1
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Leong LM, Storace DA. Imaging different cell populations in the mouse olfactory bulb using the genetically encoded voltage indicator ArcLight. NEUROPHOTONICS 2024; 11:033402. [PMID: 38288247 PMCID: PMC10823906 DOI: 10.1117/1.nph.11.3.033402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Genetically encoded voltage indicators (GEVIs) are protein-based optical sensors that allow for measurements from genetically defined populations of neurons. Although in vivo imaging in the mammalian brain with early generation GEVIs was difficult due to poor membrane expression and low signal-to-noise ratio, newer and more sensitive GEVIs have begun to make them useful for answering fundamental questions in neuroscience. We discuss principles of imaging using GEVIs and genetically encoded calcium indicators, both useful tools for in vivo imaging of neuronal activity, and review some of the recent mechanistic advances that have led to GEVI improvements. We provide an overview of the mouse olfactory bulb (OB) and discuss recent studies using the GEVI ArcLight to study different cell types within the bulb using both widefield and two-photon microscopy. Specific emphasis is placed on using GEVIs to begin to study the principles of concentration coding in the OB, how to interpret the optical signals from population measurements in the in vivo brain, and future developments that will push the field forward.
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Affiliation(s)
- Lee Min Leong
- Florida State University, Department of Biological Science, Tallahassee, Florida, United States
| | - Douglas A. Storace
- Florida State University, Department of Biological Science, Tallahassee, Florida, United States
- Florida State University, Program in Neuroscience, Tallahassee, Florida, United States
- Florida State University, Institute of Molecular Biophysics, Tallahassee, Florida, United States
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2
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Okreglak V, Ling R, Ingaramo M, Thayer NH, Millett-Sikking A, Gottschling DE. Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth. Nat Metab 2023; 5:1803-1819. [PMID: 37640943 PMCID: PMC10590757 DOI: 10.1038/s42255-023-00872-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. Here we develop a highly sensitive pH reporter and find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes before cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid phosphatidylinositol 3,5-bisphosphate, which is regulated by the cyclin-dependent kinase Pho85 (CDK5 in mammals). Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division.
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Affiliation(s)
- Voytek Okreglak
- Calico Life Sciences, LLC, South San Francisco, CA, USA.
- Altos Labs, Redwood City, CA, USA.
| | - Rachel Ling
- Calico Life Sciences, LLC, South San Francisco, CA, USA
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3
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Shen Y, Wen Y, Sposini S, Vishwanath AA, Abdelfattah AS, Schreiter ER, Lemieux MJ, de Juan-Sanz J, Perrais D, Campbell RE. Rational Engineering of an Improved Genetically Encoded pH Sensor Based on Superecliptic pHluorin. ACS Sens 2023; 8:3014-3022. [PMID: 37481776 DOI: 10.1021/acssensors.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Genetically encoded pH sensors based on fluorescent proteins are valuable tools for the imaging of cellular events that are associated with pH changes, such as exocytosis and endocytosis. Superecliptic pHluorin (SEP) is a pH-sensitive green fluorescent protein (GFP) variant widely used for such applications. Here, we report the rational design, development, structure, and applications of Lime, an improved SEP variant with higher fluorescence brightness and greater pH sensitivity. The X-ray crystal structure of Lime supports the mechanistic rationale that guided the introduction of beneficial mutations. Lime provides substantial improvements relative to SEP for imaging of endocytosis and exocytosis. Furthermore, Lime and its variants are advantageous for a broader range of applications including the detection of synaptic release and neuronal voltage changes.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yurong Wen
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Silvia Sposini
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
- Department of Metabolism, Digestion and Reproduction, Institute of Reproductive and Developmental Biology, Imperial College London, London SW7 2BX, United Kingdom
| | - Anjali Amrapali Vishwanath
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - Ahmed S Abdelfattah
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
- Department of Neuroscience, Brown University, Providence, Rhode Island 02906, United States
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jaime de Juan-Sanz
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - David Perrais
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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4
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Evans SW, Shi DQ, Chavarha M, Plitt MH, Taxidis J, Madruga B, Fan JL, Hwang FJ, van Keulen SC, Suomivuori CM, Pang MM, Su S, Lee S, Hao YA, Zhang G, Jiang D, Pradhan L, Roth RH, Liu Y, Dorian CC, Reese AL, Negrean A, Losonczy A, Makinson CD, Wang S, Clandinin TR, Dror RO, Ding JB, Ji N, Golshani P, Giocomo LM, Bi GQ, Lin MZ. A positively tuned voltage indicator for extended electrical recordings in the brain. Nat Methods 2023; 20:1104-1113. [PMID: 37429962 PMCID: PMC10627146 DOI: 10.1038/s41592-023-01913-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/15/2023] [Indexed: 07/12/2023]
Abstract
Genetically encoded voltage indicators (GEVIs) enable optical recording of electrical signals in the brain, providing subthreshold sensitivity and temporal resolution not possible with calcium indicators. However, one- and two-photon voltage imaging over prolonged periods with the same GEVI has not yet been demonstrated. Here, we report engineering of ASAP family GEVIs to enhance photostability by inversion of the fluorescence-voltage relationship. Two of the resulting GEVIs, ASAP4b and ASAP4e, respond to 100-mV depolarizations with ≥180% fluorescence increases, compared with the 50% fluorescence decrease of the parental ASAP3. With standard microscopy equipment, ASAP4e enables single-trial detection of spikes in mice over the course of minutes. Unlike GEVIs previously used for one-photon voltage recordings, ASAP4b and ASAP4e also perform well under two-photon illumination. By imaging voltage and calcium simultaneously, we show that ASAP4b and ASAP4e can identify place cells and detect voltage spikes with better temporal resolution than commonly used calcium indicators. Thus, ASAP4b and ASAP4e extend the capabilities of voltage imaging to standard one- and two-photon microscopes while improving the duration of voltage recordings.
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Affiliation(s)
- S Wenceslao Evans
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Dong-Qing Shi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Mariya Chavarha
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mark H Plitt
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Jiannis Taxidis
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Blake Madruga
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jiang Lan Fan
- UC Berkeley/UCSF Joint Program in Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Fuu-Jiun Hwang
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
| | - Siri C van Keulen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Michelle M Pang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Sharon Su
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Sungmoo Lee
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Yukun A Hao
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Guofeng Zhang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Dongyun Jiang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Lagnajeet Pradhan
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Richard H Roth
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
| | - Yu Liu
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
- Department of Ophthalmology, Stanford University Medical Center, Stanford, CA, USA
| | - Conor C Dorian
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Austin L Reese
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Adrian Negrean
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, New York, NY, USA
- Kavli Institute for Brain Science, New York, NY, USA
| | - Christopher D Makinson
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | - Sui Wang
- Department of Ophthalmology, Stanford University Medical Center, Stanford, CA, USA
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University Medical Center, Stanford, CA, USA
| | - Na Ji
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Physics, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peyman Golshani
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Semel Institute for Neuroscience and Human Behavior, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Lisa M Giocomo
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Guo-Qiang Bi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Michael Z Lin
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, USA.
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5
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Bloxham W, Brinks D, Kheifets S, Cohen AE. Linearly polarized excitation enhances signals from fluorescent voltage indicators. Biophys J 2021; 120:5333-5342. [PMID: 34710379 DOI: 10.1016/j.bpj.2021.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022] Open
Abstract
Voltage imaging in cells requires high-speed recording of small fluorescent signals, often leading to low signal/noise ratios. Because voltage indicators are membrane bound, their orientations are partially constrained by the plane of the membrane. We explored whether tuning the linear polarization of excitation light could enhance voltage indicator fluorescence. We tested a panel of dye- and protein-based voltage indicators in mammalian cells. The dye BeRST1 showed a 73% increase in brightness between the least and most favorable polarizations. The protein-based reporter ASAP1 showed a 22% increase in brightness, and QuasAr3 showed a 14% increase in brightness. In very thin neurites expressing QuasAr3, improvements were anomalously large, with a 170% increase in brightness between polarization parallel versus perpendicular to the dendrite. Signal/noise ratios of optically recorded action potentials were increased by up to 50% in neurites expressing QuasAr3. These results demonstrate that polarization control can be a facile means to enhance signals from fluorescent voltage indicators, particularly in thin neurites or in high-background environments.
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Affiliation(s)
- William Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts; Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts.
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6
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Rhee JK, Iwamoto Y, Baker BJ. Visualizing Oscillations in Brain Slices With Genetically Encoded Voltage Indicators. Front Neuroanat 2021; 15:741711. [PMID: 34795565 PMCID: PMC8592998 DOI: 10.3389/fnana.2021.741711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) expressed pan-neuronally were able to optically resolve bicuculline induced spontaneous oscillations in brain slices of the mouse motor cortex. Three GEVIs were used that differ in their timing of response to voltage transients as well as in their voltage ranges. The duration, number of cycles, and frequency of the recorded oscillations reflected the characteristics of each GEVI used. Multiple oscillations imaged in the same slice never originated at the same location, indicating the lack of a “hot spot” for induction of the voltage changes. Comparison of pan-neuronal, Ca2+/calmodulin-dependent protein kinase II α restricted, and parvalbumin restricted GEVI expression revealed distinct profiles for the excitatory and inhibitory cells in the spontaneous oscillations of the motor cortex. Resolving voltage fluctuations across space, time, and cell types with GEVIs represent a powerful approach to dissecting neuronal circuit activity.
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Affiliation(s)
- Jun Kyu Rhee
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, South Korea.,Brain Science Creative Research Center, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | | | - Bradley J Baker
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, South Korea.,Brain Science Creative Research Center, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
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7
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Monitoring of compound resting membrane potentials of cell cultures with ratiometric genetically encoded voltage indicators. Commun Biol 2021; 4:1164. [PMID: 34620975 PMCID: PMC8497494 DOI: 10.1038/s42003-021-02675-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
The cellular resting membrane potential (Vm) not only determines electrical responsiveness of excitable cells but also plays pivotal roles in non-excitable cells, mediating membrane transport, cell-cycle progression, and tumorigenesis. Studying these processes requires estimation of Vm, ideally over long periods of time. Here, we introduce two ratiometric genetically encoded Vm indicators, rArc and rASAP, and imaging and analysis procedures for measuring differences in average resting Vm between cell groups. We investigated the influence of ectopic expression of K+ channels and their disease-causing mutations involved in Andersen-Tawil (Kir2.1) and Temple-Baraitser (KV10.1) syndrome on median resting Vm of HEK293T cells. Real-time long-term monitoring of Vm changes allowed to estimate a 40–50 min latency from induction of transcription to functional Kir2.1 channels in HEK293T cells. The presented methodology is readily implemented with standard fluorescence microscopes and offers deeper insights into the role of the resting Vm in health and disease. Rühl et al. report the generation of ratiometric genetically encoded voltage indicators (GEVIs) and establish that they can be used in high-throughput automated imaging to measure compound membrane potential (Vm) in mammalian cells. This method is implementable with standard fluorescence microscopes and has the potential to offer insights into the role of the resting Vm in health and disease.
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8
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Mechanism of ArcLight derived GEVIs involves electrostatic interactions that can affect proton wires. Biophys J 2021; 120:1916-1926. [PMID: 33744263 PMCID: PMC8204334 DOI: 10.1016/j.bpj.2021.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 11/24/2022] Open
Abstract
The genetically encoded voltage indicators ArcLight and its derivatives mediate voltage-dependent optical signals by intermolecular, electrostatic interactions between neighboring fluorescent proteins (FPs). A random mutagenesis event placed a negative charge on the exterior of the FP, resulting in a greater than 10-fold improvement of the voltage-dependent optical signal. Repositioning this negative charge on the exterior of the FP reversed the polarity of voltage-dependent optical signals, suggesting the presence of “hot spots” capable of interacting with the negative charge on a neighboring FP, thereby changing the fluorescent output. To explore the potential effect on the chromophore state, voltage-clamp fluorometry was performed with alternating excitation at 390 nm followed by excitation at 470 nm, resulting in several mutants exhibiting voltage-dependent, ratiometric optical signals of opposing polarities. However, the kinetics, voltage ranges, and optimal FP fusion sites were different depending on the wavelength of excitation. These results suggest that the FP has external, electrostatic pathways capable of quenching fluorescence that are wavelength specific. One mutation to the FP (E222H) showed a voltage-dependent increase in fluorescence when excited at 390 nm, indicating the ability to affect the proton wire from the protonated chromophore to the H222 position. ArcLight-derived sensors may therefore offer a novel way to map how conditions external to the β-can structure can affect the fluorescence of the chromophore and transiently affect those pathways via conformational changes mediated by manipulating membrane potential.
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9
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Bondar A, Rybakova O, Melcr J, Dohnálek J, Khoroshyy P, Ticháček O, Timr Š, Miclea P, Sakhi A, Marková V, Lazar J. Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools. Commun Biol 2021; 4:189. [PMID: 33580182 PMCID: PMC7881160 DOI: 10.1038/s42003-021-01694-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/11/2021] [Indexed: 11/09/2022] Open
Abstract
Fluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.
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Affiliation(s)
- Alexey Bondar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Science, Nove Hrady, Czech Republic
| | - Olga Rybakova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Science, Nove Hrady, Czech Republic
| | - Josef Melcr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
| | - Petro Khoroshyy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Science, Nove Hrady, Czech Republic
| | - Ondřej Ticháček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Paul Miclea
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Science, Nove Hrady, Czech Republic
| | - Alina Sakhi
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
| | - Vendula Marková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Josef Lazar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha 6, Czech Republic.
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Science, Nove Hrady, Czech Republic.
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10
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Myšková J, Rybakova O, Brynda J, Khoroshyy P, Bondar A, Lazar J. Directionality of light absorption and emission in representative fluorescent proteins. Proc Natl Acad Sci U S A 2020; 117:32395-32401. [PMID: 33273123 PMCID: PMC7768707 DOI: 10.1073/pnas.2017379117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescent molecules are like antennas: The rate at which they absorb light depends on their orientation with respect to the incoming light wave, and the apparent intensity of their emission depends on their orientation with respect to the observer. However, the directions along which the most important fluorescent molecules in biology, fluorescent proteins (FPs), absorb and emit light are generally not known. Our optical and X-ray investigations of FP crystals have now allowed us to determine the molecular orientations of the excitation and emission transition dipole moments in the FPs mTurquoise2, eGFP, and mCherry, and the photoconvertible FP mEos4b. Our results will allow using FP directionality in studies of molecular and biological processes, but also in development of novel bioengineering and bioelectronics applications.
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Affiliation(s)
- Jitka Myšková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Olga Rybakova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Petro Khoroshyy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Alexey Bondar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Josef Lazar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic;
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
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11
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Limapichat W, Pornthanakasem W, Satitthammachart C, Chitnumsub P, Leartsakulpanich U. Real-time detection of changes in yeast plasma membrane potential using genetically encoded voltage indicator proteins. FEMS Yeast Res 2020; 20:5874255. [PMID: 32691845 DOI: 10.1093/femsyr/foaa041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/18/2020] [Indexed: 11/12/2022] Open
Abstract
In yeast, adaptation to varying conditions often requires proper regulation of the plasma membrane potential. To determine yeast membrane potential change, optical methods involving potentiometric dyes have been supplemental to the direct electrode-based method. However, the hydrophobic nature of the dyes and their slow distribution across the membrane still limits their utilization. Genetically encoded voltage indicator (GEVI) proteins employed in neuroscience offer a tantalizing alternative for monitoring yeast membrane potential change. In this work, several widely used GEVI proteins were assessed in Saccharomyces cerevisiae for their expression and function as a voltage reporter. Among them, only ArcLight and Accelerated Sensor of Action Potential (ASAP) proteins could be expressed and transported to the plasma membrane. While the voltage-sensing capability was demonstrated for both ArcLight and ASAP, ArcLight fluorescence was sensitive to the intracellular pH change concurrently with the voltage change. Therefore, we established that ASAP is the more suitable GEVI protein for reporting yeast membrane potential change. This voltage-sensing reporter for yeast based on ASAP offers a new effective strategy for real-time optical detection of yeast membrane potential change, which potentially facilitates many areas of yeast research including optimizing growth conditions for industrial use and investigating yeast ion transport system.
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Affiliation(s)
- Walrati Limapichat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chatchaya Satitthammachart
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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12
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Rhee JK, Leong LM, Mukim MSI, Kang BE, Lee S, Bilbao-Broch L, Baker BJ. Biophysical Parameters of GEVIs: Considerations for Imaging Voltage. Biophys J 2020; 119:1-8. [PMID: 32521239 PMCID: PMC7335909 DOI: 10.1016/j.bpj.2020.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/17/2020] [Accepted: 05/20/2020] [Indexed: 11/29/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) continue to evolve, resulting in many different probes with varying strengths and weaknesses. Developers of new GEVIs tend to highlight their positive features. A recent article from an independent laboratory has compared the signal/noise ratios of a number of GEVIs. Such a comparison can be helpful to investigators eager to try to image the voltage of excitable cells. In this perspective, we will present examples of how the biophysical features of GEVIs affect the imaging of excitable cells in an effort to assist researchers when considering probes for their specific needs.
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Affiliation(s)
- Jun Kyu Rhee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Lee Min Leong
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Md Sofequl Islam Mukim
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bok Eum Kang
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sungmoo Lee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Laura Bilbao-Broch
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea.
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13
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Abstract
As a "holy grail" of neuroscience, optical imaging of membrane potential could enable high resolution measurements of spiking and synaptic activity in neuronal populations. This has been partly achieved using organic voltage-sensitive dyes in vitro, or in invertebrate preparations yet unspecific staining has prevented single-cell resolution measurements from mammalian preparations in vivo. The development of genetically encoded voltage indicators (GEVIs) and chemogenetic sensors has enabled targeting voltage indicators to plasma membranes and selective neuronal populations. Here, we review recent advances in the design and use of genetic voltage indicators and discuss advantages and disadvantages of three classes of them. Although genetic voltage indicators could revolutionize neuroscience, there are still significant challenges, particularly two-photon performance. To overcome them may require cross-disciplinary collaborations, team effort, and sustained support by large-scale research initiatives.
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Affiliation(s)
- Yuki Bando
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
- Present address: Department Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Christiane Grimm
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
| | - Victor H Cornejo
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA.
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14
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Storace DA, Cohen LB, Choi Y. Using Genetically Encoded Voltage Indicators (GEVIs) to Study the Input-Output Transformation of the Mammalian Olfactory Bulb. Front Cell Neurosci 2019; 13:342. [PMID: 31417362 PMCID: PMC6684792 DOI: 10.3389/fncel.2019.00342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) are fluorescent protein reporters of membrane potential. These tools can, in principle, be used to monitor the neural activity of genetically distinct cell types in the brain. Although introduced in 1997, they have been a challenge to use to study intact neural circuits due to a combination of small signal-to-noise ratio, slow kinetics, and poor membrane expression. New strategies have yielded novel GEVIs such as ArcLight, which have improved properties. Here, we compare the in vivo properties of ArcLight with Genetically Encoded Calcium Indicators (GECIs) in the mouse olfactory bulb. We show how voltage imaging can be combined with organic calcium sensitive dyes to measure the input-output transformation of the olfactory bulb. Finally, we demonstrate that ArcLight can be targeted to olfactory bulb interneurons. The olfactory bulb contributes substantially to the perception of the concentration invariance of odor recognition.
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Affiliation(s)
- Douglas A Storace
- Department of Biological Science, Florida State University, Tallahassee, FL, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Lawrence B Cohen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, South Korea
| | - Yunsook Choi
- Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, South Korea
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15
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Kannan M, Vasan G, Pieribone VA. Optimizing Strategies for Developing Genetically Encoded Voltage Indicators. Front Cell Neurosci 2019; 13:53. [PMID: 30863283 PMCID: PMC6399427 DOI: 10.3389/fncel.2019.00053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/04/2019] [Indexed: 01/23/2023] Open
Abstract
Genetically encoded optical indicators of neuronal activity enable unambiguous recordings of input-output activity patterns from identified cells in intact circuits. Among them, genetically encoded voltage indicators (GEVIs) offer additional advantages over calcium indicators as they are direct sensors of membrane potential and can adeptly report subthreshold events and hyperpolarization. Here, we outline the major GEVI designs and give an account of properties that need to be carefully optimized during indicator engineering. While designing the ideal GEVI, one should keep in mind aspects such as membrane localization, signal size, signal-to-noise ratio, kinetics and voltage dependence of optical responses. Using ArcLight and derivatives as prototypes, we delineate how a probe should be optimized for the former properties and developed along other areas in a need-based manner. Finally, we present an overview of the GEVI engineering process and lend an insight into their discovery, delivery and diagnosis.
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Affiliation(s)
- Madhuvanthi Kannan
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Ganesh Vasan
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States
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16
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Matzke AJ, Lin WD, Matzke M. Evidence That Ion-Based Signaling Initiating at the Cell Surface Can Potentially Influence Chromatin Dynamics and Chromatin-Bound Proteins in the Nucleus. FRONTIERS IN PLANT SCIENCE 2019; 10:1267. [PMID: 31681370 PMCID: PMC6811650 DOI: 10.3389/fpls.2019.01267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/11/2019] [Indexed: 05/18/2023]
Abstract
We have developed tools and performed pilot experiments to test the hypothesis that an intracellular ion-based signaling pathway, provoked by an extracellular stimulus acting at the cell surface, can influence interphase chromosome dynamics and chromatin-bound proteins in the nucleus. The experimental system employs chromosome-specific fluorescent tags and the genome-encoded fluorescent pH sensor SEpHluorinA227D, which has been targeted to various intracellular membranes and soluble compartments in root cells of Arabidopsis thaliana. We are using this system and three-dimensional live cell imaging to visualize whether fluorescent-tagged interphase chromosome sites undergo changes in constrained motion concurrently with reductions in membrane-associated pH elicited by extracellular ATP, which is known to trigger a cascade of events in plant cells including changes in calcium ion concentrations, pH, and membrane potential. To examine possible effects of the proposed ion-based signaling pathway directly at the chromatin level, we generated a pH-sensitive fluorescent DNA-binding protein that allows pH changes to be monitored at specific genomic sites. Results obtained using these tools support the existence of a rapid, ion-based signaling pathway that initiates at the cell surface and reaches the nucleus to induce alterations in interphase chromatin mobility and the surrounding pH of chromatin-bound proteins. Such a pathway could conceivably act under natural circumstances to allow external stimuli to swiftly influence gene expression by affecting interphase chromosome movement and the structures and/or activities of chromatin-associated proteins.
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Affiliation(s)
| | | | - Marjori Matzke
- *Correspondence: Antonius J.M. Matzke, ; Marjori Matzke,
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17
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Kang BE, Lee S, Baker BJ. Optical consequences of a genetically-encoded voltage indicator with a pH sensitive fluorescent protein. Neurosci Res 2018; 146:13-21. [PMID: 30342069 DOI: 10.1016/j.neures.2018.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/20/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Abstract
Genetically-Encoded Voltage Indicators (GEVIs) are capable of converting changes in membrane potential into an optical signal. Here, we focus on recent insights into the mechanism of ArcLight-type probes and the consequences of utilizing a pH-dependent Fluorescent Protein (FP). A negative charge on the exterior of the β-can of the FP combined with a pH-sensitive FP enables voltage-dependent conformational changes to affect the fluorescence of the probe. This hypothesis implies that interaction/dimerization of the FP creates a microenvironment for the probe that is altered via conformational changes. This mechanism explains why a pH sensitive FP with a negative charge on the outside of the β-can is needed, but also suggests that pH could affect the optical signal as well. To better understand the effects of pH on the voltage-dependent signal of ArcLight, the intracellular pH (pHi) was tested at pH 6.8, 7.2, or 7.8. The resting fluorescence of ArcLight gets brighter as the pHi increases, yet only pH 7.8 significantly affected the ΔF/F. ArcLight could also simultaneously report voltage and pH changes during the acidification of a neuron firing multiple action potentials revealing different buffering capacities of the soma versus the processes of the cell.
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Affiliation(s)
- Bok Eum Kang
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sungmoo Lee
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Program in Nanoscience and Technology, Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University. Suwon, Republic of Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
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18
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Yi B, Kang BE, Lee S, Braubach S, Baker BJ. A dimeric fluorescent protein yields a bright, red-shifted GEVI capable of population signals in brain slice. Sci Rep 2018; 8:15199. [PMID: 30315245 PMCID: PMC6185910 DOI: 10.1038/s41598-018-33297-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
A bright, red-shifted Genetically Encoded Voltage Indicator (GEVI) was developed using a modified version of the fluorescent protein, tdTomato. Dimerization of the fluorescent domain for ArcLight-type GEVIs has been shown to affect the signal size of the voltage-dependent optical signal. For red-shifted GEVI development, tdTomato was split fusing a single dTomato chromophore to the voltage sensing domain. Optimization of the amino acid length and charge composition of the linker region between the voltage sensing domain and the fluorescent protein resulted in a probe that is an order of magnitude brighter than FlicR1 at a resting potential of -70 mV and exhibits a ten-fold larger change in fluorescence (ΔF) upon 100 mV depolarization of the plasma membrane in HEK 293 cells. Unlike ArcLight, the introduction of charged residues to the exterior of dTomato did not substantially improve the dynamic range of the optical signal. As a result, this new GEVI, Ilmol, yields a 3-fold improvement in the signal-to-noise ratio compared to FlicR1 despite a smaller fractional change in fluorescence of 4% per 100 mV depolarization of the plasma membrane. Ilmol expresses well in neurons resolving action potentials in neuronal cultures and reporting population signals in mouse hippocampal acute brain slice recordings. Ilmol is the brightest red-shifted GEVI to date enabling imaging with 160-fold less light than Archon1 for primary neuron recordings (50 mW/cm2 versus 8 W/cm2) and 600-fold less light than QuasAr2 for mouse brain slice recordings (500 mW/cm2 versus 300 W/cm2). This new GEVI uses a distinct mechanism from other approaches, opening an alternate engineering path to improve sensitivity and speed.
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Affiliation(s)
- Bumjun Yi
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bok Eum Kang
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Sungmoo Lee
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Department of Transdisciplinary Studies, Graduate school of Convergence Science and Technology, Seoul National University, Suwon, Republic of Korea
| | - Sophie Braubach
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Bradley J Baker
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea. .,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea.
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19
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Platisa J, Pieribone VA. Genetically encoded fluorescent voltage indicators: are we there yet? Curr Opin Neurobiol 2018; 50:146-153. [PMID: 29501950 PMCID: PMC5984684 DOI: 10.1016/j.conb.2018.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/04/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
In order to understand how brain activity produces adaptive behavior we need large-scale, high-resolution recordings of neuronal activity. Fluorescent genetically encoded voltage indicators (GEVIs) offer the potential for these recordings to be performed chronically from targeted cells in a minimally invasive manner. As the number of GEVIs successfully tested for in vivo use grows, so has the number of open questions regarding the improvements that would facilitate broad adoption of this technology that surpasses mere 'proof of principle' studies. Our aim in this review is not to provide a status check of the current state of the field, as excellent publications covering this topic already exist. Here, we discuss specific questions regarding GEVI development and application that we think are crucial in achieving this goal.
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Affiliation(s)
- Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, CT 06519, United States; Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, United States.
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, CT 06519, United States; Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, United States; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, United States
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20
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Kwon T, Sakamoto M, Peterka DS, Yuste R. Attenuation of Synaptic Potentials in Dendritic Spines. Cell Rep 2018; 20:1100-1110. [PMID: 28768195 DOI: 10.1016/j.celrep.2017.07.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 10/19/2022] Open
Abstract
Dendritic spines receive the majority of excitatory inputs in many mammalian neurons, but their biophysical properties and exact role in dendritic integration are still unclear. Here, we study spine electrical properties in cultured hippocampal neurons using an improved genetically encoded voltage indicator (ArcLight) and two-photon glutamate uncaging. We find that back-propagating action potentials (bAPs) fully invade dendritic spines. However, uncaging excitatory post-synaptic potentials (uEPSPs) generated by glutamate photorelease, ranging from 4 to 27 mV in amplitude, are attenuated by up to 4-fold as they propagate to the parent dendrites. Finally, the simultaneous occurrence of bAPs and uEPSPs results in sublinear summation of membrane potential. Our results demonstrate that spines can behave as electric compartments, reducing the synaptic inputs injected into the cell, while receiving bAPs are unmodified. The attenuation of EPSPs by spines could have important repercussions for synaptic plasticity and dendritic integration.
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Affiliation(s)
- Taekyung Kwon
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Masayuki Sakamoto
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Darcy S Peterka
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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21
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Cartailler J, Kwon T, Yuste R, Holcman D. Deconvolution of Voltage Sensor Time Series and Electro-diffusion Modeling Reveal the Role of Spine Geometry in Controlling Synaptic Strength. Neuron 2018; 97:1126-1136.e10. [PMID: 29429935 DOI: 10.1016/j.neuron.2018.01.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/09/2017] [Accepted: 01/12/2018] [Indexed: 01/03/2023]
Abstract
Most synaptic excitatory connections are made on dendritic spines. But how the voltage in spines is modulated by its geometry remains unclear. To investigate the electrical properties of spines, we combine voltage imaging data with electro-diffusion modeling. We first present a temporal deconvolution procedure for the genetically encoded voltage sensor expressed in hippocampal cultured neurons and then use electro-diffusion theory to compute the electric field and the current-voltage conversion. We extract a range for the neck resistances of 〈R〉=100±35MΩ. When a significant current is injected in a spine, the neck resistance can be inversely proportional to its radius, but not to the radius square, as predicted by Ohm's law. We conclude that the postsynaptic voltage cannot only be modulated by changing the number of receptors, but also by the spine geometry. Thus, spine morphology could be a key component in determining synaptic transduction and plasticity.
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Affiliation(s)
- Jerome Cartailler
- Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Taekyung Kwon
- Neurotechnology Center, Depts. Biological Sciences and Neuroscience, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Depts. Biological Sciences and Neuroscience, Columbia University, New York, NY 10027, USA
| | - David Holcman
- Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France.
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22
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Simine L, Lammert H, Sun L, Onuchic JN, Rossky PJ. Fluorescent Proteins Detect Host Structural Rearrangements via Electrostatic Mechanism. J Am Chem Soc 2018; 140:1203-1206. [PMID: 29328673 DOI: 10.1021/jacs.7b10851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rational design of genetically encoded fluorescent biosensors, which can detect rearrangements of target proteins via interdomain allostery, is hindered by the absence of mechanistic understanding of the underlying photophysics. Here, we focus on the modulation of fluorescence by mechanical perturbation in a popular biological probe: enhanced Green Fluorescent Protein (eGFP). Using a combination of molecular dynamics (MD) simulations and quantum chemistry, and a set of physically motivated assumptions, we construct a map of fluorescence quantum yield as a function of a 2D electric field imposed by the protein environment on the fluorophore. This map is transferable between Tsien's Class 2 GFP's, and it allows one to estimate the shifts in fluorescence intensity due to mechanical perturbations directly from MD simulations. We use it in combination with steered MD simulations to put forward a hypothesis for the mechanism of a genetically encoded voltage probe (ArcLight) whose mechanism is currently under debate.
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Affiliation(s)
- Lena Simine
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Heiko Lammert
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Li Sun
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - José N Onuchic
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Peter J Rossky
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
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23
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Abstract
Fluorescent protein-based biosensors are indispensable molecular tools for life science research. The invention and development of high-fidelity biosensors for a particular molecule or molecular event often catalyze important scientific breakthroughs. Understanding the structural and functional organization of brain activities remain a subject for which optical sensors are in desperate need and of growing interest. Here, we review genetically encoded fluorescent sensors for imaging neuronal activities with a focus on the design principles and optimizations of various sensors. New bioluminescent sensors useful for deep-tissue imaging are also discussed. By highlighting the protein engineering efforts and experimental applications of these sensors, we can consequently analyze factors influencing their performance. Finally, we remark on how future developments can fill technological gaps and lead to new discoveries.
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Affiliation(s)
- Zhijie Chen
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA
| | - Tan M. Truong
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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24
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Voltage and Calcium Imaging of Brain Activity. Biophys J 2017; 113:2160-2167. [PMID: 29102396 DOI: 10.1016/j.bpj.2017.09.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/14/2017] [Accepted: 09/21/2017] [Indexed: 01/02/2023] Open
Abstract
Sensors for imaging brain activity have been under development for almost 50 years. The development of some of these tools is relatively mature, whereas qualitative improvements of others are needed and are actively pursued. In particular, genetically encoded voltage indicators are just now starting to be used to answer neurobiological questions and, at the same time, more than 10 laboratories are working to improve them. In this Biophysical Perspective, we attempt to discuss the present state of the art and indicate areas of active development.
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25
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Toward Better Genetically Encoded Sensors of Membrane Potential. Trends Neurosci 2017; 39:277-289. [PMID: 27130905 DOI: 10.1016/j.tins.2016.02.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/25/2016] [Accepted: 02/22/2016] [Indexed: 11/24/2022]
Abstract
Genetically encoded optical sensors of cell activity are powerful tools that can be targeted to specific cell types. This is especially important in neuroscience because individual brain regions can include a multitude of different cell types. Optical imaging allows for simultaneous recording from numerous neurons or brain regions. Optical signals of membrane potential are useful because membrane potential changes are a direct sign of both synaptic and action potentials. Here we describe recent improvements in the in vitro and in vivo signal size and kinetics of genetically encoded voltage indicators (GEVIs) and discuss their relationship to alternative sensors of neural activity.
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26
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Borden PY, Ortiz AD, Waiblinger C, Sederberg AJ, Morrissette AE, Forest CR, Jaeger D, Stanley GB. Genetically expressed voltage sensor ArcLight for imaging large scale cortical activity in the anesthetized and awake mouse. NEUROPHOTONICS 2017; 4:031212. [PMID: 28491905 PMCID: PMC5416966 DOI: 10.1117/1.nph.4.3.031212] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
With the recent breakthrough in genetically expressed voltage indicators (GEVIs), there has been a tremendous demand to determine the capabilities of these sensors in vivo. Novel voltage sensitive fluorescent proteins allow for direct measurement of neuron membrane potential changes through changes in fluorescence. Here, we utilized ArcLight, a recently developed GEVI, and examined the functional characteristics in the widely used mouse somatosensory whisker pathway. We measured the resulting evoked fluorescence using a wide-field microscope and a CCD camera at 200 Hz, which enabled voltage recordings over the entire cortical region with high temporal resolution. We found that ArcLight produced a fluorescent response in the S1 barrel cortex during sensory stimulation at single whisker resolution. During wide-field cortical imaging, we encountered substantial hemodynamic noise that required additional post hoc processing through noise subtraction techniques. Over a period of 28 days, we found clear and consistent ArcLight fluorescence responses to a simple sensory input. Finally, we demonstrated the use of ArcLight to resolve cortical S1 sensory responses in the awake mouse. Taken together, our results demonstrate the feasibility of ArcLight as a measurement tool for mesoscopic, chronic imaging.
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Affiliation(s)
- Peter Y. Borden
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
| | - Alex D. Ortiz
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
| | - Christian Waiblinger
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
| | - Audrey J. Sederberg
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
| | - Arthur E. Morrissette
- Emory University, Neuroscience Program, Department of Biology, Atlanta, Georgia, United States
| | - Craig R. Forest
- Georgia Institute of Technology and Emory University, School of Mechanical Engineering, Atlanta, Georgia, United States
| | - Dieter Jaeger
- Emory University, Neuroscience Program, Department of Biology, Atlanta, Georgia, United States
| | - Garrett B. Stanley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
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27
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Bondar A, Lazar J. The G protein G i1 exhibits basal coupling but not preassembly with G protein-coupled receptors. J Biol Chem 2017; 292:9690-9698. [PMID: 28438833 DOI: 10.1074/jbc.m116.768127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/21/2017] [Indexed: 11/06/2022] Open
Abstract
The Gi/o protein family transduces signals from a diverse group of G protein-coupled receptors (GPCRs). The observed specificity of Gi/o-GPCR coupling and the high rate of Gi/o signal transduction have been hypothesized to be enabled by the existence of stable associates between Gi/o proteins and their cognate GPCRs in the inactive state (Gi/o-GPCR preassembly). To test this hypothesis, we applied the recently developed technique of two-photon polarization microscopy (2PPM) to Gαi1 subunits labeled with fluorescent proteins and four GPCRs: the α2A-adrenergic receptor, GABAB, cannabinoid receptor type 1 (CB1R), and dopamine receptor type 2. Our experiments with non-dissociating mutants of fluorescently labeled Gαi1 subunits (exhibiting impaired dissociation from activated GPCRs) showed that 2PPM is capable of detecting GPCR-G protein interactions. 2PPM experiments with non-mutated fluorescently labeled Gαi1 subunits and α2A-adrenergic receptor, GABAB, or dopamine receptor type 2 receptors did not reveal any interaction between the Gi1 protein and the non-stimulated GPCRs. In contrast, non-stimulated CB1R exhibited an interaction with the Gi1 protein. Further experiments revealed that this interaction is caused solely by CB1R basal activity; no preassembly between CB1R and the Gi1 protein could be observed. Our results demonstrate that four diverse GPCRs do not preassemble with non-active Gi1 However, we also show that basal GPCR activity allows interactions between non-stimulated GPCRs and Gi1 (basal coupling). These findings suggest that Gi1 interacts only with active GPCRs and that the well known high speed of GPCR signal transduction does not require preassembly between G proteins and GPCRs.
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Affiliation(s)
- Alexey Bondar
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 37333 Nove Hrady,
| | - Josef Lazar
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 37333 Nove Hrady.,the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague, and.,the Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
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28
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Platisa J, Vasan G, Yang A, Pieribone VA. Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight. ACS Chem Neurosci 2017; 8:513-523. [PMID: 28045247 PMCID: PMC5355904 DOI: 10.1021/acschemneuro.6b00234] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
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Genetically encoded
calcium indicators (GECIs) produce unprecedentedly
large signals that have enabled routine optical recording of single
neuron activity in vivo in rodent brain. Genetically encoded voltage
indicators (GEVIs) offer a more direct measure of neuronal electrical
status, however the signal-to-noise characteristics and signal polarity
of the probes developed to date have precluded routine use in vivo.
We applied directed evolution to target modulable areas of the fluorescent
protein in GEVI ArcLight to create the first GFP-based GEVI (Marina)
that exhibits a ΔF/ΔV with a positive slope relationship. We found that only three rounds
of site-directed mutagenesis produced a family of “brightening”
GEVIs with voltage sensitivities comparable to that seen in the parent
probe ArcLight. This shift in signal polarity is an essential first
step to producing voltage indicators with signal-to-noise characteristics
comparable to GECIs to support widespread use in vivo.
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Affiliation(s)
- Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Ganesh Vasan
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Amy Yang
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Vincent A. Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
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29
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Barnett LM, Hughes TE, Drobizhev M. Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence. PLoS One 2017; 12:e0170934. [PMID: 28182677 PMCID: PMC5300113 DOI: 10.1371/journal.pone.0170934] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/12/2017] [Indexed: 11/19/2022] Open
Abstract
The goal of this work is to determine how GCaMP6m's fluorescence is altered in response to Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for how GCaMP6m changes fluorescence in response to Ca2+ is with a four-state model, in which a Ca2+-dependent change of the chromophore protonation state, due to a shift in pKa, is the predominant factor. The pKa shift is quantitatively explained by a change in electrostatic potential around the chromophore due to the conformational changes that occur in the protein when calmodulin binds Ca2+ and interacts with the M13 peptide. The absolute pKa values for the Ca2+-free and Ca2+-saturated states of GCaMP6m are critical to its high signal-to-noise ratio. This mechanism has important implications for further improvements to GCaMP6m and potentially for other similarly designed biosensors.
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Affiliation(s)
- Lauren M. Barnett
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Thomas E. Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
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30
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Inagaki S, Nagai T. Current progress in genetically encoded voltage indicators for neural activity recording. Curr Opin Chem Biol 2016; 33:95-100. [PMID: 27322400 DOI: 10.1016/j.cbpa.2016.05.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 12/28/2022]
Abstract
Genetically Encoded Voltage Indicators (GEVIs) are powerful tools used to investigate neural activity in the brain. The spatiotemporal resolution of GEVIs is on a subcellular and millisecond scale, and is superior to that of the functional magnetic resonance imaging (fMRI) and electroencephalogram (EEG). Further, while patch-clamp techniques record membrane voltage for tens of neurons simultaneously, GEVIs can do so for hundreds of neurons. It is important for neuroscientists to understand the pros and cons of GEVIs and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available GEVIs based on voltage sensing mechanism and provide a guideline for selecting optimal GEVIs for specific applications.
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Affiliation(s)
- Shigenori Inagaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeharu Nagai
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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31
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Melcr J, Bonhenry D, Timr Š, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. J Chem Theory Comput 2016; 12:2418-25. [DOI: 10.1021/acs.jctc.5b01202] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Daniel Bonhenry
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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32
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Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions. Sci Rep 2016; 6:23865. [PMID: 27040905 PMCID: PMC4878010 DOI: 10.1038/srep23865] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/15/2016] [Indexed: 12/03/2022] Open
Abstract
An in silico search strategy was developed to identify potential voltage-sensing domains (VSD) for the development of genetically encoded voltage indicators (GEVIs). Using a conserved charge distribution in the S2 α-helix, a single in silico search yielded most voltage-sensing proteins including voltage-gated potassium channels, voltage-gated calcium channels, voltage-gated sodium channels, voltage-gated proton channels, and voltage-sensing phosphatases from organisms ranging from mammals to bacteria and plants. A GEVI utilizing the VSD from a voltage-gated proton channel identified from that search was able to optically report changes in membrane potential. In addition this sensor was capable of manipulating the internal pH while simultaneously reporting that change optically since it maintains the voltage-gated proton channel activity of the VSD. Biophysical characterization of this GEVI, Pado, demonstrated that the voltage-dependent signal was distinct from the pH-dependent signal and was dependent on the movement of the S4 α-helix. Further investigation into the mechanism of the voltage-dependent optical signal revealed that inhibiting the dimerization of the fluorescent protein greatly reduced the optical signal. Dimerization of the FP thereby enabled the movement of the S4 α-helix to mediate a fluorescent response.
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33
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Treger JS, Priest MF, Bezanilla F. Single-molecule fluorimetry and gating currents inspire an improved optical voltage indicator. eLife 2015; 4:e10482. [PMID: 26599732 PMCID: PMC4658195 DOI: 10.7554/elife.10482] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/29/2015] [Indexed: 11/13/2022] Open
Abstract
Voltage-sensing domains (VSDs) underlie the movement of voltage-gated ion channels, as well as the voltage-sensitive fluorescent responses observed from a common class of genetically encoded voltage indicators (GEVIs). Despite the widespread use and potential utility of these GEVIs, the biophysical underpinnings of the relationship between VSD movement and fluorophore response remain unclear. We investigated the recently developed GEVI ArcLight, and its close variant Arclight', at both the single-molecule and macroscopic levels to better understand their characteristics and mechanisms of activity. These studies revealed a number of previously unobserved features of ArcLight's behavior, including millisecond-scale fluorescence fluctuations in single molecules as well as a previously unreported delay prior to macroscopic fluorescence onset. Finally, these mechanistic insights allowed us to improve the optical response of ArcLight to fast or repetitive pulses with the development of ArcLightning, a novel GEVI with improved kinetics. DOI:http://dx.doi.org/10.7554/eLife.10482.001 Nerve cells, or neurons, transmit information using changes in the voltage across their cell membranes. In the brain, these neurons work together in complex networks, and so understanding how the brain processes information will require neuroscientists to analyze voltage changes in many neurons at the same time.To achieve this, scientists have developed genetically-encoded voltage indicators (or GEVIs). These commonly feature a fluorescent protein attached to a voltage-sensitive protein; when the voltage-sensitive protein moves in response to changes in electrical activity, the amount of light emitted by the fluorescent protein also changes. Treger, Priest and Bezanilla have now studied the characteristics of a popular GEVI called ArcLight by recording how fluorescence and voltage are related, both in single molecules and in groups of millions of molecules.This revealed that the fluorescence response of ArcLight does not occur instantly when a voltage change occurs. Instead the indicator fluoresces after a short delay. This delay corresponds with how quickly the voltage-sensitive protein responds. The fluorescence of a close relative of ArcLight also rapidly flickers, which deteriorates the signal quality. Using this knowledge Treger, Priest and Bezanilla engineered the voltage-sensitive protein of ArcLight to develop a new variant of the indicator, named ArcLightning. Tests revealed that ArcLightning responds much faster than ArcLight to voltage changes in neurons, although the flicker of the fluorescent protein likely remains. ArcLightning should prove to be a valuable tool for analyzing how neurons work together in living animals, but the flicker of the fluorescent protein suggests that there is further room for improvement. The rational design method used to develop ArcLightning could also be applied to improve other recently developed voltage indicators. DOI:http://dx.doi.org/10.7554/eLife.10482.002
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Affiliation(s)
- Jeremy S Treger
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Michael F Priest
- Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
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34
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Matzke AJM, Matzke M. Expression and testing in plants of ArcLight, a genetically-encoded voltage indicator used in neuroscience research. BMC PLANT BIOLOGY 2015; 15:245. [PMID: 26459340 PMCID: PMC4603945 DOI: 10.1186/s12870-015-0633-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/30/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of electrical activity at cell membranes uses genetically-encoded voltage indicators (GEVIs). Developed by neuroscientists to chart neuronal circuits in animals, GEVIs comprise a fluorescent protein that is fused to a voltage-sensing domain. One well-known GEVI, ArcLight, undergoes strong shifts in fluorescence intensity in response to voltage changes in mammalian cells. ArcLight consists of super-ecliptic (SE) pHluorin (pH-sensitive fluorescent protein) with an A227D substitution, which confers voltage sensitivity in neurons, fused to the voltage-sensing domain of the voltage-sensing phosphatase of C iona i ntestinalis (Ci-VSD). In an ongoing effort to adapt tools of optical electrophysiology for plants, we describe here the expression and testing of ArcLight and various derivatives in different membranes of root cells in Arabidopsis thaliana. RESULTS Transgenic constructs were designed to express ArcLight and various derivatives targeted to the plasma membrane and nuclear membranes of Arabidopsis root cells. In transgenic seedlings, changes in fluorescence intensity of these reporter proteins following extracellular ATP (eATP) application were monitored using a fluorescence microscope equipped with a high speed camera. Coordinate reductions in fluorescence intensity of ArcLight and Ci-VSD-containing derivatives were observed at both the plasma membrane and nuclear membranes following eATP treatments. However, similar responses were observed for derivatives lacking the Ci-VSD. The dispensability of the Ci-VSD suggests that in plants, where H(+) ions contribute substantially to electrical activities, the voltage-sensing ability of ArcLight is subordinate to the pH sensitivity of its SEpHluorin base. The transient reduction of ArcLight fluorescence triggered by eATP most likely reflects changes in pH and not membrane voltage. CONCLUSIONS The pH sensitivity of ArcLight precludes its use as a direct sensor of membrane voltage in plants. Nevertheless, ArcLight and derivatives situated in the plasma membrane and nuclear membranes may offer robust, fluorescence intensity-based pH indicators for monitoring concurrent changes in pH at these discrete membrane systems. Such tools will assist analyses of pH as a signal and/or messenger at the cell surface and the nuclear periphery in living plants.
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Affiliation(s)
- Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan.
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan.
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35
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Timr Š, Brabec J, Bondar A, Ryba T, Železný M, Lazar J, Jungwirth P. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes. J Phys Chem B 2015; 119:9706-16. [DOI: 10.1021/acs.jpcb.5b05123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Štěpán Timr
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jiří Brabec
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS-50F-1650, Berkeley, California 94720 United States
| | - Alexey Bondar
- Institute
of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, v.v.i., Zámek 136, 37333 Nové Hrady, Czech Republic
- Faculty
of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Tomáš Ryba
- Department
of Cybernetics, Faculty of Applied Sciences, University of West Bohemia, Univerzitní 8, 30614 Plzeň, Czech Republic
| | - Miloš Železný
- Department
of Cybernetics, Faculty of Applied Sciences, University of West Bohemia, Univerzitní 8, 30614 Plzeň, Czech Republic
| | - Josef Lazar
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Institute
of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, v.v.i., Zámek 136, 37333 Nové Hrady, Czech Republic
- Faculty
of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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36
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St-Pierre F, Chavarha M, Lin MZ. Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators. Curr Opin Chem Biol 2015; 27:31-8. [PMID: 26079047 DOI: 10.1016/j.cbpa.2015.05.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/04/2015] [Indexed: 11/24/2022]
Abstract
Neurons tightly regulate the electrical potential difference across the plasma membrane with millivolt accuracy and millisecond resolution. Membrane voltage dynamics underlie the generation of an impulse, the transduction of impulses from one end of the neuron to the other, and the release of neurotransmitters. Imaging these voltage dynamics in multiple neurons simultaneously is therefore crucial for understanding how neurons function together within circuits in intact brains. Genetically encoded fluorescent voltage sensors have long been desired to report voltage in defined subsets of neurons with optical readout. In this review, we discuss the diverse strategies used to design and optimize protein-based voltage sensors, and highlight the chemical mechanisms by which different classes of reporters sense voltage. To guide neuroscientists in choosing an appropriate sensor for their applications, we also describe operating trade-offs of each class of voltage indicators.
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Affiliation(s)
- François St-Pierre
- Department of Pediatrics, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mariya Chavarha
- Department of Pediatrics, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Pediatrics, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA.
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37
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Lo SQ, Koh DXP, Sng JCG, Augustine GJ. All-optical mapping of barrel cortex circuits based on simultaneous voltage-sensitive dye imaging and channelrhodopsin-mediated photostimulation. NEUROPHOTONICS 2015; 2:021013. [PMID: 26158003 PMCID: PMC4478985 DOI: 10.1117/1.nph.2.2.021013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/04/2015] [Indexed: 05/25/2023]
Abstract
We describe an experimental approach that uses light to both control and detect neuronal activity in mouse barrel cortex slices: blue light patterned by a digital micromirror array system allowed us to photostimulate specific layers and columns, while a red-shifted voltage-sensitive dye was used to map out large-scale circuit activity. We demonstrate that such all-optical mapping can interrogate various circuits in somatosensory cortex by sequentially activating different layers and columns. Further, mapping in slices from whisker-deprived mice demonstrated that chronic sensory deprivation did not significantly alter feedforward inhibition driven by layer 5 pyramidal neurons. Further development of voltage-sensitive optical probes should allow this all-optical mapping approach to become an important and high-throughput tool for mapping circuit interactions in the brain.
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Affiliation(s)
- Shun Qiang Lo
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Physiology, Singapore 117597, Singapore
- Nanyang Technological University, Lee Kong Chian School of Medicine, Proteos, Biopolis, Level 4, 61 Biopolis Drive, #04-06/07, Singapore 138673, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Proteos, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, United States
| | - Dawn X. P. Koh
- National University of Singapore, Graduate School of Integrative Sciences and Engineering, Singapore 117456, Singapore
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Pharmacology, Singapore 117599, Singapore
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, 30 Medical Drive, Singapore 117609, Singapore
| | - Judy C. G. Sng
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Pharmacology, Singapore 117599, Singapore
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, 30 Medical Drive, Singapore 117609, Singapore
| | - George J. Augustine
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Physiology, Singapore 117597, Singapore
- Nanyang Technological University, Lee Kong Chian School of Medicine, Proteos, Biopolis, Level 4, 61 Biopolis Drive, #04-06/07, Singapore 138673, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Proteos, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, United States
- Korea Institute of Science and Technology, Center for Functional Connectomics, 39-1 Hawolgokdong, Seongbukgu, Seoul 136-791, Republic of Korea
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38
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Novel in vivo techniques to visualize kidney anatomy and function. Kidney Int 2015; 88:44-51. [PMID: 25738253 PMCID: PMC4490063 DOI: 10.1038/ki.2015.65] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/05/2015] [Accepted: 01/06/2015] [Indexed: 12/11/2022]
Abstract
Intravital imaging using multiphoton microscopy (MPM) has become an increasingly popular and widely used experimental technique in kidney research over the past few years. MPM allows deep optical sectioning of the intact, living kidney tissue with submicron resolution which is unparalleled among intravital imaging approaches. MPM has solved a long-standing critical technical barrier in renal research to study several complex and inaccessible cell types and anatomical structures in vivo in their native environment. Comprehensive and quantitative kidney structure and function MPM studies helped our better understanding of the cellular and molecular mechanisms of the healthy and diseased kidney. This review summarizes recent in vivo MPM studies with a focus on the glomerulus and the filtration barrier, although select, glomerulus-related renal vascular and tubular functions are also mentioned. The latest applications of serial MPM of the same glomerulus in vivo, in the intact kidney over several days, during the progression of glomerular disease are discussed. This visual approach, in combination with genetically encoded fluorescent markers of cell lineage, has helped to track the fate and function (e.g. cell calcium changes) of single podocytes during the development of glomerular pathologies, and provided visual proof for the highly dynamic rather than static nature of the glomerular environment. Future intravital imaging applications have the promise to further push the limits of optical microscopy, and to advance our understanding of the mechanisms of kidney injury. Also, MPM will help to study new mechanisms of tissue repair and regeneration, a cutting edge area of kidney research.
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