1
|
Zhuang B, Vos MH. Photoswitching Behavior of Flavin-Inhibitor Complex in a Nonphotocatalytic Flavoenzyme. J Am Chem Soc 2022; 144:11569-11573. [PMID: 35727223 DOI: 10.1021/jacs.2c04763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An unprecedented photoswitching phenomenon of flavin-inhibitor complexes in a flavoenzyme was revealed by femtosecond transient absorption spectroscopy. The vast majority of flavoenzymes, including monomeric sarcosine oxidase (MSOX), perform non-light-driven physiological functions. Yet, the participation of flavin cofactors in photoinduced electron transfer reactions is widespread. MSOX catalyzes the oxidative demethylation of sarcosine; methylthioacetate (MTA) is a substrate analog inhibitor that forms a complex with MSOX exhibiting intense absorption bands over the whole visible range due to flavin-MTA charge transfer (CT) interactions. Here, we demonstrate that upon excitation, these CT interactions vanish during a barrierless high quantum yield reaction in ∼300 fs. The initial complex subsequently geminately re-forms in a few nanoseconds near room temperature in a thermally activated way with an activation energy of 28 kJ/mol. We attribute this hitherto undocumented process to a well-defined photoinduced isomerization of MTA in the active site, as corroborated by experiments with the heavier ligand methylselenoacetate. Photoisomerization phenomena involving CT transitions may be further explored in photocatalytic and photoswitching applications of flavoenzymes.
Collapse
Affiliation(s)
- Bo Zhuang
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Marten H Vos
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| |
Collapse
|
2
|
Waadt R, Kudla J, Kollist H. Multiparameter in vivo imaging in plants using genetically encoded fluorescent indicator multiplexing. PLANT PHYSIOLOGY 2021; 187:537-549. [PMID: 35237819 PMCID: PMC8491039 DOI: 10.1093/plphys/kiab399] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/03/2021] [Indexed: 05/20/2023]
Abstract
Biological processes are highly dynamic, and during plant growth, development, and environmental interactions, they occur and influence each other on diverse spatiotemporal scales. Understanding plant physiology on an organismic scale requires analyzing biological processes from various perspectives, down to the cellular and molecular levels. Ideally, such analyses should be conducted on intact and living plant tissues. Fluorescent protein (FP)-based in vivo biosensing using genetically encoded fluorescent indicators (GEFIs) is a state-of-the-art methodology for directly monitoring cellular ion, redox, sugar, hormone, ATP and phosphatidic acid dynamics, and protein kinase activities in plants. The steadily growing number of diverse but technically compatible genetically encoded biosensors, the development of dual-reporting indicators, and recent achievements in plate-reader-based analyses now allow for GEFI multiplexing: the simultaneous recording of multiple GEFIs in a single experiment. This in turn enables in vivo multiparameter analyses: the simultaneous recording of various biological processes in living organisms. Here, we provide an update on currently established direct FP-based biosensors in plants, discuss their functional principles, and highlight important biological findings accomplished by employing various approaches of GEFI-based multiplexing. We also discuss challenges and provide advice for FP-based biosensor analyses in plants.
Collapse
Affiliation(s)
- Rainer Waadt
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster 48149, Germany
- Author for communication:
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster 48149, Germany
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| |
Collapse
|
3
|
Gheorghiu M, Polonschii C, Popescu O, Gheorghiu E. Advanced Optogenetic-Based Biosensing and Related Biomaterials. MATERIALS 2021; 14:ma14154151. [PMID: 34361345 PMCID: PMC8347019 DOI: 10.3390/ma14154151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
The ability to stimulate mammalian cells with light, brought along by optogenetic control, has significantly broadened our understanding of electrically excitable tissues. Backed by advanced (bio)materials, it has recently paved the way towards novel biosensing concepts supporting bio-analytics applications transversal to the main biomedical stream. The advancements concerning enabling biomaterials and related novel biosensing concepts involving optogenetics are reviewed with particular focus on the use of engineered cells for cell-based sensing platforms and the available toolbox (from mere actuators and reporters to novel multifunctional opto-chemogenetic tools) for optogenetic-enabled real-time cellular diagnostics and biosensor development. The key advantages of these modified cell-based biosensors concern both significantly faster (minutes instead of hours) and higher sensitivity detection of low concentrations of bioactive/toxic analytes (below the threshold concentrations in classical cellular sensors) as well as improved standardization as warranted by unified analytic platforms. These novel multimodal functional electro-optical label-free assays are reviewed among the key elements for optogenetic-based biosensing standardization. This focused review is a potential guide for materials researchers interested in biosensing based on light-responsive biomaterials and related analytic tools.
Collapse
Affiliation(s)
- Mihaela Gheorghiu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
- Correspondence: (M.G.); (E.G.)
| | - Cristina Polonschii
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
| | - Octavian Popescu
- Molecular Biology Center, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai-University, 400084 Cluj-Napoca, Romania;
- Institute of Biology Bucharest, Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Eugen Gheorghiu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
- Correspondence: (M.G.); (E.G.)
| |
Collapse
|
4
|
Lysyk L, Brassard R, Arutyunova E, Siebert V, Jiang Z, Takyi E, Morrison M, Young HS, Lemberg MK, O'Donoghue AJ, Lemieux MJ. Insights into the catalytic properties of the mitochondrial rhomboid protease PARL. J Biol Chem 2021; 296:100383. [PMID: 33556373 PMCID: PMC7966987 DOI: 10.1016/j.jbc.2021.100383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The rhomboid protease PARL is a critical regulator of mitochondrial homeostasis through its cleavage of substrates such as PINK1, PGAM5, and Smac/Diablo, which have crucial roles in mitochondrial quality control and apoptosis. However, the catalytic properties of PARL, including the effect of lipids on the protease, have never been characterized in vitro. To address this, we isolated human PARL expressed in yeast and used FRET-based kinetic assays to measure proteolytic activity in vitro. We show that PARL activity in detergent is enhanced by cardiolipin, a lipid enriched in the mitochondrial inner membrane. Significantly higher turnover rates were observed for PARL reconstituted in proteoliposomes, with Smac/Diablo being cleaved most rapidly at a rate of 1 min−1. In contrast, PGAM5 is cleaved with the highest efficiency (kcat/KM) compared with PINK1 and Smac/Diablo. In proteoliposomes, a truncated β-cleavage form of PARL, a physiological form known to affect mitochondrial fragmentation, is more active than the full-length enzyme for hydrolysis of PINK1, PGAM5, and Smac/Diablo. Multiplex profiling of 228 peptides reveals that PARL prefers substrates with a bulky side chain such as Phe in P1, which is distinct from the preference for small side chain residues typically found with bacterial rhomboid proteases. This study using recombinant PARL provides fundamental insights into its catalytic activity and substrate preferences that enhance our understanding of its role in mitochondrial function and has implications for specific inhibitor design.
Collapse
Affiliation(s)
- Laine Lysyk
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Raelynn Brassard
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Verena Siebert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Emmanuella Takyi
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Melissa Morrison
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
5
|
Abstract
The electromechanical function of the heart involves complex, coordinated activity over time and space. Life-threatening cardiac arrhythmias arise from asynchrony in these space-time events; therefore, therapies for prevention and treatment require fundamental understanding and the ability to visualize, perturb and control cardiac activity. Optogenetics combines optical and molecular biology (genetic) approaches for light-enabled sensing and actuation of electrical activity with unprecedented spatiotemporal resolution and parallelism. The year 2020 marks a decade of developments in cardiac optogenetics since this technology was adopted from neuroscience and applied to the heart. In this Review, we appraise a decade of advances that define near-term (immediate) translation based on all-optical electrophysiology, including high-throughput screening, cardiotoxicity testing and personalized medicine assays, and long-term (aspirational) prospects for clinical translation of cardiac optogenetics, including new optical therapies for rhythm control. The main translational opportunities and challenges for optogenetics to be fully embraced in cardiology are also discussed.
Collapse
|
6
|
Somuncu ÖS, Berns HM, Sanchez JG. New Pioneers of Optogenetics in Neuroscience. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1288:47-60. [PMID: 31983055 DOI: 10.1007/5584_2019_473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Optogenetics have recently increased in popularity as tools to study behavior in response to the brain and how these trends relate back to a neuronal circuit. Additionally, the high demand for human cerebral tissue in research has led to the generation of a new model to investigate human brain development and disease. Human Pluripotent Stem Cells (hPSCs) have been previously used to recapitulate the development of several tissues such as intestine, stomach and liver and to model disease in a human context, recently new improvements have been made in the field of hPSC-derived brain organoids to better understand overall brain development but more specifically, to mimic inter-neuronal communication. This review aims to highlight the recent advances in these two separate approaches of brain research and to emphasize the need for overlap. These two novel approaches would combine the study of behavior along with the specific circuits required to produce the signals causing such behavior. This review is focused on the current state of the field, as well as the development of novel optogenetic technologies and their potential for current scientific study and potential therapeutic use.
Collapse
Affiliation(s)
- Ö Sezin Somuncu
- Department of Medical Biology, Bahçeşehir University Faculty of Medicine, İstanbul, Turkey.
| | - H Matthew Berns
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - J Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| |
Collapse
|
7
|
Sun F, Zhou J, Dai B, Qian T, Zeng J, Li X, Zhuo Y, Zhang Y, Wang Y, Qian C, Tan K, Feng J, Dong H, Lin D, Cui G, Li Y. Next-generation GRAB sensors for monitoring dopaminergic activity in vivo. Nat Methods 2020; 17:1156-1166. [PMID: 33087905 PMCID: PMC7648260 DOI: 10.1038/s41592-020-00981-9] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022]
Abstract
Dopamine (DA) plays a critical role in the brain, and the ability to directly measure dopaminergic activity is essential for understanding its physiological functions. We therefore developed red fluorescent G-protein-coupled receptor-activation-based DA (GRABDA) sensors and optimized versions of green fluorescent GRABDA sensors. In response to extracellular DA, both the red and green GRABDA sensors exhibit a large increase in fluorescence, with subcellular resolution, subsecond kinetics and nanomolar-to-submicromolar affinity. Moreover, the GRABDA sensors resolve evoked DA release in mouse brain slices, detect evoked compartmental DA release from a single neuron in live flies and report optogenetically elicited nigrostriatal DA release as well as mesoaccumbens dopaminergic activity during sexual behavior in freely behaving mice. Coexpressing red GRABDA with either green GRABDA or the calcium indicator GCaMP6s allows tracking of dopaminergic signaling and neuronal activity in distinct circuits in vivo.
Collapse
Affiliation(s)
- Fangmiao Sun
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Jingheng Zhou
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Bing Dai
- Neuroscience Institute, Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Tongrui Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Jianzhi Zeng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Xuelin Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yizhou Zhuo
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Yajun Zhang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Yipan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Cheng Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ke Tan
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Jiesi Feng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Hui Dong
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Dayu Lin
- Neuroscience Institute, Department of Psychiatry, New York University School of Medicine, New York, NY, USA.
| | - Guohong Cui
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, China.
| |
Collapse
|
8
|
Intensiometric biosensors visualize the activity of multiple small GTPases in vivo. Nat Commun 2019; 10:211. [PMID: 30643148 PMCID: PMC6331645 DOI: 10.1038/s41467-018-08217-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/22/2018] [Indexed: 01/21/2023] Open
Abstract
Ras and Rho small GTPases are critical for numerous cellular processes including cell division, migration, and intercellular communication. Despite extensive efforts to visualize the spatiotemporal activity of these proteins, achieving the sensitivity and dynamic range necessary for in vivo application has been challenging. Here, we present highly sensitive intensiometric small GTPase biosensors visualizing the activity of multiple small GTPases in single cells in vivo. Red-shifted sensors combined with blue light-controllable optogenetic modules achieved simultaneous monitoring and manipulation of protein activities in a highly spatiotemporal manner. Our biosensors revealed spatial dynamics of Cdc42 and Ras activities upon structural plasticity of single dendritic spines, as well as a broad range of subcellular Ras activities in the brains of freely behaving mice. Thus, these intensiometric small GTPase sensors enable the spatiotemporal dissection of complex protein signaling networks in live animals. FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.
Collapse
|
9
|
Kim J, Heo WD. Synergistic Ensemble of Optogenetic Actuators and Dynamic Indicators in Cell Biology. Mol Cells 2018; 41:809-817. [PMID: 30157546 PMCID: PMC6182222 DOI: 10.14348/molcells.2018.0295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bioimaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.
Collapse
Affiliation(s)
- Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141,
Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| |
Collapse
|
10
|
Walia A, Waadt R, Jones AM. Genetically Encoded Biosensors in Plants: Pathways to Discovery. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:497-524. [PMID: 29719164 DOI: 10.1146/annurev-arplant-042817-040104] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genetically encoded biosensors that directly interact with a molecule of interest were first introduced more than 20 years ago with fusion proteins that served as fluorescent indicators for calcium ions. Since then, the technology has matured into a diverse array of biosensors that have been deployed to improve our spatiotemporal understanding of molecules whose dynamics have profound influence on plant physiology and development. In this review, we address several types of biosensors with a focus on genetically encoded calcium indicators, which are now the most diverse and advanced group of biosensors. We then consider the discoveries in plant biology made by using biosensors for calcium, pH, reactive oxygen species, redox conditions, primary metabolites, phytohormones, and nutrients. These discoveries were dependent on the engineering, characterization, and optimization required to develop a successful biosensor; they were also dependent on the methodological developments required to express, detect, and analyze the readout of such biosensors.
Collapse
Affiliation(s)
- Ankit Walia
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, United Kingdom;
| | - Rainer Waadt
- Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander M Jones
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, United Kingdom;
| |
Collapse
|
11
|
Bielecki J, Garm A. Vision Made Easy: Cubozoans Can Advance Our Understanding of Systems-Level Visual Information Processing. Results Probl Cell Differ 2018; 65:599-624. [PMID: 30083938 DOI: 10.1007/978-3-319-92486-1_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Animals relying on vision as their main sensory modality reserve a large part of their central nervous system to appropriately navigate their environment. In general, neural involvement correlates to the complexity of the visual system and behavioural repertoire. In humans, one third of the available neural capacity supports our single-chambered general-purpose eyes, whereas animals with less elaborate visual systems need less computational power, and generally have smaller brains, and thereby lack in visual behaviour. As a consequence, both traditional model animals (mice, zebrafish, and flies) and more experimentally tractable animals (Hydra, Planaria, and C. elegans) cannot contribute to our understanding of systems-level visual information processing-a Goldilocks case of too big and too small.However, one animal, the box jellyfish Tripedalia cystophora, possesses a rather complex visual system, displays multiple visual behaviours, yet processes visual information by means of a relatively simple central nervous system. This-just right-model system could not only provide information on how visual stimuli are processed through distinct combinations of neural circuitry but also provide a processing algorithm for extracting specific information from a complex visual scene.
Collapse
Affiliation(s)
- Jan Bielecki
- GEOMAR - Helmholtz Centre for Ocean Research, Kiel, Germany.
- Institute of Physiology, Christian Albrechts University, Kiel, Germany.
| | - Anders Garm
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
12
|
Koopman CD, Zimmermann WH, Knöpfel T, de Boer TP. Cardiac optogenetics: using light to monitor cardiac physiology. Basic Res Cardiol 2017; 112:56. [PMID: 28861604 PMCID: PMC5579185 DOI: 10.1007/s00395-017-0645-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/28/2017] [Indexed: 12/12/2022]
Abstract
Our current understanding of cardiac excitation and its coupling to contraction is largely based on ex vivo studies utilising fluorescent organic dyes to assess cardiac action potentials and signal transduction. Recent advances in optogenetic sensors open exciting new possibilities for cardiac research and allow us to answer research questions that cannot be addressed using the classic organic dyes. Especially thrilling is the possibility to use optogenetic sensors to record parameters of cardiac excitation and contraction in vivo. In addition, optogenetics provide a high spatial resolution, as sensors can be coupled to motifs and targeted to specific cell types and subcellular domains of the heart. In this review, we will give a comprehensive overview of relevant optogenetic sensors, how they can be utilised in cardiac research and how they have been applied in cardiac research up to now.
Collapse
Affiliation(s)
- Charlotte D Koopman
- Department of Medical Physiology, University Medical Center Utrecht, Yalelaan 50, 3584CM, Utrecht, The Netherlands.,Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, 3584CT, Utrecht, The Netherlands
| | - Wolfram H Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany.,DHZK (German Center for Cardiovascular Research), Partner Site, Göttingen, Germany
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London, UK.,Centre for Neurotechnology, Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Teun P de Boer
- Department of Medical Physiology, University Medical Center Utrecht, Yalelaan 50, 3584CM, Utrecht, The Netherlands.
| |
Collapse
|
13
|
Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
Collapse
Affiliation(s)
- Martin Pelosse
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Cécile Cottet-Rousselle
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Alexei Grichine
- Inserm, U1055 and U1209, Grenoble, France.,Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | | | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France. .,Inserm, U1055 and U1209, Grenoble, France.
| |
Collapse
|
14
|
Chernov KG, Redchuk TA, Omelina ES, Verkhusha VV. Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes. Chem Rev 2017; 117:6423-6446. [DOI: 10.1021/acs.chemrev.6b00700] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Konstantin G. Chernov
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Taras A. Redchuk
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Evgeniya S. Omelina
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Vladislav V. Verkhusha
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
- Department
of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
15
|
Photoswitchable dual-color fluorescent particles from seeded emulsion polymerization and role of some affecting parameters on FRET process. Eur Polym J 2017. [DOI: 10.1016/j.eurpolymj.2017.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Spangler SM, Bruchas MR. Optogenetic approaches for dissecting neuromodulation and GPCR signaling in neural circuits. Curr Opin Pharmacol 2017; 32:56-70. [PMID: 27875804 PMCID: PMC5395328 DOI: 10.1016/j.coph.2016.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022]
Abstract
Optogenetics has revolutionized neuroscience by providing means to control cell signaling with spatiotemporal control in discrete cell types. In this review, we summarize four major classes of optical tools to manipulate neuromodulatory GPCR signaling: opsins (including engineered chimeric receptors); photoactivatable proteins; photopharmacology through caging-photoswitchable molecules; fluorescent protein based reporters and biosensors. Additionally, we highlight technologies to utilize these tools in vitro and in vivo, including Cre dependent viral vector expression and two-photon microscopy. These emerging techniques targeting specific members of the GPCR signaling pathway offer an expansive base for investigating GPCR signaling in behavior and disease states, in addition to paving a path to potential therapeutic developments.
Collapse
Affiliation(s)
- Skylar M Spangler
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R Bruchas
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
17
|
Karreman MA, Hyenne V, Schwab Y, Goetz JG. Intravital Correlative Microscopy: Imaging Life at the Nanoscale. Trends Cell Biol 2016; 26:848-863. [DOI: 10.1016/j.tcb.2016.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 01/04/2023]
|
18
|
Abdelfattah AS, Farhi SL, Zhao Y, Brinks D, Zou P, Ruangkittisakul A, Platisa J, Pieribone VA, Ballanyi K, Cohen AE, Campbell RE. A Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices. J Neurosci 2016; 36:2458-72. [PMID: 26911693 PMCID: PMC4764664 DOI: 10.1523/jneurosci.3484-15.2016] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/16/2015] [Accepted: 01/15/2016] [Indexed: 01/09/2023] Open
Abstract
Optical imaging of voltage indicators based on green fluorescent proteins (FPs) or archaerhodopsin has emerged as a powerful approach for detecting the activity of many individual neurons with high spatial and temporal resolution. Relative to green FP-based voltage indicators, a bright red-shifted FP-based voltage indicator has the intrinsic advantages of lower phototoxicity, lower autofluorescent background, and compatibility with blue-light-excitable channelrhodopsins. Here, we report a bright red fluorescent voltage indicator (fluorescent indicator for voltage imaging red; FlicR1) with properties that are comparable to the best available green indicators. To develop FlicR1, we used directed protein evolution and rational engineering to screen libraries of thousands of variants. FlicR1 faithfully reports single action potentials (∼3% ΔF/F) and tracks electrically driven voltage oscillations at 100 Hz in dissociated Sprague Dawley rat hippocampal neurons in single trial recordings. Furthermore, FlicR1 can be easily imaged with wide-field fluorescence microscopy. We demonstrate that FlicR1 can be used in conjunction with a blue-shifted channelrhodopsin for all-optical electrophysiology, although blue light photoactivation of the FlicR1 chromophore presents a challenge for applications that require spatially overlapping yellow and blue excitation.
Collapse
Affiliation(s)
- Ahmed S Abdelfattah
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Samouil L Farhi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yongxin Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520, Neurobiology, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Physics, Harvard University, Cambridge, Massachusetts 02138, and Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada,
| |
Collapse
|
19
|
Song C, Knöpfel T. Optogenetics enlightens neuroscience drug discovery. Nat Rev Drug Discov 2015; 15:97-109. [DOI: 10.1038/nrd.2015.15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Zhao M, Alleva R, Ma H, Daniel AGS, Schwartz TH. Optogenetic tools for modulating and probing the epileptic network. Epilepsy Res 2015; 116:15-26. [PMID: 26354163 PMCID: PMC4567692 DOI: 10.1016/j.eplepsyres.2015.06.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/29/2015] [Accepted: 06/14/2015] [Indexed: 12/01/2022]
Abstract
Epilepsy affects roughly 1% of the population worldwide. Although effective treatments with antiepileptic drugs are available, more than 20% of patients have seizures that are refractory to medical therapy and many patients experience adverse effects. Hence, there is a continued need for novel therapies for those patients. A new technique called "optogenetics" may offer a new hope for these refractory patients. Optogenetics is a technology based on the combination of optics and genetics, which can control or record neural activity with light. Following delivery of light-sensitive opsin genes such as channelrhodopsin-2 (ChR2), halorhodopsin (NpHR), and others into brain, excitation or inhibition of specific neurons in precise brain areas can be controlled by illumination at different wavelengths with very high temporal and spatial resolution. Neuromodulation with the optogenetics toolbox have already been shown to be effective at treating seizures in animal models of epilepsy. This review will outline the most recent advances in epilepsy research with optogenetic techniques and discuss how this technology can contribute to our understanding and treatment of epilepsy in the future.
Collapse
Affiliation(s)
- Mingrui Zhao
- Department of Neurological Surgery, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA.
| | - Rose Alleva
- Department of Neurological Surgery, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA.
| | - Hongtao Ma
- Department of Neurological Surgery, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA.
| | - Andy G S Daniel
- Department of Neurological Surgery, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA.
| | - Theodore H Schwartz
- Department of Neurological Surgery, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA; Department of Otolaryngology, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA; Department of Neuroscience, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10021, USA.
| |
Collapse
|
22
|
Li D, Liu L, Li WH. Genetic targeting of a small fluorescent zinc indicator to cell surface for monitoring zinc secretion. ACS Chem Biol 2015; 10:1054-63. [PMID: 25572404 DOI: 10.1021/cb5007536] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Numerous mammalian cells contain Zn2+ in their secretory granules. During secretion, Zn2+ is coreleased with granular cargos into extracellular medium so Zn2+ serves as a convenient surrogate marker for tracking the dynamics of secretion. Fluorescent Zn2+ sensors that can be selectively targeted to cells of interest would be invaluable tools for imaging Zn2+ release in multicellular systems including tissues and live animals. Exploiting the HaloTag labeling technology and using an optimized linker, we have engineered a fluorescent Zn2+ indicator that displayed a 15-fold fluorescence enhancement upon Zn2+ binding while reacting efficiently with a HaloTag enzyme in a cellular environment. Two-color imaging of ZIMIR-HaloTag and a red-emitting calcium indicator in pancreatic islet beta cells demonstrated that photoactivation of a channelrhodopsin was able to induce exocytosis of Zn2+/insulin granules and revealed heterogeneity in secretory activity along the cell membrane that was uncoupled from cellular Ca2+ activity. This integrated photonic approach for imaging and controlling the release of large dense core granules provides exquisite cellular selectivity and should facilitate future studies of stimulus-secretion coupling and paracrine signaling in secretory cells.
Collapse
Affiliation(s)
- Daliang Li
- Departments of Cell Biology
and Biochemistry, University of Texas Southwestern Medical Center, 6000
Harry Hines Boulevard, Dallas, Texas 75390-9039, United States
| | - Lin Liu
- Departments of Cell Biology
and Biochemistry, University of Texas Southwestern Medical Center, 6000
Harry Hines Boulevard, Dallas, Texas 75390-9039, United States
| | - Wen-Hong Li
- Departments of Cell Biology
and Biochemistry, University of Texas Southwestern Medical Center, 6000
Harry Hines Boulevard, Dallas, Texas 75390-9039, United States
| |
Collapse
|
23
|
Mundell NA, Beier KT, Pan YA, Lapan SW, Göz Aytürk D, Berezovskii VK, Wark AR, Drokhlyansky E, Bielecki J, Born RT, Schier AF, Cepko CL. Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms. J Comp Neurol 2015; 523:1639-63. [PMID: 25688551 PMCID: PMC4458151 DOI: 10.1002/cne.23761] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/03/2015] [Accepted: 02/10/2015] [Indexed: 12/20/2022]
Abstract
Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV‐G) or its own glycoprotein (VSV‐G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods. J. Comp. Neurol. 523:1639–1663, 2015. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Nathan A Mundell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Kevin T Beier
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Y Albert Pan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts, 01238
| | - Sylvain W Lapan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Didem Göz Aytürk
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | | | - Abigail R Wark
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115
| | - Eugene Drokhlyansky
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Jan Bielecki
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, 93106
| | - Richard T Born
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115
| | - Alexander F Schier
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts, 01238
| | - Constance L Cepko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115
| |
Collapse
|
24
|
Abstract
Genetically encoded optical actuators and indicators have changed the landscape of neuroscience, enabling targetable control and readout of specific components of intact neural circuits in behaving animals. Here, we review the development of optical neural interfaces, focusing on hardware designed for optical control of neural activity, integrated optical control and electrical readout, and optical readout of population and single-cell neural activity in freely moving mammals.
Collapse
Affiliation(s)
- Melissa R Warden
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853;
| | | | | |
Collapse
|
25
|
Takamura A, Hattori M, Yoshimura H, Ozawa T. Simultaneous time-lamination imaging of protein association using a split fluorescent timer protein. Anal Chem 2015; 87:3366-72. [PMID: 25679333 DOI: 10.1021/ac504583t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of temporal behaviors of protein association in living cells are crucially important for elucidating the fundamental roles and the mechanism of interactive coordination for cell activities. We developed a method for investigating the temporal alternation of a particular protein assembly using monomeric fluorescent proteins, fluorescent timers (FTs), of which the fluorescent color changes from blue to red over time. We identified a dissection site of the FTs, which allows complementation of the split FT fragments. The split fragments of each FT variant recovered their fluorescence and maintained inherent rates of the color changes upon the reassembly of the fragments in vitro. We applied this method to visualize the aggregation process of α-synuclein in living cells. The size of the aggregates with the temporal information was analyzed from ratio values of the blue and red fluorescence of the reconstituted FTs, from which the aggregation rates were evaluated. This method using the split FT fragments enables tracing and visualizing temporal alternations of various protein associations by single fluorescence measurements at a given time point.
Collapse
Affiliation(s)
- Ayari Takamura
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuru Hattori
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
26
|
Mishina Y, Mutoh H, Song C, Knöpfel T. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain. Front Mol Neurosci 2014; 7:78. [PMID: 25324718 PMCID: PMC4179510 DOI: 10.3389/fnmol.2014.00078] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/14/2014] [Indexed: 11/13/2022] Open
Abstract
Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviors. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs) has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP) prototypical design or on the voltage-dependent state transitions of microbial opsins. We recently introduced a new VSFP design in which the voltage-sensing domain (VSD) is sandwiched between a fluorescence resonance energy transfer pair of fluorescent proteins (termed VSFP-Butterflies) and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.
Collapse
Affiliation(s)
- Yukiko Mishina
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute Wako, Japan ; Centre for Global Communication Strategies, The University of Tokyo Tokyo, Japan
| | - Hiroki Mutoh
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute Wako, Japan ; Department of Neurophysiology, Hamamatsu University School of Medicine Shizuoka, Japan
| | - Chenchen Song
- Division of Brain Sciences, Department of Medicine, Imperial College London London, UK
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute Wako, Japan ; Division of Brain Sciences, Department of Medicine, Imperial College London London, UK
| |
Collapse
|
27
|
Abstract
Any bilayer lipid membrane can support a membrane voltage. The combination of optical perturbation and optical readout of membrane voltage opens the door to studies of electrophysiology in a huge variety of systems previously inaccessible to electrode-based measurements. Yet, the application of optogenetic electrophysiology requires careful reconsideration of the fundamentals of bioelectricity. Rules of thumb appropriate for neuroscience and cardiology may not apply in systems with dramatically different sizes, lipid compositions, charge carriers, or protein machinery. Optogenetic tools are not electrodes; thus, optical and electrode-based measurements have different quirks. Here we review the fundamental aspects of bioelectricity with the aim of laying a conceptual framework for all-optical electrophysiology.
Collapse
Affiliation(s)
- Adam E Cohen
- Department of Chemistry and Chemical Biology and
| | | |
Collapse
|
28
|
Waadt R, Hitomi K, Nishimura N, Hitomi C, Adams SR, Getzoff ED, Schroeder JI. FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis. eLife 2014; 3:e01739. [PMID: 24737861 PMCID: PMC3985518 DOI: 10.7554/elife.01739] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abscisic acid (ABA) is a plant hormone that regulates plant growth and development and mediates abiotic stress responses. Direct cellular monitoring of dynamic ABA concentration changes in response to environmental cues is essential for understanding ABA action. We have developed ABAleons: ABA-specific optogenetic reporters that instantaneously convert the phytohormone-triggered interaction of ABA receptors with PP2C-type phosphatases to send a fluorescence resonance energy transfer (FRET) signal in response to ABA. We report the design, engineering and use of ABAleons with ABA affinities in the range of 100–600 nM to map ABA concentration changes in plant tissues with spatial and temporal resolution. High ABAleon expression can partially repress Arabidopsis ABA responses. ABAleons report ABA concentration differences in distinct cell types, ABA concentration increases in response to low humidity and NaCl in guard cells and to NaCl and osmotic stress in roots and ABA transport from the hypocotyl to the shoot and root. DOI:http://dx.doi.org/10.7554/eLife.01739.001 Plants are able to respond to detrimental changes in their environment—when, for example, water becomes scarce or the soil becomes too salty—in ways that minimize stress and damage caused by these changes. Hormones are chemicals that trigger the plant’s response under these circumstances. Abscisic acid is the hormone that regulates how plants respond to drought and salt stress and that controls the plant growth in these conditions. In the past, it was possible to measure the average level of this hormone in a given tissue, but not the level in individual cells in a living plant. Moreover, it was difficult to follow directly how abscisic acid moved between the plant cells, tissues or organs. Now, Waadt et al. (and independently Jones et al.) have developed tools that can measure the levels of abscisic acid within individual cells in living plants and in real time. The plants were genetically engineered to produce sensor proteins with two properties: they can bind to abscisic acid in a reversible manner, and they contain two ‘tags’ that fluoresce at different wavelengths. Shining light onto the plant at a specific wavelength that is only absorbed by one of the tags actually causes both of the tags on the sensor proteins to fluoresce. However, the sensors fluoresce more at one wavelength when they are bound to abscisic acid, and more at the other wavelength when they are not bound to abscisic acid. Hence, measuring the ratio of these two wavelengths in the light that is given off by the sensor proteins can be used as a measure of the concentration of abscisic acid in a plant cell. Waadt et al. developed sensor proteins called ‘ABAleons’, and used one of these to analyze the uptake, distribution and movement of abscisic acid in different tissues in the model plant Arabidopsis thaliana. Changes in the level of abscisic acid could be detected at the level of an individual plant cell, and over time scales of fractions of seconds to hours. ABAleons also revealed that the concentration of abscisic acid in guard cells—specialized cells that help stop the loss of water vapor from a leaf—increases when humidity levels are low, or when salt levels are high. Low water levels, or high salt levels, also slowly increased the concentration of abscisic acid in the roots of the plant. Furthermore, Waadt et al. saw that abscisic acid moved long distances from the base of the stem up into the shoot, and down to the root. Waadt et al. also report that the ABAleons made plants less responsive to abscisic acid, possibly because binding to the ABAleons reduced the amount of abscisic acid that was available to perform its role as a hormone. The next challenge is to engineer ABAleons that minimize this unwanted side effect, and then go on to use ABAleons to study environmental conditions and proteins involved in plant hormone responses. DOI:http://dx.doi.org/10.7554/eLife.01739.002
Collapse
Affiliation(s)
- Rainer Waadt
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, United States
| | | | | | | | | | | | | |
Collapse
|
29
|
Pollock JD, Wu DY, Satterlee JS. Molecular neuroanatomy: a generation of progress. Trends Neurosci 2014; 37:106-23. [PMID: 24388609 PMCID: PMC3946666 DOI: 10.1016/j.tins.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 11/22/2022]
Abstract
The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.
Collapse
Affiliation(s)
- Jonathan D Pollock
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA.
| | - Da-Yu Wu
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - John S Satterlee
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
| |
Collapse
|
30
|
Carlson HJ, Campbell RE. Circular permutated red fluorescent proteins and calcium ion indicators based on mCherry. Protein Eng Des Sel 2013; 26:763-72. [PMID: 24151339 DOI: 10.1093/protein/gzt052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Red fluorescent indicators for calcium ion (Ca(2+)) are preferable, relative to blue-shifted alternatives, for biological imaging applications due to the lower phototoxicity, lower autofluorescent background and deeper tissue penetration associated with longer wavelength light. Accordingly, we undertook the development of a genetically encoded Ca(2+) indicator based on the popular and widely utilized Discosoma-derived red fluorescent protein, mCherry. Starting from a promising but dimly fluorescent circular permutated variant of mCherry, we first engineered a 13-fold brighter variant (cp196V1.2) through directed evolution. This bright cp196V1.2 was then used as the scaffold for creation of eight distinct libraries of potential Ca(2+) indicators via permutation at different sites within the 7th and 10th β-strands, and fusion of calmodulin and M13 to the new termini. Screening of these libraries led to the conclusion that, consistent with previous investigations of homologous fluorescent proteins, the 146-145 site in β-strand 7 is the most promising permutation site for construction of useful Ca(2+) indicators. Further rounds of directed evolution ultimately led to an indicator that exhibits a 250% change in intrinsic brightness in response to Ca(2+) and an exceptionally high affinity (Kd = 6 nM) for Ca(2+).
Collapse
Affiliation(s)
- Haley J Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | | |
Collapse
|
31
|
Wu J, Liu L, Matsuda T, Zhao Y, Rebane A, Drobizhev M, Chang YF, Araki S, Arai Y, March K, Hughes TE, Sagou K, Miyata T, Nagai T, Li WH, Campbell RE. Improved orange and red Ca²± indicators and photophysical considerations for optogenetic applications. ACS Chem Neurosci 2013; 4:963-72. [PMID: 23452507 PMCID: PMC3689190 DOI: 10.1021/cn400012b] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/01/2013] [Indexed: 11/30/2022] Open
Abstract
We have used protein engineering to expand the palette of genetically encoded calcium ion (Ca(2+)) indicators to include orange and improved red fluorescent variants, and validated the latter for combined use with optogenetic activation by channelrhodopsin-2 (ChR2). These indicators feature intensiometric signal changes that are 1.7- to 9.7-fold improved relatively to the progenitor Ca(2+) indicator, R-GECO1. In the course of this work, we discovered a photoactivation phenomenon in red fluorescent Ca(2+) indicators that, if not appreciated and accounted for, can cause false-positive artifacts in Ca(2+) imaging traces during optogenetic activation with ChR2. We demonstrate, in both a beta cell line and slice culture of developing mouse neocortex, that these artifacts can be avoided by using an appropriately low intensity of blue light for ChR2 activation.
Collapse
Affiliation(s)
- Jiahui Wu
- Department of Chemistry, University
of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lin Liu
- Departments of Cell Biology and of
Biochemistry, University of Texas Southwestern Medical
Center, 6000 Harry Hines Blvd, Dallas, Texas 75390-9039,
United States
| | - Tomoki Matsuda
- The Institute
of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047 Japan
| | - Yongxin Zhao
- Department of Chemistry, University
of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Aleksander Rebane
- Department of Physics, Montana
State University, Bozeman, Montana 59717, United States
| | - Mikhail Drobizhev
- Department of Physics, Montana
State University, Bozeman, Montana 59717, United States
| | - Yu-Fen Chang
- The Institute
of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047 Japan
| | - Satoko Araki
- The Institute
of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047 Japan
| | - Yoshiyuki Arai
- The Institute
of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047 Japan
| | - Kelsey March
- 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
| | - Ken Sagou
- Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Takaki Miyata
- Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Takeharu Nagai
- The Institute
of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047 Japan
| | - Wen-hong Li
- Departments of Cell Biology and of
Biochemistry, University of Texas Southwestern Medical
Center, 6000 Harry Hines Blvd, Dallas, Texas 75390-9039,
United States
| | - Robert E. Campbell
- Department of Chemistry, University
of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
32
|
Li WH, Li D. Fluorescent probes for monitoring regulated secretion. Curr Opin Chem Biol 2013; 17:672-81. [PMID: 23711436 DOI: 10.1016/j.cbpa.2013.04.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 01/14/2023]
Abstract
Numerous secretory cells use the regulated secretory pathway to release signaling molecules. Regulated secretion is an essential component of the intercellular communication network of a multicellular organism and serves diverse functions in neurobiology, endocrinology, and many other aspects of animal physiology. Probes that can monitor a specific exocytotic event with high temporal and spatial resolution would be invaluable tools for studying the molecular and cellular mechanisms underlying stimulus-secretion coupling, and for characterizing secretion defects that are found in different human diseases. This review summarizes different strategies and recent progress in developing fluorescent sensors for imaging regulated cell secretion.
Collapse
Affiliation(s)
- Wen-hong Li
- Department of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9039, United States.
| | | |
Collapse
|
33
|
Reynolds III JE, Josowicz M, Tyler P, Vegh RB, Solntsev KM. Spectral and redox properties of the GFP synthetic chromophores as a function of pH in buffered media. Chem Commun (Camb) 2013; 49:7788-90. [DOI: 10.1039/c3cc44113j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|