by the acquisition parameters such as the temporal characteristics of the imaging system. Herein, we investigate the effect of various gate widths on the accuracy of estimation of FRET parameters with focus on the near-infrared spectral window. Experiments were performed in silico, in vitro, and in vivo with gate width sizes ranging from 300 ps to 1000 ps in intervals of 100 ps. For all cases, the FRET parameters were retrieved accurately and the imaging acquisition time was decreased three-fold. These results indicate that increasing the gate width up to 1000 ps still allows for accurate quantification of FRET interactions even in the case of short lifetimes such as those encountered with near-infrared FRET pairs.
Collapse
Affiliation(s)
| | | | - Xavier Intes
- Author to whom correspondence should be addressed; ; Tel.: +1-518-276-6964
| |
Collapse
|
67
|
Guzmán C, Oetken-Lindholm C, Abankwa D. Automated High-Throughput Fluorescence Lifetime Imaging Microscopy to Detect Protein-Protein Interactions. ACTA ACUST UNITED AC 2015; 21:238-45. [PMID: 26384400 DOI: 10.1177/2211068215606048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/16/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is widely used to study conformational changes of macromolecules and protein-protein, protein-nucleic acid, and protein-small molecule interactions. FRET biosensors can serve as valuable secondary assays in drug discovery and for target validation in mammalian cells. Fluorescence lifetime imaging microscopy (FLIM) allows precise quantification of the FRET efficiency in intact cells, as FLIM is independent of fluorophore concentration, detection efficiency, and fluorescence intensity. We have developed an automated FLIM system using a commercial frequency domain FLIM attachment (Lambert Instruments) for wide-field imaging. Our automated FLIM system is capable of imaging and analyzing up to 50 different positions of a slide in less than 4 min, or the inner 60 wells of a 96-well plate in less than 20 min. Automation is achieved using a motorized stage and controller (Prior Scientific) coupled with a Zeiss Axio Observer body and full integration into the Lambert Instruments FLIM acquisition software. As an application example, we analyze the interaction of the oncoprotein Ras and its effector Raf after drug treatment. In conclusion, our automated FLIM imaging system requires only commercial components and may therefore allow for a broader use of this technique in chemogenomics projects.
Collapse
Affiliation(s)
- Camilo Guzmán
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | | | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| |
Collapse
|
68
|
Abstract
Multiple biological processes are regulated by complicated interaction networks formed by protein-protein or protein-RNA interactions. Nuclear bodies (NBs) are a class of membrane-less subnuclear structures, acting as reaction sites, storage and modification sites, or transcription regulating sites involved in signaling transduction. Biochemical and fluorescence-based methods are widely used to study protein-protein interactions, but false-positive results are a major issue, especially for some fluorescence-based methods. Moreover, these methods fail to be applied to study the formation of NBs, which were characterized by a popular bacterial Lac operator and/or repressor (LacO/LacI) system in mammalian cells. Methods investigating assembly of plant NBs are not available. We have recently developed a nucleolar marker protein nucleolin2 (Nuc2)-based method named Nucleolus-tethering System (NoTS) and showed its application in interaction assay among nucleoplasmic proteins and initiation of plant specific NBs, photobodies. In this extraview, we will compare NoTS with the traditional methods and discuss the assembly mechanisms of NBs, in addition to advantages, limitations, and perspectives about the application of NoTS.
Collapse
Affiliation(s)
- Yin Liu
- a National Key Laboratory of Plant Molecular Genetics; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | | |
Collapse
|
69
|
Cosentino K, Ros U, García-Sáez AJ. Assembling the puzzle: Oligomerization of α-pore forming proteins in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:457-466. [PMID: 26375417 DOI: 10.1016/j.bbamem.2015.09.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 12/21/2022]
Abstract
Pore forming proteins (PFPs) share the ability of creating pores that allow the passage of ions, proteins or other constituents through a wide variety of target membranes, ranging from bacteria to humans. They often cause cell death, as pore formation disrupts the membrane permeability barrier required for maintaining cell homeostasis. The organization into supramolecular complexes or oligomers that pierce the membrane is a common feature of PFPs. However, the molecular pathway of self-assembly and pore opening remains unclear. Here, we review the most recent discoveries in the mechanism of membrane oligomerization and pore formation of a subset of PFPs, the α-PFPs, whose pore-forming domains are formed by helical segments. Only now we are starting to grasp the molecular details of their function, mainly thanks to the introduction of single molecule microscopy and nanoscopy techniques. This article is part of a Special Issue entitled: Pore-forming toxins edited by Mauro Dalla Serra and Franco Gambale.
Collapse
Affiliation(s)
- Katia Cosentino
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Uris Ros
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany.,Center for Protein Studies, Havana University, Havana, Cuba
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany
| |
Collapse
|
70
|
De Los Santos C, Chang CW, Mycek MA, Cardullo RA. FRAP, FLIM, and FRET: Detection and analysis of cellular dynamics on a molecular scale using fluorescence microscopy. Mol Reprod Dev 2015; 82:587-604. [PMID: 26010322 PMCID: PMC4515154 DOI: 10.1002/mrd.22501] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/01/2015] [Indexed: 01/01/2023]
Abstract
The combination of fluorescent-probe technology plus modern optical microscopes allows investigators to monitor dynamic events in living cells with exquisite temporal and spatial resolution. Fluorescence recovery after photobleaching (FRAP), for example, has long been used to monitor molecular dynamics both within cells and on cellular surfaces. Although bound by the diffraction limit imposed on all optical microscopes, the combination of digital cameras and the application of fluorescence intensity information on large-pixel arrays have allowed such dynamic information to be monitored and quantified. Fluorescence lifetime imaging microscopy (FLIM), on the other hand, utilizes the information from an ensemble of fluorophores to probe changes in the local environment. Using either fluorescence-intensity or lifetime approaches, fluorescence resonance energy transfer (FRET) microscopy provides information about molecular interactions, with Ångstrom resolution. In this review, we summarize the theoretical framework underlying these methods and illustrate their utility in addressing important problems in reproductive and developmental systems.
Collapse
Affiliation(s)
- Carla De Los Santos
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
| | - Ching-Wei Chang
- Department of Bioengineering, University of California, Berkeley 94720
| | - Mary-Ann Mycek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Richard A. Cardullo
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
| |
Collapse
|
71
|
Luo S, Jiang Y, Liang Z, Wu J. Quantitative detection of in vivo physical protein-protein interactions based on DNA sequence recognition. J Mol Cell Biol 2015; 7:383-6. [PMID: 26078363 DOI: 10.1093/jmcb/mjv036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Siwei Luo
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science & Technology of China, Hefei, China
| | - Yihua Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science & Technology of China, Hefei, China
| | - Zhi Liang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science & Technology of China, Hefei, China
| | - Jiarui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science & Technology of China, Hefei, China Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China School of Life Science and Technology, Shanghai Tech University, Shanghai, China Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
72
|
Senutovitch N, Vernetti L, Boltz R, DeBiasio R, Gough A, Taylor DL. Fluorescent protein biosensors applied to microphysiological systems. Exp Biol Med (Maywood) 2015; 240:795-808. [PMID: 25990438 PMCID: PMC4464952 DOI: 10.1177/1535370215584934] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This mini-review discusses the evolution of fluorescence as a tool to study living cells and tissues in vitro and the present role of fluorescent protein biosensors (FPBs) in microphysiological systems (MPSs). FPBs allow the measurement of temporal and spatial dynamics of targeted cellular events involved in normal and perturbed cellular assay systems and MPSs in real time. FPBs evolved from fluorescent analog cytochemistry (FAC) that permitted the measurement of the dynamics of purified proteins covalently labeled with environmentally insensitive fluorescent dyes and then incorporated into living cells, as well as a large list of diffusible fluorescent probes engineered to measure environmental changes in living cells. In parallel, a wide range of fluorescence microscopy methods were developed to measure the chemical and molecular activities of the labeled cells, including ratio imaging, fluorescence lifetime, total internal reflection, 3D imaging, including super-resolution, as well as high-content screening. FPBs evolved from FAC by combining environmentally sensitive fluorescent dyes with proteins in order to monitor specific physiological events such as post-translational modifications, production of metabolites, changes in various ion concentrations, and the dynamic interaction of proteins with defined macromolecules in time and space within cells. Original FPBs involved the engineering of fluorescent dyes to sense specific activities when covalently attached to particular domains of the targeted protein. The subsequent development of fluorescent proteins (FPs), such as the green fluorescent protein, dramatically accelerated the adoption of studying living cells, since the genetic "labeling" of proteins became a relatively simple method that permitted the analysis of temporal-spatial dynamics of a wide range of proteins. Investigators subsequently engineered the fluorescence properties of the FPs for environmental sensitivity that, when combined with targeted proteins/peptides, created a new generation of FPBs. Examples of FPBs that are useful in MPS are presented, including the design, testing, and application in a liver MPS.
Collapse
Affiliation(s)
- Nina Senutovitch
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA University of Pittsburgh Department of Computational & Systems Biology, Pittsburgh, PA 15260, USA
| | - Lawrence Vernetti
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA University of Pittsburgh Department of Computational & Systems Biology, Pittsburgh, PA 15260, USA
| | - Robert Boltz
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA University of Pittsburgh Department of Computational & Systems Biology, Pittsburgh, PA 15260, USA
| | - Richard DeBiasio
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA
| | - Albert Gough
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA University of Pittsburgh Department of Computational & Systems Biology, Pittsburgh, PA 15260, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15260, USA University of Pittsburgh Department of Computational & Systems Biology, Pittsburgh, PA 15260, USA
| |
Collapse
|
73
|
Hirsch M, Helm M. Live cell imaging of duplex siRNA intracellular trafficking. Nucleic Acids Res 2015; 43:4650-60. [PMID: 25870407 PMCID: PMC4482072 DOI: 10.1093/nar/gkv307] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/27/2015] [Indexed: 01/08/2023] Open
Abstract
Intracellular distribution of siRNA after in vitro transfection typically depends on lipopolyplexes, which must release the siRNA into the cytosol. Here, the fate of siRNAs was monitored by FRET-based live cell imaging. Subsequent to in situ observation of uptake and release processes, this approach allowed the observation of a number of hitherto uncharacterized intracellular distribution and degradation processes, commencing with a burst of endosomal releases, followed, in some cases, by fast siRNA influx into the nucleus. The continued observation of intact siRNA against a background of free fluorophores resulting from advanced degradation was possible by a specifically developed imaging algorithm, which identified populations of intact siRNA in pixels based on FRET. This proved to be essential in the end point definition of siRNA distribution, which typically featured partially degraded siRNA pools in perinuclear structures. Our results depict the initial 4 h as a critical time window, characterized by fast initial burst release into the cytosol, which lay the foundations for subsequent intracellular distribution of siRNA. Combination with a subsequent slower, but sustained release from endosomal reservoirs may contribute to the efficiency and duration of RNAi, and explain the success of lipopolyplexes in RNAi experiments in cell culture.
Collapse
Affiliation(s)
- Markus Hirsch
- Institute of Pharmacy and Biochemistry, University of Mainz, D-55128 Mainz, Germany Institute of Pharmacy und Molecular Biotechnology, University of Heidelberg, D-69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, University of Mainz, D-55128 Mainz, Germany Institute of Pharmacy und Molecular Biotechnology, University of Heidelberg, D-69120 Heidelberg, Germany
| |
Collapse
|
74
|
Miller KE, Kim Y, Huh WK, Park HO. Bimolecular Fluorescence Complementation (BiFC) Analysis: Advances and Recent Applications for Genome-Wide Interaction Studies. J Mol Biol 2015; 427:2039-2055. [PMID: 25772494 DOI: 10.1016/j.jmb.2015.03.005] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 12/09/2022]
Abstract
Complex protein networks are involved in nearly all cellular processes. To uncover these vast networks of protein interactions, various high-throughput screening technologies have been developed. Over the last decade, bimolecular fluorescence complementation (BiFC) assay has been widely used to detect protein-protein interactions (PPIs) in living cells. This technique is based on the reconstitution of a fluorescent protein in vivo. Easy quantification of the BiFC signals allows effective cell-based high-throughput screenings for protein binding partners and drugs that modulate PPIs. Recently, with the development of large screening libraries, BiFC has been effectively applied for genome-wide PPI studies and has uncovered novel protein interactions, providing new insight into protein functions. In this review, we describe the development of reagents and methods used for BiFC-based screens in yeast, plants, and mammalian cells. We also discuss the advantages and drawbacks of these methods and highlight the application of BiFC in large-scale studies.
Collapse
Affiliation(s)
- Kristi E Miller
- Molecular Cellular Developmental Biology Program, Ohio State University, OH, USA
| | - Yeonsoo Kim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Hay-Oak Park
- Molecular Cellular Developmental Biology Program, Ohio State University, OH, USA
| |
Collapse
|
75
|
Löchte S, Waichman S, Beutel O, You C, Piehler J. Live cell micropatterning reveals the dynamics of signaling complexes at the plasma membrane. ACTA ACUST UNITED AC 2015; 207:407-18. [PMID: 25385185 PMCID: PMC4226739 DOI: 10.1083/jcb.201406032] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The use of micropatterned surfaces that bind HaloTag fusion proteins allows spatial organization of plasma membrane proteins for efficient visualization and quantification of protein–protein interactions in live cells. Interactions of proteins in the plasma membrane are notoriously challenging to study under physiological conditions. We report in this paper a generic approach for spatial organization of plasma membrane proteins into micropatterns as a tool for visualizing and quantifying interactions with extracellular, intracellular, and transmembrane proteins in live cells. Based on a protein-repellent poly(ethylene glycol) polymer brush, micropatterned surface functionalization with the HaloTag ligand for capturing HaloTag fusion proteins and RGD peptides promoting cell adhesion was devised. Efficient micropatterning of the type I interferon (IFN) receptor subunit IFNAR2 fused to the HaloTag was achieved, and highly specific IFN binding to the receptor was detected. The dynamics of this interaction could be quantified on the single molecule level, and IFN-induced receptor dimerization in micropatterns could be monitored. Assembly of active signaling complexes was confirmed by immunostaining of phosphorylated Janus family kinases, and the interaction dynamics of cytosolic effector proteins recruited to the receptor complex were unambiguously quantified by fluorescence recovery after photobleaching.
Collapse
Affiliation(s)
- Sara Löchte
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sharon Waichman
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Oliver Beutel
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| |
Collapse
|
76
|
Mattheyses AL, Marcus AI. Förster resonance energy transfer (FRET) microscopy for monitoring biomolecular interactions. Methods Mol Biol 2015; 1278:329-339. [PMID: 25859959 DOI: 10.1007/978-1-4939-2425-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Förster or Fluorescence resonance energy transfer (FRET) can be used to detect protein-protein interactions. When combined with microscopy, FRET has high temporal and spatial resolution, allowing the interaction dynamics of proteins within specific subcellular compartments to be detected in cells. FRET microscopy has become a powerful technique to assay the direct binding interaction of two proteins in vivo. Here, we describe a sensitized emission method to determine the presence and dynamics of protein-protein interactions in living cells.
Collapse
Affiliation(s)
- Alexa L Mattheyses
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA,
| | | |
Collapse
|
77
|
Guidolin D, Agnati LF, Marcoli M, Borroto-Escuela DO, Fuxe K. G-protein-coupled receptor type A heteromers as an emerging therapeutic target. Expert Opin Ther Targets 2014; 19:265-83. [PMID: 25381716 DOI: 10.1517/14728222.2014.981155] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The discovery of receptor-receptor interactions (RRIs) in the early 1980s provided evidence that G-protein-coupled receptors (GPCRs) operate not only as monomers but also as heteromers, in which integration of the incoming signals takes place already at the plasma membrane level through allosteric RRIs. These integrative mechanisms give sophisticated dynamics to the structure and function of these receptor assemblies in terms of modulation of recognition, G-protein signaling and selectivity and switching to β-arrestin signaling. AREAS COVERED The present review briefly describes the concept of direct RRI and the available data on the mechanisms of oligomer formation. Further, pharmacological data concerning the best characterized heteromers involving type A GPCRs will be analyzed to evaluate their profile as possible targets for the treatment of various diseases, in particular of impacting diseases of the CNS. EXPERT OPINION GPCR heteromers have the potential to open a completely new field for pharmacology with likely a major impact in molecular medicine. Novel pharmacological strategies for the treatment of several pathologies have already been proposed. However, several challenges still exist to accurately characterize the role of the identified heteroreceptor complexes in pathology and to develop heteromer-specific ligands capable of efficiently exploiting their pharmacological features.
Collapse
Affiliation(s)
- Diego Guidolin
- University of Padova, Department of Molecular Medicine , via Gabelli 65, 35121 Padova , Italy +39 049 8272316 ; +39 049 8272319 ;
| | | | | | | | | |
Collapse
|
78
|
Gilbert RJ, Serra MD, Froelich CJ, Wallace MI, Anderluh G. Membrane pore formation at protein–lipid interfaces. Trends Biochem Sci 2014; 39:510-6. [DOI: 10.1016/j.tibs.2014.09.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 11/15/2022]
|
79
|
Implementation of transportation distance for analyzing FLIM and FRET experiments. Bull Math Biol 2014; 76:2596-626. [PMID: 25253276 DOI: 10.1007/s11538-014-0025-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
Abstract
Analysis of fluorescence lifetime imaging microscopy (FLIM) and Förster resonance energy transfer (FRET) experiments in living cells is usually based on mean lifetimes computations. However, these mean lifetimes can induce misinterpretations. We propose in this work the implementation of the transportation distance for FLIM and FRET experiments in vivo. This non-fitting indicator, which is easy to compute, reflects the similarity between two distributions and can be used for pixels clustering to improve the estimation of the FRET parameters. We study the robustness and the discriminating power of this transportation distance, both theoretically and numerically. In addition, a comparison study with the largely used mean lifetime differences is performed. We finally demonstrate practically the benefits of the transportation distance over the usual mean lifetime differences for both FLIM and FRET experiments in living cells.
Collapse
|
80
|
Ma Y, Nagamune T, Kawahara M. Split focal adhesion kinase for probing protein–protein interactions. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
81
|
Detecting protein-protein interactions based on kinase-mediated growth induction of mammalian cells. Sci Rep 2014; 4:6127. [PMID: 25135216 PMCID: PMC4137342 DOI: 10.1038/srep06127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/01/2014] [Indexed: 01/04/2023] Open
Abstract
Detection of protein–protein interactions (PPIs) is important for understanding numerous processes in mammalian cells; however, existing PPI detection methods often give significant background signals. Here, we propose a novel PPI-detection method based on kinase-mediated growth induction of mammalian cells. In this method, target proteins are fused to the intracellular domain of c-kit (c-kit ICD) and expressed in interleukin-3-dependent mammalian cells. The PPI induces dimerization and activation of c-kit ICDs, which leads to cell growth in the absence of interleukin-3. Using this system, we successfully detected the ligand-dependent homo-interaction of FKBPF36V and hetero-interaction of FKBP and FRBT2098L, as well as the constitutive interaction between MDM2 and a known peptide inhibitor. Intriguingly, cells expressing high-affinity peptide chimeras are selected from the mixture of the cell populations dominantly expressing low-affinity peptide chimeras. These results indicate that this method can detect PPIs with low background levels and is suitable for peptide inhibitor screening.
Collapse
|
82
|
Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014; 5:263. [PMID: 25177341 PMCID: PMC4133750 DOI: 10.3389/fgene.2014.00263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks.
Collapse
Affiliation(s)
- Robert H Newman
- Department of Biology, North Carolina Agricultural and Technical State University Greensboro, NC, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; High-Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University Baltimore, MD, USA
| |
Collapse
|
83
|
Zhao Y, Ren J, Padilla-Parra S, Fry EE, Stuart DI. Lysosome sorting of β-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor. Nat Commun 2014; 5:4321. [PMID: 25027712 PMCID: PMC4104448 DOI: 10.1038/ncomms5321] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/05/2014] [Indexed: 01/25/2023] Open
Abstract
The integral membrane protein LIMP-2 has been a paradigm for mannose 6-phosphate receptor (MPR) independent lysosomal targeting, binding to β-glucocerebrosidase (β-GCase) and directing it to the lysosome, before dissociating in the late-endosomal/lysosomal compartments. Here we report structural results illuminating how LIMP-2 binds and releases β-GCase according to changes in pH, via a histidine trigger, and suggesting that LIMP-2 localizes the ceramide portion of the substrate adjacent to the β-GCase catalytic site. Remarkably, we find that LIMP-2 bears P-Man9GlcNAc2 covalently attached to residue N325, and that it binds MPR, via mannose 6-phosphate, with a similar affinity to that observed between LIMP-2 and β-GCase. The binding sites for β-GCase and the MPR are functionally separate, so that a stable ternary complex can be formed. By fluorescence lifetime imaging microscopy, we also demonstrate that LIMP-2 interacts with MPR in living cells. These results revise the accepted view of LIMP-2-β-GCase lysosomal targeting.
Collapse
Affiliation(s)
- Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- These authors contributed equally to this work
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- These authors contributed equally to this work
| | - Sergi Padilla-Parra
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| |
Collapse
|
84
|
Liu Y, Liu Q, Yan Q, Shi L, Fang Y. Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model. Mol Biol Cell 2014; 25:1366-73. [PMID: 24554768 PMCID: PMC3983000 DOI: 10.1091/mbc.e13-09-0527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/27/2014] [Accepted: 02/13/2014] [Indexed: 01/08/2023] Open
Abstract
Protein-protein interactions play essential roles in regulating many biological processes. At the cellular level, many proteins form nuclear foci known as nuclear bodies in which many components interact with each other. Photobodies are nuclear bodies containing proteins for light-signaling pathways in plants. What initiates the formation of photobodies is poorly understood. Here we develop a nucleolar marker protein nucleolin2 (Nuc2)-based method called the nucleolus-tethering system (NoTS) by artificially tethering a protein of interest to the nucleolus to analyze the initiation of photobodies. A candidate initiator is evaluated by visualizing whether a protein fused with Nuc2 forms body-like structures at the periphery of the nucleolus, and other components are recruited to the de novo-formed bodies. The interaction between two proteins can also be revealed through relocation and recruitment of interacting proteins to the nucleolus. Using the NoTS, we test the interactions among components in photobodies. In addition, we demonstrate that components of photobodies such as CONSTITUTIVELY PHOTOMORPHOGENIC 1, photoreceptors, and transcription factors tethered to the nucleolus have the capacity to form body-like structures at the periphery of the nucleolus, which contain other components of photobodies, suggesting a self-organization model for the biogenesis of photobodies.
Collapse
Affiliation(s)
- Yin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingqing Yan
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Leilei Shi
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
85
|
Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
Collapse
Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
| |
Collapse
|
86
|
Moreira JMA, Thorsen SB, Brünner N, Stenvang J. Proximity probing assays for simultaneous visualization of protein complexes in situ. Expert Rev Proteomics 2014; 10:219-21. [PMID: 23777212 DOI: 10.1586/epr.13.22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
EVALUATION OF: Leuchowius KJ, Clausson CM, Grannas K et al. Parallel visualization of multiple protein complexes in individual cells in tumor tissue. Mol. Cell Proteomics doi:10.1074/mcp.O112.023374 (2013) (Epub ahead of print). Techniques for in situ detection and quantification of proteins in fixed tissue remain an important element of both basic biological analyses and clinical biomarker research. The practical importance of such techniques can be exemplified by the everyday clinical use of immunohistochemical detection of the estrogen receptor and HER2 in tissues from breast cancer patients. Several techniques are currently available for detection of single proteins and post-translational modifications, but very few are suitable for detection of protein complexes. Methods that enable simultaneous detection and quantification of protein complexes provide novel possibilities for understanding the biological role(s) of protein complexes and may open new opportunities to improve clinical biomarker research. Leuchowius et al. describe an improved proximity ligation assay for in situ detection of protein complexes, which is able to detect and quantify several protein complexes simultaneously in the same tissue specimen.
Collapse
Affiliation(s)
- José Manuel Afonso Moreira
- Sino-Danish Breast Cancer Research Centre and Danish Centre for Translational Breast Cancer Research, Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 88, 1870 Frederiksberg C, Denmark
| | | | | | | |
Collapse
|
87
|
Piehler J. Spectroscopic techniques for monitoring protein interactions in living cells. Curr Opin Struct Biol 2014; 24:54-62. [DOI: 10.1016/j.sbi.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 12/21/2022]
|
88
|
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.
Collapse
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.
| |
Collapse
|
89
|
Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
90
|
Hanson MR, Sattarzadeh A. Fluorescent labeling and confocal microscopic imaging of chloroplasts and non-green plastids. Methods Mol Biol 2014; 1132:125-43. [PMID: 24599850 DOI: 10.1007/978-1-62703-995-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
While chlorophyll has served as an excellent label for plastids in green tissue, the development of fluorescent proteins has allowed their ready visualization in all tissues of the plants, revealing new features of their morphology and motility. Gene regulatory sequences in plastid transgenes can be optimized through the use of fluorescent protein reporters. Fluorescent labeling of plastids simultaneously with other subcellular locations reveals dynamic interactions and mutant phenotypes. Transient expression of fluorescent protein fusions is particularly valuable to determine whether or not a protein of unknown function is targeted to the plastid. Particle bombardment and agroinfiltration methods described here are convenient for imaging fluorescent proteins in plant organelles. With proper selection of fluorophores for labeling the components of the plant cell, confocal microscopy can produce extremely informative images at high resolution at depths not feasible by standard epifluorescence microscopy.
Collapse
Affiliation(s)
- Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|
91
|
Gulin-Sarfraz T, Sarfraz J, Didem Şen Karaman DŞK, Zhang J, Oetken-Lindholm C, Duchanoy A, Rosenholm JM, Abankwa D. FRET-reporter nanoparticles to monitor redox-induced intracellular delivery of active compounds. RSC Adv 2014. [DOI: 10.1039/c4ra00270a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
FRET-reporter particles for redox-induced release of active compounds in cells were developed. This particle system allowed following the intracellular cleavage of delivered compounds after particle internalization.
Collapse
Affiliation(s)
- Tina Gulin-Sarfraz
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Jawad Sarfraz
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | | | - Jixi Zhang
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | | | - Alain Duchanoy
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Jessica M. Rosenholm
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Daniel Abankwa
- Turku Centre for Biotechnology
- Åbo Akademi University
- 20520 Turku, Finland
| |
Collapse
|
92
|
Jeoung M, Galperin E. Visualizing of signaling proteins on endosomes utilizing knockdown and reconstitution approach. Methods Enzymol 2014; 534:47-63. [PMID: 24359947 DOI: 10.1016/b978-0-12-397926-1.00003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Spatial distribution of intracellular signaling molecules and assembly of signaling complexes are yet to be fully understood. Studies of signaling events in time or space present a particular challenge due to the adverse effects that overexpression of signaling proteins may have on their functions and localization. To follow the distribution of signaling proteins in living cells we developed a methodology named knockdown and reconstitution (KDAR) that allows one to visualize proteins at levels of expression that are close to physiological. This methodology provides a stable expression of "endogenous" shRNA for long-term silencing of the targeted gene and simultaneous expression of a DNA cassette coding for a fluorescently labeled protein, which is insensitive to the targeting shRNA. In this chapter we discuss the needed reagents and outline two experimental approaches to generate KDAR stable cell lines. First, we demonstrate how the plasmid-mediated KDAR approach is successfully utilized to visualize spatial distribution of the GFP-labeled MEK2 in living cells. We then show how the lentivirus-mediated KDAR approach is used to reconstitute and visualize expression of the ERK1/2 scaffold protein Shoc2.
Collapse
Affiliation(s)
- Myoungkun Jeoung
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA.
| |
Collapse
|
93
|
Mérola F, Fredj A, Betolngar DB, Ziegler C, Erard M, Pasquier H. Newly engineered cyan fluorescent proteins with enhanced performances for live cell FRET imaging. Biotechnol J 2013; 9:180-91. [DOI: 10.1002/biot.201300198] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/17/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
|
94
|
Gomes I, Fujita W, Chandrakala MV, Devi LA. Disease-specific heteromerization of G-protein-coupled receptors that target drugs of abuse. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:207-65. [PMID: 23663971 DOI: 10.1016/b978-0-12-386931-9.00009-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Drugs of abuse such as morphine or marijuana exert their effects through the activation of G-protein-coupled receptors (GPCRs), the opioid and cannabinoid receptors, respectively. Moreover, interactions between either of these receptors have been shown to be involved in the rewarding effects of drugs of abuse. Recent advances in the field, using a variety of approaches, have demonstrated that many GPCRs, including opioid, cannabinoid, and dopamine receptors, can form associations between different receptor subtypes or with other GPCRs to form heteromeric complexes. The formation of these complexes, in turn, leads to the modulation of the properties of individual protomers. The development of tools that can selectively disrupt GPCR heteromers as well as monoclonal antibodies that can selectively block signaling by specific heteromer pairs has indicated that heteromers involving opioid, cannabinoid, or dopamine receptors may play a role in various disease states. In this review, we describe evidence for opioid, cannabinoid, and dopamine receptor heteromerization and the potential role of GPCR heteromers in pathophysiological conditions.
Collapse
Affiliation(s)
- Ivone Gomes
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, USA
| | | | | | | |
Collapse
|
95
|
Espenel C, Acharya BR, Kreitzer G. A biosensor of local kinesin activity reveals roles of PKC and EB1 in KIF17 activation. ACTA ACUST UNITED AC 2013; 203:445-55. [PMID: 24189273 PMCID: PMC3824023 DOI: 10.1083/jcb.201305023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We showed previously that the kinesin-2 motor KIF17 regulates microtubule (MT) dynamics and organization to promote epithelial differentiation. How KIF17 activity is regulated during this process remains unclear. Several kinesins, including KIF17, adopt compact and extended conformations that reflect autoinhibited and active states, respectively. We designed biosensors of KIF17 to monitor its activity directly in single cells using fluorescence lifetime imaging to detect Förster resonance energy transfer. Lifetime data are mapped on a phasor plot, allowing us to resolve populations of active and inactive motors in individual cells. Using this biosensor, we demonstrate that PKC contributes to the activation of KIF17 and that this is required for KIF17 to stabilize MTs in epithelia. Furthermore, we show that EB1 recruits KIF17 to dynamic MTs, enabling its accumulation at MT ends and thus promoting MT stabilization at discrete cellular domains.
Collapse
Affiliation(s)
- Cedric Espenel
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY 10021
| | | | | |
Collapse
|
96
|
Binding of the rhesus TRIM5α PRYSPRY domain to capsid is necessary but not sufficient for HIV-1 restriction. Virology 2013; 448:217-28. [PMID: 24314652 DOI: 10.1016/j.virol.2013.10.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/11/2013] [Accepted: 10/07/2013] [Indexed: 11/23/2022]
Abstract
The PRYSPRY domain of TRIM5α provides specificity and the capsid recognition motif to retroviral restriction. Restriction of HIV-1 by rhesus TRIM5α (TRIM5αrh) has been correlated to its ability to bind to the HIV-1 core, suggesting that capsid binding is required for restriction. This work explores whether the PRYSPRY domain of TRIM5αrh exhibits an additional function besides binding to the HIV-1 core. Using our recently described structure of the PRYSPRY domain, we performed an exhaustive structure-function study of the surface and interior residues of the PRYSPRY domain. Testing retroviral restriction and capsid binding of an extensive collection of 60 TRIM5αrh PRYSPRY variants revealed that binding is necessary but not sufficient for restriction. In support of this hypothesis, we showed that some human tripartite motif proteins bind the HIV-1 capsid but do not restrict HIV-1 infection, such as human TRIM6 and TRIM34. Overall this work suggested that the PRYSPRY domain serves an unknown function, distinct from the binding of TRIM5αrh to the HIV-1 core, to block HIV-1 infection.
Collapse
|
97
|
Leavesley SJ, Britain AL, Cichon LK, Nikolaev VO, Rich TC. Assessing FRET using spectral techniques. Cytometry A 2013; 83:898-912. [PMID: 23929684 DOI: 10.1002/cyto.a.22340] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/13/2013] [Accepted: 06/28/2013] [Indexed: 01/21/2023]
Abstract
Förster resonance energy transfer (FRET) techniques have proven invaluable for probing the complex nature of protein-protein interactions, protein folding, and intracellular signaling events. These techniques have traditionally been implemented with the use of one or more fluorescence band-pass filters, either as fluorescence microscopy filter cubes, or as dichroic mirrors and band-pass filters in flow cytometry. In addition, new approaches for measuring FRET, such as fluorescence lifetime and acceptor photobleaching, have been developed. Hyperspectral techniques for imaging and flow cytometry have also shown to be promising for performing FRET measurements. In this study, we have compared traditional (filter-based) FRET approaches to three spectral-based approaches: the ratio of acceptor-to-donor peak emission, linear spectral unmixing, and linear spectral unmixing with a correction for direct acceptor excitation. All methods are estimates of FRET efficiency, except for one-filter set and three-filter set FRET indices, which are included for consistency with prior literature. In the first part of this study, spectrofluorimetric data were collected from a CFP-Epac-YFP FRET probe that has been used for intracellular cAMP measurements. All comparisons were performed using the same spectrofluorimetric datasets as input data, to provide a relevant comparison. Linear spectral unmixing resulted in measurements with the lowest coefficient of variation (0.10) as well as accurate fits using the Hill equation. FRET efficiency methods produced coefficients of variation of less than 0.20, while FRET indices produced coefficients of variation greater than 8.00. These results demonstrate that spectral FRET measurements provide improved response over standard, filter-based measurements. Using spectral approaches, single-cell measurements were conducted through hyperspectral confocal microscopy, linear unmixing, and cell segmentation with quantitative image analysis. Results from these studies confirmed that spectral imaging is effective for measuring subcellular, time-dependent FRET dynamics and that additional fluorescent signals can be readily separated from FRET signals, enabling multilabel studies of molecular interactions. © 2013 International Society for Advancement of Cytometry.
Collapse
Affiliation(s)
- Silas J Leavesley
- Department of Chemical and Biomolecular Engineering, University of South Alabama, Mobile, Alabama, 36688; Department of Pharmacology, University of South Alabama, Mobile, Alabama, 36688
| | | | | | | | | |
Collapse
|
98
|
Leray A, Padilla-Parra S, Roul J, Héliot L, Tramier M. Spatio-Temporal Quantification of FRET in living cells by fast time-domain FLIM: a comparative study of non-fitting methods [corrected]. PLoS One 2013; 8:e69335. [PMID: 23874948 PMCID: PMC3715500 DOI: 10.1371/journal.pone.0069335] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/09/2013] [Indexed: 11/30/2022] Open
Abstract
Förster Resonance Energy Transfer (FRET) measured with Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique to investigate spatio-temporal regulation of protein-protein interactions in living cells. When using standard fitting methods to analyze time domain FLIM, the correct estimation of the FRET parameters requires a high number of photons and therefore long acquisition times which are incompatible with the observation of dynamic protein-protein interactions. Recently, non-fitting strategies have been developed for the analysis of FLIM images: the polar plot or "phasor" and the minimal fraction of interacting donor mfD . We propose here a novel non-fitting strategy based on the calculation of moments. We then compare the performance of these three methods when shortening the acquisition time: either by reducing the number of counted photons N or the number of temporal channels Nch , which is particularly adapted for the original fast-FLIM prototype presented in this work that employs the time gated approach. Based on theoretical calculations, Monte Carlo simulations and experimental data, we determine the domain of validity of each method. We thus demonstrate that the polar approach remains accurate for a large range of conditions (low N, Nch or small fractions of interacting donor fD ). The validity domain of the moments method is more restricted (not applicable when fD <0.25 or when Nch = 4) but it is more precise than the polar approach. We also demonstrate that the mfD is robust in all conditions and it is the most precise strategy; although it does not strictly provide the fraction of interacting donor. We show using the fast-FLIM prototype (with an acquisition rate up to 1 Hz) that these non-fitting strategies are very powerful for on-line analysis on a standard computer and thus for quantifying automatically the spatio-temporal activation of Rac-GTPase in living cells by FRET.
Collapse
Affiliation(s)
- Aymeric Leray
- Institut de Recherche Interdisciplinaire, USR 3078 CNRS, Université de Lille-Nord de France, Biophotonique Cellulaire Fonctionnelle, Villeneuve d'Ascq, France.
| | | | | | | | | |
Collapse
|
99
|
Sun Y, Rombola C, Jyothikumar V, Periasamy A. Förster resonance energy transfer microscopy and spectroscopy for localizing protein-protein interactions in living cells. Cytometry A 2013; 83:780-93. [PMID: 23813736 DOI: 10.1002/cyto.a.22321] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/15/2022]
Abstract
The fundamental theory of Förster resonance energy transfer (FRET) was established in the 1940s. Its great power was only realized in the past 20 years after different techniques were developed and applied to biological experiments. This success was made possible by the availability of suitable fluorescent probes, advanced optics, detectors, microscopy instrumentation, and analytical tools. Combined with state-of-the-art microscopy and spectroscopy, FRET imaging allows scientists to study a variety of phenomena that produce changes in molecular proximity, thereby leading to many significant findings in the life sciences. In this review, we outline various FRET imaging techniques and their strengths and limitations; we also provide a biological model to demonstrate how to investigate protein-protein interactions in living cells using both intensity- and fluorescence lifetime-based FRET microscopy methods.
Collapse
Affiliation(s)
- Yuansheng Sun
- The W.M. Keck Center for Cellular Imaging (KCCI), Department of Biology, Physical and Life Sciences Building, University of Virginia, Charlottesville, Virginia
| | | | | | | |
Collapse
|
100
|
Zeug A, Woehler A, Neher E, Ponimaskin EG. Quantitative intensity-based FRET approaches--a comparative snapshot. Biophys J 2013. [PMID: 23199910 DOI: 10.1016/j.bpj.2012.09.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically encoded FRET-based biosensors. A variety of procedures have been described for measuring FRET efficiency or the relative abundance of donor-acceptor complexes, based on analysis of the donor fluorescence lifetime or the spectrally resolved fluorescence intensity. The latter methods are preferable if one wants to not only quantify the apparent FRET efficiencies but also calculate donor-acceptor stoichiometry and observe fast dynamic changes in the interactions among donor and acceptor molecules in live cells. This review focuses on a comparison of the available intensity-based approaches used to measure FRET. We discuss their strengths and weaknesses in terms of FRET quantification, and provide several examples of biological applications.
Collapse
Affiliation(s)
- André Zeug
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Hannover, Germany
| | | | | | | |
Collapse
|