1
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Tchasovnikarova IA, Marr SK, Damle M, Kingston RE. TRACE generates fluorescent human reporter cell lines to characterize epigenetic pathways. Mol Cell 2022; 82:479-491.e7. [PMID: 34963054 PMCID: PMC8796053 DOI: 10.1016/j.molcel.2021.11.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023]
Abstract
Genetically encoded biosensors are powerful tools to monitor cellular behavior, but the difficulty in generating appropriate reporters for chromatin factors hampers our ability to dissect epigenetic pathways. Here, we present TRACE (transgene reporters across chromatin environments), a high-throughput, genome-wide technique to generate fluorescent human reporter cell lines responsive to manipulation of epigenetic factors. By profiling GFP expression from a large pool of individually barcoded lentiviral integrants in the presence and absence of a perturbation, we identify reporters responsive to pharmacological inhibition of the histone lysine demethylase LSD1 and genetic ablation of the PRC2 subunit SUZ12. Furthermore, by manipulating the HIV-1 host factor LEDGF through targeted deletion or fusion to chromatin reader domains, we alter lentiviral integration site preferences, thus broadening the types of chromatin examined by TRACE. The phenotypic reporters generated through TRACE will allow the genetic interrogation of a broad range of epigenetic pathways, furthering our mechanistic understanding of chromatin biology.
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Affiliation(s)
- Iva A. Tchasovnikarova
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA,The Gurdon Institute, University of Cambridge, Tennis Court
Road, Cambridge, CB2 1QN, UK,Lead Contact,Correspondence should be addressed to:
,
| | - Sharon K. Marr
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA
| | - Robert E. Kingston
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA,Correspondence should be addressed to:
,
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2
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Hardy JC, Mehta S, Zhang J. Measuring Spatiotemporal cAMP Dynamics Within an Endogenous Signaling Compartment Using FluoSTEP-ICUE. Methods Mol Biol 2022; 2483:351-366. [PMID: 35286687 PMCID: PMC9994038 DOI: 10.1007/978-1-0716-2245-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
cAMP is a ubiquitous second messenger involved in the regulation of diverse cellular processes. Spatiotemporal regulation of cAMP through compartmentalization within various subcellular microdomains is essential to ensure specific signaling. In the following protocol, we describe a method for directly visualizing signaling dynamics within cAMP microdomains using fluorescent sensors targeted to endogenous proteins (FluoSTEPs). Instead of overexpressing a biosensor-tagged protein of interest to target a microdomain, FluoSTEP Indicator of cAMP using Epac (FluoSTEP-ICUE) utilizes spontaneously complementing split GFP and CRISPR-Cas9 genome editing to localize a FRET-based cAMP biosensor to an endogenously expressed protein of interest. Utilizing this approach, FluoSTEP-ICUE can be used to measure cAMP levels within endogenous signaling compartments, thus providing a powerful tool for studying the spatiotemporal regulation of cAMP signaling.
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Affiliation(s)
- Julia C Hardy
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, University of California San Diego, La Jolla, CA, USA. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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3
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Kierzek M, Deal PE, Miller EW, Mukherjee S, Wachten D, Baumann A, Kaupp UB, Strünker T, Brenker C. Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes. eLife 2021; 10:e63129. [PMID: 34859780 PMCID: PMC8700268 DOI: 10.7554/elife.63129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Fluorescent probes that change their spectral properties upon binding to small biomolecules, ions, or changes in the membrane potential (Vm) are invaluable tools to study cellular signaling pathways. Here, we introduce a novel technique for simultaneous recording of multiple probes at millisecond time resolution: frequency- and spectrally-tuned multiplexing (FASTM). Different from present multiplexing approaches, FASTM uses phase-sensitive signal detection, which renders various combinations of common probes for Vm and ions accessible for multiplexing. Using kinetic stopped-flow fluorimetry, we show that FASTM allows simultaneous recording of rapid changes in Ca2+, pH, Na+, and Vm with high sensitivity and minimal crosstalk. FASTM is also suited for multiplexing using single-cell microscopy and genetically encoded FRET biosensors. Moreover, FASTM is compatible with optochemical tools to study signaling using light. Finally, we show that the exceptional time resolution of FASTM also allows resolving rapid chemical reactions. Altogether, FASTM opens new opportunities for interrogating cellular signaling.
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Affiliation(s)
- Michelina Kierzek
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- CiM-IMPRS Graduate School, University of MünsterMünsterGermany
| | - Parker E Deal
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Evan W Miller
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular & Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States
| | - Shatanik Mukherjee
- Molecular Sensory Systems, Center of Advanced European Studies and ResearchBonnGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Department of Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Arnd Baumann
- Institute of Biological Information Processing (IBI-1), Research Center JülichJülichGermany
| | - U Benjamin Kaupp
- Life & Medical Sciences Institute (LIMES), University of BonnBonnGermany
| | - Timo Strünker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- Cells in Motion Interfaculty Centre, University of MünsterMünsterGermany
| | - Christoph Brenker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
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4
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Srinivasan P, Griffin NM, Thakur D, Joshi P, Nguyen-Le A, McCotter S, Jain A, Saeidi M, Kulkarni P, Eisdorfer JT, Rothman J, Montell C, Theogarajan L. An Autonomous Molecular Bioluminescent Reporter (AMBER) for Voltage Imaging in Freely Moving Animals. Adv Biol (Weinh) 2021; 5:e2100842. [PMID: 34761564 PMCID: PMC8858017 DOI: 10.1002/adbi.202100842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/08/2021] [Indexed: 11/12/2022]
Abstract
Genetically encoded reporters have greatly increased our understanding of biology. While fluorescent reporters have been widely used, photostability and phototoxicity have hindered their use in long-term experiments. Bioluminescence overcomes some of these challenges but requires the addition of an exogenous luciferin limiting its use. Using a modular approach, Autonomous Molecular BioluminEscent Reporter (AMBER), an indicator of membrane potential is engineered. Unlike other bioluminescent systems, AMBER is a voltage-gated luciferase coupling the functionalities of the Ciona voltage-sensing domain (VSD) and bacterial luciferase, luxAB. When co-expressed with the luciferin-producing genes, AMBER reversibly switches the bioluminescent intensity as a function of membrane potential. Using biophysical and biochemical methods, it is shown that AMBER switches its enzymatic activity from an OFF to an ON state as a function of the membrane potential. Upon depolarization, AMBER switches from a low to a high enzymatic activity state, showing a several-fold increase in the bioluminescence output (ΔL/L). AMBER in the pharyngeal muscles and mechanosensory touch neurons of Caenorhabditis elegans is expressed. Using the compressed sensing approach, the electropharingeogram of the C. elegans pharynx is reconstructed, validating the sensor in vivo. Thus, AMBER represents the first fully genetically encoded bioluminescent reporter without requiring exogenous luciferin addition.
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Affiliation(s)
- Prasanna Srinivasan
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
- Center for Bioengineering, Institute for Collaborative Biotechnologies, University of California Santa Barbara, CA 93106
| | - Nicole M Griffin
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, 93106, USA
- Center for Bioengineering, Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Dhananjay Thakur
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, CA 93106
- The Neuroscience Research Institute, University of California Santa Barbara, CA 93106
| | - Pradeep Joshi
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, CA 93106
| | - Alex Nguyen-Le
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
- Current address: Department of Electrical Engineering, University of Pennsylvania, Philadelphia, PA
| | - Sean McCotter
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
| | - Akshar Jain
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
| | - Mitra Saeidi
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
| | - Prajakta Kulkarni
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
| | - Jaclyn T. Eisdorfer
- College of Creative Studies,University of California Santa Barbara, CA 93106 Current address: Dept. of Bioengineering, Temple University, Philadelphia, PA 19122
| | - Joel Rothman
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, CA 93106
| | - Craig Montell
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, CA 93106
- The Neuroscience Research Institute, University of California Santa Barbara, CA 93106
| | - Luke Theogarajan
- Department of Electrical and Computer Engineering, University of California Santa Barbara, CA 93106
- Center for Bioengineering, Institute for Collaborative Biotechnologies, University of California Santa Barbara, CA 93106
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5
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Zhang L, Takahashi Y, Schroeder JI. Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells. PLANT PHYSIOLOGY 2021; 187:527-536. [PMID: 35142856 PMCID: PMC8491035 DOI: 10.1093/plphys/kiab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/16/2021] [Indexed: 05/15/2023]
Abstract
Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor's working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.
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Affiliation(s)
- Li Zhang
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Yohei Takahashi
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
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6
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Yang Q, Liberali P. Collective behaviours in organoids. Curr Opin Cell Biol 2021; 72:81-90. [PMID: 34332339 PMCID: PMC8533486 DOI: 10.1016/j.ceb.2021.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Abstract
Collective behaviour emerges from interacting units within communities, such as migrating herds, swimming fish schools, and cells within tissues. At the microscopic level, collective behaviours include collective cell migration in development and cancer invasion, rhythmic gene expression in pattern formation, cell competition in homeostasis and cancer, force generation and mechano-sensing in morphogenesis. Studying the initiation and the maintenance of collective cell behaviours is key to understand the principles of development, regeneration and disease. However, the manifold influences of contributing factors in in vivo environments challenge the dissection of causalities in animal models. As an alternative model that has emerged to overcome this difficulty, in vitro three-dimensional organoid cultures provide a reductionist approach yet retain similarities with the in vivo tissue in cellular composition and tissue organisation. Here, we focus on recent progresses in studying collective behaviours in different organoid systems and discuss their advantages and the possibility of improvement for future applications.
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Affiliation(s)
- Qiutan Yang
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel. Petersplatz 1, 4001 Basel, Switzerland.
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7
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Mahlandt EK, Arts JJG, van der Meer WJ, van der Linden FH, Tol S, van Buul JD, Gadella TWJ, Goedhart J. Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor. J Cell Sci 2021; 134:272101. [PMID: 34357388 PMCID: PMC8445605 DOI: 10.1242/jcs.258823] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Rho GTPases are regulatory proteins, which orchestrate cell features such as morphology, polarity and movement. Therefore, probing Rho GTPase activity is key to understanding processes such as development and cell migration. Localization-based reporters for active Rho GTPases are attractive probes to study Rho GTPase-mediated processes in real time with subcellular resolution in living cells and tissue. Until now, relocation Rho biosensors (sensors that relocalize to the native location of active Rho GTPase) seem to have been only useful in certain organisms and have not been characterized well. In this paper, we systematically examined the contribution of the fluorescent protein and Rho-binding peptides on the performance of localization-based sensors. To test the performance, we compared relocation efficiency and specificity in cell-based assays. We identified several improved localization-based, genetically encoded fluorescent biosensors for detecting endogenous Rho activity. This enables a broader application of Rho relocation biosensors, which was demonstrated by using the improved biosensor to visualize Rho activity during several cellular processes, such as cell division, migration and G protein-coupled receptor signaling. Owing to the improved avidity of the new biosensors for Rho activity, cellular processes regulated by Rho can be better understood. This article has an associated First Person interview with the first author of the paper. Summary: The dT-2xrGBD location-based Rho biosensor relocalizes more efficiently than other sensors of this type, and this sensor enables the observation of endogenous Rho activity in cultured cells.
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Affiliation(s)
- Eike K Mahlandt
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Janine J G Arts
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Werner J van der Meer
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franka H van der Linden
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Simon Tol
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Jaap D van Buul
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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8
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Linghu C, Johnson SL, Valdes PA, Shemesh OA, Park WM, Park D, Piatkevich KD, Wassie AT, Liu Y, An B, Barnes SA, Celiker OT, Yao CC, Yu CCJ, Wang R, Adamala KP, Bear MF, Keating AE, Boyden ES. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics. Cell 2020; 183:1682-1698.e24. [PMID: 33232692 DOI: 10.1016/j.cell.2020.10.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022]
Abstract
In order to analyze how a signal transduction network converts cellular inputs into cellular outputs, ideally one would measure the dynamics of many signals within the network simultaneously. We found that, by fusing a fluorescent reporter to a pair of self-assembling peptides, it could be stably clustered within cells at random points, distant enough to be resolved by a microscope but close enough to spatially sample the relevant biology. Because such clusters, which we call signaling reporter islands (SiRIs), can be modularly designed, they permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple nodes of a signal transduction network within single cells. We created SiRIs for indicators of second messengers and kinases and used them, in hippocampal neurons in culture and intact brain slices, to discover relationships between the speed of calcium signaling, and the amplitude of PKA signaling, upon receiving a cAMP-driving stimulus.
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Affiliation(s)
- Changyang Linghu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Shannon L Johnson
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Pablo A Valdes
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Or A Shemesh
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Department of Neurobiology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Demian Park
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Kiryl D Piatkevich
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Asmamaw T Wassie
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Yixi Liu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Bobae An
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Stephanie A Barnes
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Orhan T Celiker
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Chun-Chen Yao
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Chih-Chieh Jay Yu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Ru Wang
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark F Bear
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Amy E Keating
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward S Boyden
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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9
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Hamilton N, Claudio NM, Armstrong RJ, Pucci F. Cell Surface Labeling by Engineered Extracellular Vesicles. ACTA ACUST UNITED AC 2020; 4:e2000007. [PMID: 32390342 DOI: 10.1002/adbi.202000007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023]
Abstract
Extracellular vesicles (EVs) can mediate local and long-range intercellular communication via cell surface signaling. In order to perform in vivo studies of unmanipulated, endogenously released EVs, sensitive but stringent approaches able to detect EV-cell surface interactions are needed. However, isolation and reinfusion of EVs can introduce biases. A rigorous way to study EVs in vivo is by genetically engineering membrane-bound reporters into parental cells. Still, the amount of reporter molecules that EVs can carry is relatively small, and thus, the sensitivity of the approach is suboptimal. This work addresses this issue by engineering EVs to display a membrane-bound form of Sortase A (SrtA), a bacterial transpeptidase that can catalyze the transfer of reporter molecules on the much bigger surface of EV-binding cells. SrtA design and reaction requirements are optimized and validated. Efficient in vitro labeling of EV-binding cells is achieved, even in the presence of only one N-terminal glycine on cell surface proteins. As compared to indirect labeling of EV-binding cells (e.g., using CD63-GFP fusion), the SrtA-based approach shows 1-2 log increase in sensitivity, depending on the EV source. This novel approach will be useful to identify and study the full set of host cells interacting with native EVs in vivo.
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Affiliation(s)
- Nicklas Hamilton
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Natalie M Claudio
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Randall J Armstrong
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Cancer Early Detection Advanced Research (CEDAR), Oregon Health and Science University, Portland, OR, USA
| | - Ferdinando Pucci
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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10
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Bers DM, Xiang YK, Zaccolo M. Whole-Cell cAMP and PKA Activity are Epiphenomena, Nanodomain Signaling Matters. Physiology (Bethesda) 2020; 34:240-249. [PMID: 31165682 DOI: 10.1152/physiol.00002.2019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Novel targeted fluorescent biosensors provide key insights into very local nanodomains of cAMP and PKA activity, and how they respond differently to β-adrenergic activation in cardiac myocytes. This unique spatiotemporal detail in living cells is not available with biochemical measurements of total cellular cAMP and PKA, and provides unique physiological insights.
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Affiliation(s)
- Donald M Bers
- Department of Pharmacology, University of California , Davis, California
| | - Yang K Xiang
- Department of Pharmacology, University of California , Davis, California
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford , Oxford , United Kingdom
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11
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O'Shaughnessy EC, Stone OJ, LaFosse PK, Azoitei ML, Tsygankov D, Heddleston JM, Legant WR, Wittchen ES, Burridge K, Elston TC, Betzig E, Chew TL, Adalsteinsson D, Hahn KM. Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor. J Cell Biol 2019; 218:3153-3160. [PMID: 31444239 PMCID: PMC6719445 DOI: 10.1083/jcb.201903019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/28/2019] [Accepted: 07/25/2019] [Indexed: 11/22/2022] Open
Abstract
O’Shaughnessy et al. present new software called ImageTank to process lattice light-sheet images of FRET biosensors. ImageTank efficiently handles large 3D datasets and includes tools for visualization and analysis. Its capabilities are demonstrated using a new Rap1 biosensor in motile cells. Lattice light-sheet microscopy (LLSM) is valuable for its combination of reduced photobleaching and outstanding spatiotemporal resolution in 3D. Using LLSM to image biosensors in living cells could provide unprecedented visualization of rapid, localized changes in protein conformation or posttranslational modification. However, computational manipulations required for biosensor imaging with LLSM are challenging for many software packages. The calculations require processing large amounts of data even for simple changes such as reorientation of cell renderings or testing the effects of user-selectable settings, and lattice imaging poses unique challenges in thresholding and ratio imaging. We describe here a new software package, named ImageTank, that is specifically designed for practical imaging of biosensors using LLSM. To demonstrate its capabilities, we use a new biosensor to study the rapid 3D dynamics of the small GTPase Rap1 in vesicles and cell protrusions.
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Affiliation(s)
- Ellen C O'Shaughnessy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Orrin J Stone
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Paul K LaFosse
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mihai L Azoitei
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Denis Tsygankov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA
| | - John M Heddleston
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Wesley R Legant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Erika S Wittchen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Keith Burridge
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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12
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Nguyen C, Upadhyay H, Murphy M, Borja G, Rozsahegyi EJ, Barnett A, Brookings T, McManus OB, Werley CA. Simultaneous voltage and calcium imaging and optogenetic stimulation with high sensitivity and a wide field of view. BIOMEDICAL OPTICS EXPRESS 2019; 10:789-806. [PMID: 30800515 PMCID: PMC6377900 DOI: 10.1364/boe.10.000789] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Transmembrane voltage and intracellular calcium concentration are coupled parameters essential to the function of neurons, cardiomyocytes, and other excitable cells. Here we introduce the Firefly-HR microscope for simultaneous optogenetic stimulation and voltage and calcium imaging with fluorescent proteins using three spectrally distinct visible color bands. Firefly-HR combines patterned stimulation, near-total internal reflection laser excitation through a prism located between the sample and a water-immersion objective, and concurrent imaging of three color channels. The microscope has efficient light collection, low fluorescent background, and a large field of view (0.24 x 1.2 mm @ 1000 frames/sec). We characterize optical crosstalk and demonstrate capabilities with three applications: (1) probing synaptically connected neuronal microcircuits, (2) examining the coupling between neuronal action potentials and calcium influx, and (3) studying the pharmacology of paced human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) via simultaneous recordings of voltage, calcium, and contraction.
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13
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Ross B, Wong SH, Snell NE, Zhang J, Rizzo MA. Triple Fluorescence Anisotropy Reporter Imaging in Living Cells. Bio Protoc 2019; 9:ew3226. [PMID: 31423459 DOI: 10.21769/bioprotoc.3226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
FRET-based genetically encoded biosensors incorporate two fluorescent proteins into their design to enable ratiometric biosensing of signaling activities in live cells. While emission ratios are generally useful for quantitative studies, they leave little room in the optical spectrum for additional sensors and optogenetic tools. Homotransfer-based reporters, such as the FLuorescence Anisotropy REporters (FLAREs), incorporate two fluorescent proteins of the same color into their design. Conversion to a single color opens the visible spectrum for the use of complementary sensors. Here, we present a protocol for measuring three independent intracellular signals in living cells. We describe the configuration and calibration of a widefield microscope for multicolor FLARE imaging. Three FLARE sensors for intracellular calcium, MAPK activity, and PKA phosphorylation are co-transfected into HEK293 cells, and triple FRET imaging is performed. Compared to heterotransfer FRET biosensors, the polarization-based multiplex imaging can track multiple signaling activities concurrently in a targeted cell population.
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Affiliation(s)
- Brian Ross
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States.,Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, United States
| | - Shenq Huey Wong
- Department of Physiology, University of Maryland Baltimore, Maryland, United States
| | - Nicole E Snell
- Department of Physiology, University of Maryland Baltimore, Maryland, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States.,Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - M A Rizzo
- Department of Physiology, University of Maryland Baltimore, Maryland, United States
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14
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Snell NE, Rao VP, Seckinger KM, Liang J, Leser J, Mancini AE, Rizzo MA. Homotransfer of FRET Reporters for Live Cell Imaging. BIOSENSORS-BASEL 2018; 8:bios8040089. [PMID: 30314323 PMCID: PMC6316388 DOI: 10.3390/bios8040089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
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Affiliation(s)
- Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Vishnu P Rao
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Kendra M Seckinger
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Junyi Liang
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Jenna Leser
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Allison E Mancini
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
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15
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Zhang Z, Chen W, Zhao Y, Yang Y. Spatiotemporal Imaging of Cellular Energy Metabolism with Genetically-Encoded Fluorescent Sensors in Brain. Neurosci Bull 2018; 34:875-886. [PMID: 29679217 PMCID: PMC6129245 DOI: 10.1007/s12264-018-0229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/24/2018] [Indexed: 12/21/2022] Open
Abstract
The brain has very high energy requirements and consumes 20% of the oxygen and 25% of the glucose in the human body. Therefore, the molecular mechanism underlying how the brain metabolizes substances to support neural activity is a fundamental issue for neuroscience studies. A well-known model in the brain, the astrocyte-neuron lactate shuttle, postulates that glucose uptake and glycolytic activity are enhanced in astrocytes upon neuronal activation and that astrocytes transport lactate into neurons to fulfill their energy requirements. Current evidence for this hypothesis has yet to reach a clear consensus, and new concepts beyond the shuttle hypothesis are emerging. The discrepancy is largely attributed to the lack of a critical method for real-time monitoring of metabolic dynamics at cellular resolution. Recent advances in fluorescent protein-based sensors allow the generation of a sensitive, specific, real-time readout of subcellular metabolites and fill the current technological gap. Here, we summarize the development of genetically encoded metabolite sensors and their applications in assessing cell metabolism in living cells and in vivo, and we believe that these tools will help to address the issue of elucidating neural energy metabolism.
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Affiliation(s)
- Zhuo Zhang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weicai Chen
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China.
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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16
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Werley CA, Chien MP, Cohen AE. Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation. BIOMEDICAL OPTICS EXPRESS 2017; 8:5794-5813. [PMID: 29296505 PMCID: PMC5745120 DOI: 10.1364/boe.8.005794] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/16/2017] [Accepted: 10/31/2017] [Indexed: 05/08/2023]
Abstract
The rapid increase in the number and quality of fluorescent reporters and optogenetic actuators has yielded a powerful set of tools for recording and controlling cellular state and function. To achieve the full benefit of these tools requires improved optical systems with high light collection efficiency, high spatial and temporal resolution, and patterned optical stimulation, in a wide field of view (FOV). Here we describe our 'Firefly' microscope, which achieves these goals in a Ø6 mm FOV. The Firefly optical system is optimized for simultaneous photostimulation and fluorescence imaging in cultured cells. All but one of the optical elements are commercially available, yet the microscope achieves 10-fold higher light collection efficiency at its design magnification than the comparable commercially available microscope using the same objective. The Firefly microscope enables all-optical electrophysiology ('Optopatch') in cultured neurons with a throughput and information content unmatched by other neuronal phenotyping systems. This capability opens possibilities in disease modeling and phenotypic drug screening. We also demonstrate applications of the system to voltage and calcium recordings in human induced pluripotent stem cell derived cardiomyocytes.
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Affiliation(s)
- Christopher A. Werley
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
| | - Miao-Ping Chien
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
| | - Adam E. Cohen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, 17 Oxford St, Cambridge, MA 02138, USA
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17
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Mastop M, Bindels DS, Shaner NC, Postma M, Gadella TWJ, Goedhart J. Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2. Sci Rep 2017; 7:11999. [PMID: 28931898 PMCID: PMC5607329 DOI: 10.1038/s41598-017-12212-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/05/2017] [Indexed: 01/13/2023] Open
Abstract
The performance of Förster Resonance Energy Transfer (FRET) biosensors depends on brightness and photostability, which are dependent on the characteristics of the fluorescent proteins that are employed. Yellow fluorescent protein (YFP) is often used as an acceptor but YFP is prone to photobleaching and pH changes. In this study, we evaluated the properties of a diverse set of acceptor fluorescent proteins in combination with the optimized CFP variant mTurquoise2 as the donor. To determine the theoretical performance of acceptors, the Förster radius was determined. The practical performance was determined by measuring FRET efficiency and photostability of tandem fusion proteins in mammalian cells. Our results show that mNeonGreen is the most efficient acceptor for mTurquoise2 and that the photostability is better than SYFP2. The non-fluorescent YFP variant sREACh is an efficient acceptor, which is useful in lifetime-based FRET experiments. Among the orange and red fluorescent proteins, mCherry and mScarlet-I are the best performing acceptors. Several new pairs were applied in a multimolecular FRET based sensor for detecting activation of a heterotrimeric G-protein by G-protein coupled receptors. Overall, the sensor with mNeonGreen as acceptor and mTurquoise2 as donor showed the highest dynamic range in ratiometric FRET imaging experiments with the G-protein sensor.
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Affiliation(s)
- Marieke Mastop
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Daphne S Bindels
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Nathan C Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, United States of America
| | - Marten Postma
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands.
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18
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Ni Q, Mehta S, Zhang J. Live-cell imaging of cell signaling using genetically encoded fluorescent reporters. FEBS J 2017; 285:203-219. [PMID: 28613457 DOI: 10.1111/febs.14134] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/09/2017] [Indexed: 12/31/2022]
Abstract
Synergistic advances in fluorescent protein engineering and live-cell imaging techniques in recent years have fueled the concurrent development and application of genetically encoded fluorescent reporters that are tailored for tracking signaling dynamics in living systems over multiple length and time scales. These biosensors are uniquely suited for this challenging task, owing to their specificity, sensitivity, and versatility, as well as to the noninvasive and nondestructive nature of fluorescence and the power of genetic encoding. Over the past 10 years, a growing number of fluorescent reporters have been developed for tracking a wide range of biological signals in living cells and animals, including second messenger and metabolite dynamics, enzyme activation and activity, and cell cycle progression and neuronal activity. Many of these biosensors are gaining wide use and are proving to be indispensable for unraveling the complex biological functions of individual signaling molecules in their native environment, the living cell, shedding new light on the structural and molecular underpinnings of cell signaling. In this review, we highlight recent advances in protein engineering that are likely to help expand and improve the design and application of these valuable tools. We then turn our focus to specific examples of live-cell imaging using genetically encoded fluorescent reporters as an important platform for advancing our understanding of G protein-coupled receptor signaling and neuronal activity.
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Affiliation(s)
- Qiang Ni
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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19
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Zhang H, Cohen AE. Optogenetic Approaches to Drug Discovery in Neuroscience and Beyond. Trends Biotechnol 2017; 35:625-639. [PMID: 28552428 PMCID: PMC5495001 DOI: 10.1016/j.tibtech.2017.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/08/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022]
Abstract
Recent advances in optogenetics have opened new routes to drug discovery, particularly in neuroscience. Physiological cellular assays probe functional phenotypes that connect genomic data to patient health. Optogenetic tools, in particular tools for all-optical electrophysiology, now provide a means to probe cellular disease models with unprecedented throughput and information content. These techniques promise to identify functional phenotypes associated with disease states and to identify compounds that improve cellular function regardless of whether the compound acts directly on a target or through a bypass mechanism. This review discusses opportunities and unresolved challenges in applying optogenetic techniques throughout the discovery pipeline - from target identification and validation, to target-based and phenotypic screens, to clinical trials.
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Affiliation(s)
- Hongkang Zhang
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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20
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Newman RH, Zhang J. Integrated Strategies to Gain a Systems-Level View of Dynamic Signaling Networks. Methods Enzymol 2017; 589:133-170. [PMID: 28336062 DOI: 10.1016/bs.mie.2017.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to survive and function properly in the face of an ever changing environment, cells must be able to sense changes in their surroundings and respond accordingly. Cells process information about their environment through complex signaling networks composed of many discrete signaling molecules. Individual pathways within these networks are often tightly integrated and highly dynamic, allowing cells to respond to a given stimulus (or, as is typically the case under physiological conditions, a combination of stimuli) in a specific and appropriate manner. However, due to the size and complexity of many cellular signaling networks, it is often difficult to predict how cellular signaling networks will respond under a particular set of conditions. Indeed, crosstalk between individual signaling pathways may lead to responses that are nonintuitive (or even counterintuitive) based on examination of the individual pathways in isolation. Therefore, to gain a more comprehensive view of cell signaling processes, it is important to understand how signaling networks behave at the systems level. This requires integrated strategies that combine quantitative experimental data with computational models. In this chapter, we first examine some of the progress that has recently been made toward understanding the systems-level regulation of cellular signaling networks, with a particular emphasis on phosphorylation-dependent signaling networks. We then discuss how genetically targetable fluorescent biosensors are being used together with computational models to gain unique insights into the spatiotemporal regulation of signaling networks within single, living cells.
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Affiliation(s)
- Robert H Newman
- North Carolina Agricultural and Technical State University, Greensboro, NC, United States.
| | - Jin Zhang
- University of California, San Diego, San Diego, CA, United States.
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21
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Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.
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Affiliation(s)
- Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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22
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Tenner B, Mehta S, Zhang J. Optical sensors to gain mechanistic insights into signaling assemblies. Curr Opin Struct Biol 2016; 41:203-210. [PMID: 27611602 PMCID: PMC5423777 DOI: 10.1016/j.sbi.2016.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022]
Abstract
Protein complexes play a major role in transducing information from outside the cell into instructions for growth and survival, and understanding how these complexes relay and shape intracellular signals has been a central question in signaling biology. Fluorescent proteins have proven paramount in opening windows for researchers to peer into the architecture and inner workings of signaling assemblies within the living cell and in real-time. In this review, we will provide readers with a current perspective on the development and use of genetically encoded optical probes to dissect the function of signaling complexes.
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Affiliation(s)
- Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States.
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23
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Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR. Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling. Annu Rev Cell Dev Biol 2016; 32:713-741. [DOI: 10.1146/annurev-cellbio-111315-125001] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kazuki Tainaka
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
- PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Shimpei I. Kubota
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatzya Murakami
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka 565-0871, Japan;
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24
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Afsari HS, Cardoso Dos Santos M, Lindén S, Chen T, Qiu X, van Bergen en Henegouwen PMP, Jennings TL, Susumu K, Medintz IL, Hildebrandt N, Miller LW. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging. SCIENCE ADVANCES 2016; 2:e1600265. [PMID: 27386579 PMCID: PMC4928903 DOI: 10.1126/sciadv.1600265] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/19/2016] [Indexed: 05/20/2023]
Abstract
Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions.
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Affiliation(s)
- Hamid Samareh Afsari
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Marcelina Cardoso Dos Santos
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Stina Lindén
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Ting Chen
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Xue Qiu
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | | | | | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Sotera Defense Solutions, Columbia, MD 21046, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Niko Hildebrandt
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
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25
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Leahy M, Thompson K, Zafar H, Alexandrov S, Foley M, O'Flatharta C, Dockery P. Functional imaging for regenerative medicine. Stem Cell Res Ther 2016; 7:57. [PMID: 27095443 PMCID: PMC4837501 DOI: 10.1186/s13287-016-0315-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In vivo imaging is a platform technology with the power to put function in its natural structural context. With the drive to translate stem cell therapies into pre-clinical and clinical trials, early selection of the right imaging techniques is paramount to success. There are many instances in regenerative medicine where the biological, biochemical, and biomechanical mechanisms behind the proposed function of stem cell therapies can be elucidated by appropriate imaging. Imaging techniques can be divided according to whether labels are used and as to whether the imaging can be done in vivo. In vivo human imaging places additional restrictions on the imaging tools that can be used. Microscopies and nanoscopies, especially those requiring fluorescent markers, have made an extraordinary impact on discovery at the molecular and cellular level, but due to their very limited ability to focus in the scattering tissues encountered for in vivo applications they are largely confined to superficial imaging applications in research laboratories. Nanoscopy, which has tremendous benefits in resolution, is limited to the near-field (e.g. near-field scanning optical microscope (NSNOM)) or to very high light intensity (e.g. stimulated emission depletion (STED)) or to slow stochastic events (photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM)). In all cases, nanoscopy is limited to very superficial applications. Imaging depth may be increased using multiphoton or coherence gating tricks. Scattering dominates the limitation on imaging depth in most tissues and this can be mitigated by the application of optical clearing techniques that can impose mild (e.g. topical application of glycerol) or severe (e.g. CLARITY) changes to the tissue to be imaged. Progression of therapies through to clinical trials requires some thought as to the imaging and sensing modalities that should be used. Smoother progression is facilitated by the use of comparable imaging modalities throughout the discovery and trial phases, giving label-free techniques an advantage wherever they can be used, although this is seldom considered in the early stages. In this paper, we will explore the techniques that have found success in aiding discovery in stem cell therapies and try to predict the likely technologies best suited to translation and future directions.
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Affiliation(s)
- Martin Leahy
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland. .,Chair of Applied Physics, National University of Ireland (NUI), Galway, Ireland.
| | - Kerry Thompson
- Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | - Haroon Zafar
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Sergey Alexandrov
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Mark Foley
- Medical Physics Research Cluster, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Cathal O'Flatharta
- Regenerative Medicine Institute (REMEDI), National University of Ireland (NUI), Galway, Ireland
| | - Peter Dockery
- Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
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26
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Depry C, Mehta S, Li R, Zhang J. Visualization of Compartmentalized Kinase Activity Dynamics Using Adaptable BimKARs. ACTA ACUST UNITED AC 2015; 22:1470-1479. [PMID: 26548610 DOI: 10.1016/j.chembiol.2015.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/14/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
The ability to monitor kinase activity dynamics in live cells greatly aids the study of how signaling events are spatiotemporally regulated. Here, we report on the adaptability of bimolecular kinase activity reporters (bimKARs) as molecular tools to enhance the real-time visualization of kinase activity. We demonstrate that the bimKAR design is truly versatile and can be used to monitor a variety of kinases, including JNK, ERK, and AMPK. Furthermore, bimKARs can have significantly enhanced dynamic ranges over their unimolecular counterparts, allowing the elucidation of previously undetectable kinase activity dynamics. Using these newly designed bimKARs, we investigate the regulation of AMPK by protein kinase A (PKA) in the plasma membrane, and demonstrate that PKA can both negatively and positively regulate AMPK activity in the same cell.
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Affiliation(s)
- Charlene Depry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA
| | - Ruojing Li
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA.
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27
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Rowland CE, Brown CW, Medintz IL, Delehanty JB. Intracellular FRET-based probes: a review. Methods Appl Fluoresc 2015; 3:042006. [PMID: 29148511 DOI: 10.1088/2050-6120/3/4/042006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.
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Affiliation(s)
- Clare E Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA. National Research Council, Washington, DC 20036, USA
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28
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Zhang X, Liu C, Wang H, Wang H, Li Z. Rare Earth Ion Mediated Fluorescence Accumulation on a Single Microbead: An Ultrasensitive Strategy for the Detection of Protein Kinase Activity at the Single-Cell Level. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Zhang X, Liu C, Wang H, Wang H, Li Z. Rare Earth Ion Mediated Fluorescence Accumulation on a Single Microbead: An Ultrasensitive Strategy for the Detection of Protein Kinase Activity at the Single-Cell Level. Angew Chem Int Ed Engl 2015; 54:15186-90. [DOI: 10.1002/anie.201507580] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/13/2015] [Indexed: 01/01/2023]
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30
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Dushek O, Lellouch AC, Vaux DJ, Shahrezaei V. Biosensor architectures for high-fidelity reporting of cellular signaling. Biophys J 2015; 107:773-782. [PMID: 25099816 PMCID: PMC4129486 DOI: 10.1016/j.bpj.2014.06.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/26/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022] Open
Abstract
Understanding mechanisms of information processing in cellular signaling networks requires quantitative measurements of protein activities in living cells. Biosensors are molecular probes that have been developed to directly track the activity of specific signaling proteins and their use is revolutionizing our understanding of signal transduction. The use of biosensors relies on the assumption that their activity is linearly proportional to the activity of the signaling protein they have been engineered to track. We use mechanistic mathematical models of common biosensor architectures (single-chain FRET-based biosensors), which include both intramolecular and intermolecular reactions, to study the validity of the linearity assumption. As a result of the classic mechanism of zero-order ultrasensitivity, we find that biosensor activity can be highly nonlinear so that small changes in signaling protein activity can give rise to large changes in biosensor activity and vice versa. This nonlinearity is abolished in architectures that favor the formation of biosensor oligomers, but oligomeric biosensors produce complicated FRET states. Based on this finding, we show that high-fidelity reporting is possible when a single-chain intermolecular biosensor is used that cannot undergo intramolecular reactions and is restricted to forming dimers. We provide phase diagrams that compare various trade-offs, including observer effects, which further highlight the utility of biosensor architectures that favor intermolecular over intramolecular binding. We discuss challenges in calibrating and constructing biosensors and highlight the utility of mathematical models in designing novel probes for cellular signaling.
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Affiliation(s)
- Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom; Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, United Kingdom.
| | - Annemarie C Lellouch
- Aix Marseille Université, Laboratoire d'Adhésion et Inflammation, Marseille, France; Institut National de la Santé et de la Recherche Médicale U1067, Marseille, France; Centre National de la Recherche Scientifique UMR 7333, Marseille, France
| | - David J Vaux
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, United Kingdom.
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31
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Patel N, Gold MG. The genetically encoded tool set for investigating cAMP: more than the sum of its parts. Front Pharmacol 2015; 6:164. [PMID: 26300778 PMCID: PMC4526808 DOI: 10.3389/fphar.2015.00164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/24/2015] [Indexed: 11/13/2022] Open
Abstract
Intracellular fluctuations of the second messenger cyclic AMP (cAMP) are regulated with spatial and temporal precision. This regulation is supported by the sophisticated arrangement of cyclases, phosphodiesterases, anchoring proteins, and receptors for cAMP. Discovery of these nuances to cAMP signaling has been facilitated by the development of genetically encodable tools for monitoring and manipulating cAMP and the proteins that support cAMP signaling. In this review, we discuss the state-of-the-art in development of different genetically encoded tools for sensing cAMP and the activity of its primary intracellular receptor protein kinase A (PKA). We introduce sequences for encoding adenylyl cyclases that enable cAMP levels to be artificially elevated within cells. We chart the evolution of sequences for selectively modifying protein-protein interactions that support cAMP signaling, and for driving cAMP sensors and manipulators to different subcellular locations. Importantly, these different genetically encoded tools can be applied synergistically, and we highlight notable instances that take advantage of this property. Finally, we consider prospects for extending the utility of the tool set to support further insights into the role of cAMP in health and disease.
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Affiliation(s)
- Neha Patel
- Department of Neuroscience, Physiology and Pharmacology, University College London London, UK
| | - Matthew G Gold
- Department of Neuroscience, Physiology and Pharmacology, University College London London, UK
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32
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Venkatachalam V, Cohen AE. Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J 2015; 107:1554-63. [PMID: 25296307 DOI: 10.1016/j.bpj.2014.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/02/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
To study the impact of neural activity on cellular physiology, one would like to combine precise control of firing patterns with highly sensitive probes of cellular physiology. Light-gated ion channels, e.g., Channelrhodopsin-2, enable precise control of firing patterns; green fluorescent protein-based reporters, e.g., the GCaMP6f Ca(2+) reporter, enable highly sensitive probing of cellular physiology. However, for most actuator-reporter combinations, spectral overlap prevents straightforward combination within a single cell. Here we explore multiwavelength control of channelrhodopsins to circumvent this limitation. The "stoplight" technique described in this article uses channelrhodopsin variants that are opened by blue light and closed by orange light. Cells are illuminated with constant blue light to excite fluorescence of a green fluorescent protein-based reporter. Modulated illumination with orange light negatively regulates activation of the channelrhodopsin. We performed detailed photophysical characterization and kinetic modeling of four candidate stoplight channelrhodopsins. The variant with the highest contrast, sdChR(C138S,E154A), enabled all-optical measurements of activity-induced calcium transients in cultured rat hippocampal neurons, although cell-to-cell variation in expression levels presents a challenge for quantification.
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Affiliation(s)
- Veena Venkatachalam
- Biophysics Program, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland.
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33
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Zhou X, Clister TL, Lowry PR, Seldin MM, Wong GW, Zhang J. Dynamic Visualization of mTORC1 Activity in Living Cells. Cell Rep 2015; 10:1767-1777. [PMID: 25772363 DOI: 10.1016/j.celrep.2015.02.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 01/15/2015] [Accepted: 02/09/2015] [Indexed: 12/18/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) senses diverse signals to regulate cell growth and metabolism. It has become increasingly clear that mTORC1 activity is regulated in time and space inside the cell, but direct interrogation of such spatiotemporal regulation is challenging. Here, we describe a genetically encoded mTORC1 activity reporter (TORCAR) that exhibits a change in FRET in response to phosphorylation by mTORC1. Co-imaging mTORC1 activity and calcium dynamics revealed that a growth-factor-induced calcium transient contributes to mTORC1 activity. Dynamic activity maps generated with the use of subcellularly targeted TORCAR uncovered mTORC1 activity not only in cytosol and at the lysosome but also in the nucleus and at the plasma membrane. Furthermore, a wide distribution of activities was observed upon growth factor stimulation, whereas leucine ester, an amino acid surrogate, induces more compartmentalized activities at the lysosome and in the nucleus. Thus, mTORC1 activities are spatiotemporally regulated in a signal-specific manner.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Terri L Clister
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pamela R Lowry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marcus M Seldin
- Department of Physiology and Center for Metabolism and Obesity Research, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - G William Wong
- Department of Physiology and Center for Metabolism and Obesity Research, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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34
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Stein V, Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol 2015; 33:101-10. [DOI: 10.1016/j.tibtech.2014.11.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 12/22/2022]
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35
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Mehta S, Zhang J. Dynamic visualization of calcium-dependent signaling in cellular microdomains. Cell Calcium 2015; 58:333-41. [PMID: 25703691 DOI: 10.1016/j.ceca.2015.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/17/2022]
Abstract
Cells rely on the coordinated action of diverse signaling molecules to sense, interpret, and respond to their highly dynamic external environment. To ensure the specific and robust flow of information, signaling molecules are often spatially organized to form distinct signaling compartments, and our understanding of the molecular mechanisms that guide intracellular signaling hinges on the ability to directly probe signaling events within these cellular microdomains. Ca(2+) signaling in particular owes much of its functional versatility to this type of exquisite spatial regulation. As discussed below, a number of methods have been developed to investigate the mechanistic and functional implications of microdomains of Ca(2+) signaling, ranging from the application of Ca(2+) buffers to the direct and targeted visualization of Ca(2+) signaling microdomains using genetically encoded fluorescent reporters.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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36
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Horch M, Hildebrandt P, Zebger I. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes. Phys Chem Chem Phys 2015; 17:18222-37. [DOI: 10.1039/c5cp02447a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
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37
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Shui B, Lee JC, Reining S, Lee FK, Kotlikoff MI. Optogenetic sensors and effectors: CHROMus-the Cornell Heart Lung Blood Institute Resource for Optogenetic Mouse Signaling. Front Physiol 2014; 5:428. [PMID: 25414670 PMCID: PMC4222331 DOI: 10.3389/fphys.2014.00428] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 01/21/2023] Open
Abstract
Significant progress has been made in the last decade in the development of optogenetic effectors and sensors that can be deployed to understand complex biological signaling in mammals at a molecular level, without disrupting the distributed, lineage specific signaling circuits that comprise nuanced physiological responses. A major barrier to the widespread exploitation of these imaging tools, however, is the lack of readily available genetic reagents that can be easily combined to probe complex biological processes. Ideally, one could envision purpose–produced mouse lines expressing optically compatible sensors and effectors, sensor pairs in distinct lineages, or sensor pairs in discrete subcellular compartments, such that they could be crossed to enable in vivo imaging studies of unprecedented scientific power. Such lines could also be combined with mice to determine the alteration in signaling accompanying targeted gene deletion or addition. In order to address this lack, the National Heart Lung and Blood Institute has recently funded an optogenetic resource designed to create optically compatible, combinatorial mouse lines that will advance NHLBI research. Here we review recent advances in optogenetic sensor and effectors and describe the rationale and goals for the establishment of the Cornell/National Heart Lung Blood Resource for Optogenetic Mouse Signaling (CHROMus).
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Affiliation(s)
- Bo Shui
- Department of Biomedical Sciences, College of Veteirnary Medicine, Cornell University Ithaca, NY, USA
| | - Jane C Lee
- Department of Biomedical Sciences, College of Veteirnary Medicine, Cornell University Ithaca, NY, USA
| | - Shaun Reining
- Department of Biomedical Sciences, College of Veteirnary Medicine, Cornell University Ithaca, NY, USA
| | - Frank K Lee
- Department of Biomedical Sciences, College of Veteirnary Medicine, Cornell University Ithaca, NY, USA
| | - Michael I Kotlikoff
- Department of Biomedical Sciences, College of Veteirnary Medicine, Cornell University Ithaca, NY, USA
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38
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Hou JH, Kralj JM, Douglass AD, Engert F, Cohen AE. Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents. Front Physiol 2014; 5:344. [PMID: 25309445 PMCID: PMC4161048 DOI: 10.3389/fphys.2014.00344] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/22/2014] [Indexed: 01/31/2023] Open
Abstract
The cardiac action potential (AP) and the consequent cytosolic Ca2+ transient are key indicators of cardiac function. Natural developmental processes, as well as many drugs and pathologies change the waveform, propagation, or variability (between cells or over time) of these parameters. Here we apply a genetically encoded dual-function calcium and voltage reporter (CaViar) to study the development of the zebrafish heart in vivo between 1.5 and 4 days post fertilization (dpf). We developed a high-sensitivity spinning disk confocal microscope and associated software for simultaneous three-dimensional optical mapping of voltage and calcium. We produced a transgenic zebrafish line expressing CaViar under control of the heart-specific cmlc2 promoter, and applied ion channel blockers at a series of developmental stages to map the maturation of the action potential in vivo. Early in development, the AP initiated via a calcium current through L-type calcium channels. Between 90 and 102 h post fertilization (hpf), the ventricular AP switched to a sodium-driven upswing, while the atrial AP remained calcium driven. In the adult zebrafish heart, a sodium current drives the AP in both the atrium and ventricle. Simultaneous voltage and calcium imaging with genetically encoded reporters provides a new approach for monitoring cardiac development, and the effects of drugs on cardiac function.
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Affiliation(s)
- Jennifer H Hou
- Department of Physics, Harvard University Cambridge, MA, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University Cambridge, MA, USA
| | - Adam D Douglass
- Department of Molecular and Cellular Biology, Harvard University Cambridge, MA, USA
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University Cambridge, MA, USA
| | - Adam E Cohen
- Department of Physics, Harvard University Cambridge, MA, USA ; Department of Chemistry and Chemical Biology, Harvard University Cambridge, MA, USA ; Howard Hughes Medical Institute Chevy Chase, MD, USA
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39
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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.
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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
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40
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Qi H, Kastenmüller W, Germain RN. Spatiotemporal basis of innate and adaptive immunity in secondary lymphoid tissue. Annu Rev Cell Dev Biol 2014; 30:141-67. [PMID: 25150013 DOI: 10.1146/annurev-cellbio-100913-013254] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Secondary lymphoid tissues are the sites of both innate and adaptive host defense. Aside from the relatively static nonhematopoietic stromal elements and some macrophages and dendritic cells, most of the cells in these tissues are in constant movement, but the organs maintain a defined microanatomy with preferred locations for the bulk of T cells, B cells, and other lymphocytes and subsets of myeloid cells. Here we describe both the cell dynamics and spatial organization of lymph nodes and review how both physical features and molecular cues guide cell movement to optimize host defense. We emphasize the role of locality in improving the efficiency of a system requiring rare cells to find each other and interact productively through membrane-bound or short-range secreted mediators and highlight how changes in steady-state cell positioning during an infectious challenge contribute to rapid generation of productive responses.
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Affiliation(s)
- Hai Qi
- Tsinghua-Peking Center for Life Sciences, Laboratory of Dynamic Immunobiology, School of Medicine, Tsinghua University, Beijing 100084, China;
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41
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Mehta S, Aye-Han NN, Ganesan A, Oldach L, Gorshkov K, Zhang J. Calmodulin-controlled spatial decoding of oscillatory Ca2+ signals by calcineurin. eLife 2014; 3:e03765. [PMID: 25056880 PMCID: PMC4141273 DOI: 10.7554/elife.03765] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Calcineurin is responsible for mediating a wide variety of cellular processes in response to dynamic calcium (Ca(2+)) signals, yet the precise mechanisms involved in the spatiotemporal control of calcineurin signaling are poorly understood. Here, we use genetically encoded fluorescent biosensors to directly probe the role of cytosolic Ca(2+) oscillations in modulating calcineurin activity dynamics in insulin-secreting MIN6 β-cells. We show that Ca(2+) oscillations induce distinct temporal patterns of calcineurin activity in the cytosol and plasma membrane vs at the ER and mitochondria in these cells. Furthermore, we found that these differential calcineurin activity patterns are determined by variations in the subcellular distribution of calmodulin (CaM), indicating that CaM plays an active role in shaping both the spatial and temporal aspects of calcineurin signaling. Together, our findings provide new insights into the mechanisms by which oscillatory signals are decoded to generate specific functional outputs within different cellular compartments.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Nwe-Nwe Aye-Han
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ambhighainath Ganesan
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, United States
| | - Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kirill Gorshkov
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, United States Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
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42
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Cheow LF, Sarkar A, Kolitz S, Lauffenburger D, Han J. Detecting kinase activities from single cell lysate using concentration-enhanced mobility shift assay. Anal Chem 2014; 86:7455-62. [PMID: 25025773 PMCID: PMC4144746 DOI: 10.1021/ac502185v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrokinetic preconcentration coupled with mobility shift assays can give rise to very high detection sensitivities. We describe a microfluidic device that utilizes this principle to detect cellular kinase activities by simultaneously concentrating and separating substrate peptides with different phosphorylation states. This platform is capable of reliably measuring kinase activities of single adherent cells cultured in nanoliter volume microwells. We also describe a novel method utilizing spacer peptides that significantly increase separation resolution while maintaining high concentration factors in this device. Thus, multiplexed kinase measurements can be implemented with single cell sensitivity. Multiple kinase activity profiling from single cell lysate could potentially allow us to study heterogeneous activation of signaling pathways that can lead to multiple cell fates.
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Affiliation(s)
- Lih Feng Cheow
- Department of Electrical Engineering and Computer Science and ‡Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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43
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Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell 2014; 55:332-41. [PMID: 25002142 DOI: 10.1016/j.molcel.2014.06.003] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/21/2014] [Accepted: 05/20/2014] [Indexed: 12/29/2022]
Abstract
Obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. We recently developed a method to map proteomes in living cells with an engineered peroxidase (APEX) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when applied to unbounded regions that allow APEX-generated radicals to escape. Here, we combine APEX technology with a SILAC-based ratiometric tagging strategy to substantially reduce unwanted background and achieve nanometer spatial resolution. This is applied to map the proteome of the mitochondrial intermembrane space (IMS), which can freely exchange small molecules with the cytosol. Our IMS proteome of 127 proteins has >94% specificity and includes nine newly discovered mitochondrial proteins. This approach will enable scientists to map proteomes of cellular regions that were previously inaccessible.
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Affiliation(s)
- Victoria Hung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyun-Woo Rhee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | | | - Valentin Cracan
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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44
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Brox D, Schwering M, Engelhardt J, Herten DP. Reversible Chemical Reactions for Single-Color Multiplexing Microscopy. Chemphyschem 2014; 15:2331-6. [DOI: 10.1002/cphc.201402012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 11/09/2022]
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45
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Sample V, Mehta S, Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J Cell Sci 2014; 127:1151-60. [PMID: 24634506 PMCID: PMC3953811 DOI: 10.1242/jcs.099994] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/22/2013] [Indexed: 01/05/2023] Open
Abstract
In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction.
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Affiliation(s)
- Vedangi Sample
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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46
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Sarkar A, Kolitz S, Lauffenburger DA, Han J. Microfluidic probe for single-cell analysis in adherent tissue culture. Nat Commun 2014; 5:3421. [PMID: 24594667 PMCID: PMC4179103 DOI: 10.1038/ncomms4421] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 02/10/2014] [Indexed: 12/12/2022] Open
Abstract
Single-cell analysis provides information critical to understanding key disease processes that are characterized by significant cellular heterogeneity. Few current methods allow single-cell measurement without removing cells from the context of interest, which not only destroys contextual information but also may perturb the process under study. Here we present a microfluidic probe that lyses single adherent cells from standard tissue culture and captures the contents to perform single-cell biochemical assays. We use this probe to measure kinase and housekeeping protein activities, separately or simultaneously, from single human hepatocellular carcinoma cells in adherent culture. This tool has the valuable ability to perform measurements that clarify connections between extracellular context, signals and responses, especially in cases where only a few cells exhibit a characteristic of interest.
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Affiliation(s)
- Aniruddh Sarkar
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah Kolitz
- Department of Biological Engineering Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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47
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Oldach L, Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. ACTA ACUST UNITED AC 2014; 21:186-97. [PMID: 24485761 DOI: 10.1016/j.chembiol.2013.12.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
Fluorescence-based, genetically encodable biosensors are widely used tools for real-time analysis of biological processes. Over the last few decades, the number of available genetically encodable biosensors and the types of processes they can monitor have increased rapidly. Here, we aim to introduce the reader to general principles and practices in biosensor development and highlight ways in which biosensors can be used to illuminate outstanding questions of biological function. Specifically, we focus on sensors developed for monitoring kinase activity and use them to illustrate some common considerations for biosensor design. We describe several uses to which kinase and second-messenger biosensors have been put, and conclude with considerations for the use of biosensors once they are developed. Overall, as fluorescence-based biosensors continue to diversify and improve, we expect them to continue to be widely used as reliable and fruitful tools for gaining deeper insights into cellular and organismal function.
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Affiliation(s)
- Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Department of Oncology, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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48
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Mehta S, Zhang J. Using a kinase-inducible bimolecular switch to control enzyme activity in living cells. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2014; 5:227-37. [PMID: 24391085 DOI: 10.1002/9780470559277.ch130090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular switches have been instrumental in the development of powerful and versatile genetic tools for directly probing biochemical processes, such as intracellular signaling, within their native contexts. A molecular switch can be broadly defined as a molecular system capable of existing in either of two states (e.g., conformations), which can be converted from one state to the other by a specific input stimulus. This protocol outlines a method for using a kinase-inducible bimolecular switch, along with live-cell fluorescence microscopy, to directly control and monitor the activity of a specific enzyme in living cells.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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49
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Using a genetically encoded FRET-based reporter to visualize calcineurin phosphatase activity in living cells. Methods Mol Biol 2014; 1071:139-49. [PMID: 24052386 DOI: 10.1007/978-1-62703-622-1_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Calcineurin is an evolutionarily conserved, ubiquitously expressed protein phosphatase that serves as a major effector of Ca(2+) signals, regulating diverse biological processes such as gene expression, tissue differentiation, immune responses, and neural plasticity. The following method describes how to monitor real-time calcineurin activity in cultured mammalian cells using a fluorescence resonance energy transfer (FRET)-based activity reporter.
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50
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Stennett EMS, Ciuba MA, Levitus M. Photophysical processes in single molecule organic fluorescent probes. Chem Soc Rev 2014; 43:1057-75. [DOI: 10.1039/c3cs60211g] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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