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Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Varizhuk AM, Podgorny OV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C. FEBS Open Bio 2023; 13:2047-2060. [PMID: 37650870 PMCID: PMC10626279 DOI: 10.1002/2211-5463.13702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023] Open
Abstract
Genetically encoded calcium indicators based on truncated troponin C are attractive probes for calcium imaging due to their relatively small molecular size and twofold reduced calcium ion buffering. However, the best-suited members of this family, YTnC and cNTnC, suffer from low molecular brightness, limited dynamic range, and/or poor sensitivity to calcium transients in neurons. To overcome these limitations, we developed an enhanced version of YTnC, named YTnC2. Compared with YTnC, YTnC2 had 5.7-fold higher molecular brightness and 6.4-fold increased dynamic range in vitro. YTnC2 was successfully used to reveal calcium transients in the cytosol and in the lumen of mitochondria of both mammalian cells and cultured neurons. Finally, we obtained and analyzed the crystal structure of the fluorescent domain of the YTnC2 mutant.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Anna V. Vlaskina
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Yulia K. Agapova
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Alena Y. Nikolaeva
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
- Bach Institute of BiochemistryResearch Centre of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical‐Chemical Medicine of Federal Medical Biological AgencyMoscowRussia
- Moscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic ChemistryRASMoscowRussia
- Center for Precision Genome Editing and Genetic Technologies for BiomedicinePirogov Russian National Research Medical UniversityMoscowRussia
- Federal Center of Brain Research and Neurotechnologies of Federal Medical Biological AgencyMoscowRussia
| | - Kiryl D. Piatkevich
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Maxim V. Patrushev
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Konstantin M. Boyko
- Bach Institute of BiochemistryResearch Centre of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Fedor V. Subach
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
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2
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Lambert GG, Crespo EL, Murphy J, Boassa D, Luong S, Celinskis D, Venn S, Hu J, Sprecher B, Tree MO, Orcutt R, Heydari D, Bell AB, Torreblanca-Zanca A, Hakimi A, Lipscombe D, Moore CI, Hochgeschwender U, Shaner NC. CaBLAM! A high-contrast bioluminescent Ca 2+ indicator derived from an engineered Oplophorus gracilirostris luciferase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546478. [PMID: 37425712 PMCID: PMC10327125 DOI: 10.1101/2023.06.25.546478] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Ca2+ plays many critical roles in cell physiology and biochemistry, leading researchers to develop a number of fluorescent small molecule dyes and genetically encodable probes that optically report changes in Ca2+ concentrations in living cells. Though such fluorescence-based genetically encoded Ca2+ indicators (GECIs) have become a mainstay of modern Ca2+ sensing and imaging, bioluminescence-based GECIs-probes that generate light through oxidation of a small-molecule by a luciferase or photoprotein-have several distinct advantages over their fluorescent counterparts. Bioluminescent tags do not photobleach, do not suffer from nonspecific autofluorescent background, and do not lead to phototoxicity since they do not require the extremely bright extrinsic excitation light typically required for fluorescence imaging, especially with 2-photon microscopy. Current BL GECIs perform poorly relative to fluorescent GECIs, producing small changes in bioluminescence intensity due to high baseline signal at resting Ca2+ concentrations and suboptimal Ca2+ affinities. Here, we describe the development of a new bioluminescent GECI, "CaBLAM," which displays a much higher contrast (dynamic range) than previously described bioluminescent GECIs coupled with a Ca2+ affinity suitable for capturing physiological changes in cytosolic Ca2+ concentration. Derived from a new variant of Oplophorus gracilirostris luciferase with superior in vitro properties and a highly favorable scaffold for insertion of sensor domains, CaBLAM allows for single-cell and subcellular resolution imaging of Ca2+ dynamics at high frame rates in cultured neurons. CaBLAM marks a significant milestone in the GECI timeline, enabling Ca2+ recordings with high spatial and temporal resolution without perturbing cells with intense excitation light.
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Affiliation(s)
- Gerard G. Lambert
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
| | | | - Jeremy Murphy
- Carney Institute for Brain Sciences, Department of Neuroscience, Brown University, Providence, RI USA
| | - Daniela Boassa
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
| | - Selena Luong
- University of California San Diego, La Jolla, CA USA
| | - Dmitrijs Celinskis
- Carney Institute for Brain Sciences, Department of Neuroscience, Brown University, Providence, RI USA
| | - Stephanie Venn
- College of Medicine, Central Michigan University, Mt. Pleasant, MI USA
| | - Junru Hu
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA USA
| | - Brittany Sprecher
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
| | - Maya O. Tree
- College of Medicine, Central Michigan University, Mt. Pleasant, MI USA
| | - Richard Orcutt
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
| | - Daniel Heydari
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
| | - Aidan B. Bell
- University of California San Diego, La Jolla, CA USA
| | | | | | - Diane Lipscombe
- College of Medicine, Central Michigan University, Mt. Pleasant, MI USA
| | - Christopher I. Moore
- Carney Institute for Brain Sciences, Department of Neuroscience, Brown University, Providence, RI USA
| | | | - Nathan C. Shaner
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA USA
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3
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Subach OM, Varfolomeeva L, Vlaskina AV, Agapova YK, Nikolaeva AY, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. FNCaMP, ratiometric green calcium indicator based on mNeonGreen protein. Biochem Biophys Res Commun 2023; 665:169-177. [PMID: 37163937 DOI: 10.1016/j.bbrc.2023.04.108] [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: 04/18/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]
Abstract
Neurobiologists widely use green genetically encoded calcium indicators (GECIs) for visualization of neuronal activity. Among them, ratiometric GECIs allow imaging of both active and non-active neuronal populations. However, they are not popular, since their properties are inferior to intensiometric GCaMP series of GECIs. The most characterized and developed ratiometric green GECI is FGCaMP7. However, the dynamic range and sensitivity of its large Stock's shift green (LSS-Green) form is significantly lower than its Green form and its molecular design is not optimal. To address these drawbacks, we engineered a ratiometric green calcium indicator, called FNCaMP, which is based on bright mNeonGreen protein and calmodulin from A. niger and has optimal NTnC-like design. We compared the properties of the FNCaMP and FGCaMP7 indicators in vitro, in mammalian cells, and in neuronal cultures. Finally, we obtained and analyzed X-ray structure of the FNCaMP indicator.
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Affiliation(s)
- Oksana M Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Larisa Varfolomeeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Anna V Vlaskina
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Yulia K Agapova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Alena Y Nikolaeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
| | - Maxim V Patrushev
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Fedor V Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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4
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Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Anokhin KV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers. Int J Mol Sci 2023; 24:ijms24043279. [PMID: 36834686 PMCID: PMC9963904 DOI: 10.3390/ijms24043279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yulia K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D. Piatkevich
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
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5
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FRCaMP, a Red Fluorescent Genetically Encoded Calcium Indicator Based on Calmodulin from Schizosaccharomyces Pombe Fungus. Int J Mol Sci 2020; 22:ijms22010111. [PMID: 33374320 PMCID: PMC7794825 DOI: 10.3390/ijms22010111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Red fluorescent genetically encoded calcium indicators (GECIs) have expanded the available pallet of colors used for the visualization of neuronal calcium activity in vivo. However, their calcium-binding domain is restricted by calmodulin from metazoans. In this study, we developed red GECI, called FRCaMP, using calmodulin (CaM) from Schizosaccharomyces pombe fungus as a calcium binding domain. Compared to the R-GECO1 indicator in vitro, the purified protein FRCaMP had similar spectral characteristics, brightness, and pH stability but a 1.3-fold lower ΔF/F calcium response and 2.6-fold tighter calcium affinity with Kd of 441 nM and 2.4-6.6-fold lower photostability. In the cytosol of cultured HeLa cells, FRCaMP visualized calcium transients with a ΔF/F dynamic range of 5.6, which was similar to that of R-GECO1. FRCaMP robustly visualized the spontaneous activity of neuronal cultures and had a similar ΔF/F dynamic range of 1.7 but 2.1-fold faster decay kinetics vs. NCaMP7. On electrically stimulated cultured neurons, FRCaMP demonstrated 1.8-fold faster decay kinetics and 1.7-fold lower ΔF/F values per one action potential of 0.23 compared to the NCaMP7 indicator. The fungus-originating CaM of the FRCaMP indicator version with a deleted M13-like peptide did not interact with the cytosolic environment of the HeLa cells in contrast to the metazoa-originating CaM of the similarly truncated version of the GCaMP6s indicator with a deleted M13-like peptide. Finally, we generated a split version of the FRCaMP indicator, which allowed the simultaneous detection of calcium transients and the heterodimerization of bJun/bFos interacting proteins in the nuclei of HeLa cells with a ΔF/F dynamic range of 9.4 and a contrast of 2.3-3.5, respectively.
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6
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Pal A, Tian L. Imaging voltage and brain chemistry with genetically encoded sensors and modulators. Curr Opin Chem Biol 2020; 57:166-176. [PMID: 32823064 DOI: 10.1016/j.cbpa.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/21/2023]
Abstract
Neurons and glia are functionally organized into circuits and higher-order structures that allow the precise information processing required for complex behaviors. To better understand the structure and function of the brain, we must understand synaptic connectivity, action potential generation and propagation, as well as well-orchestrated molecular signaling. Recently, dramatically improved sensors for voltage, intracellular calcium, and neurotransmitters/modulators, combined with advanced microscopy provide new opportunities for in vivo dissection of cellular and circuit activity in awake, behaving animals. This review focuses on the current trends in genetically encoded sensors for molecules and cellular events and their potential applicability to the study of nervous system in health and disease.
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Affiliation(s)
- Akash Pal
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
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7
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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8
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Barykina NV, Sotskov VP, Gruzdeva AM, Wu YK, Portugues R, Subach OM, Chefanova ES, Plusnin VV, Ivashkina OI, Anokhin KV, Vlaskina AV, Korzhenevskiy DA, Nikolaeva AY, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Subach FV. FGCaMP7, an Improved Version of Fungi-Based Ratiometric Calcium Indicator for In Vivo Visualization of Neuronal Activity. Int J Mol Sci 2020; 21:ijms21083012. [PMID: 32344594 PMCID: PMC7215472 DOI: 10.3390/ijms21083012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) have become a widespread tool for the visualization of neuronal activity. As compared to popular GCaMP GECIs, the FGCaMP indicator benefits from calmodulin and M13-peptide from the fungi Aspergillus niger and Aspergillus fumigatus, which prevent its interaction with the intracellular environment. However, FGCaMP exhibits a two-phase fluorescence behavior with the variation of calcium ion concentration, has moderate sensitivity in neurons (as compared to the GCaMP6s indicator), and has not been fully characterized in vitro and in vivo. To address these limitations, we developed an enhanced version of FGCaMP, called FGCaMP7. FGCaMP7 preserves the ratiometric phenotype of FGCaMP, with a 3.1-fold larger ratiometric dynamic range in vitro. FGCaMP7 demonstrates 2.7- and 8.7-fold greater photostability compared to mEGFP and mTagBFP2 fluorescent proteins in vitro, respectively. The ratiometric response of FGCaMP7 is 1.6- and 1.4-fold higher, compared to the intensiometric response of GCaMP6s, in non-stimulated and stimulated neuronal cultures, respectively. We reveal the inertness of FGCaMP7 to the intracellular environment of HeLa cells using its truncated version with a deleted M13-like peptide; in contrast to the similarly truncated variant of GCaMP6s. We characterize the crystal structure of the parental FGCaMP indicator. Finally, we test the in vivo performance of FGCaMP7 in mouse brain using a two-photon microscope and an NVista miniscope; and in zebrafish using two-color ratiometric confocal imaging.
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Affiliation(s)
- Natalia V. Barykina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna M. Gruzdeva
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - You Kure Wu
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - Ruben Portugues
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Elizaveta S. Chefanova
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Viktor V. Plusnin
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Olga I. Ivashkina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tatiana V. Rakitina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna M. Varizhuk
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Galina E. Pozmogova
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196-7100-3389
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9
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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Ijomone OM, Aluko OM, Okoh COA, Martins AC, Aschner M. Role for calcium signaling in manganese neurotoxicity. J Trace Elem Med Biol 2019; 56:146-155. [PMID: 31470248 DOI: 10.1016/j.jtemb.2019.08.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Calcium is an essential macronutrient that is involved in many cellular processes. Homeostatic control of intracellular levels of calcium ions [Ca2+] is vital to maintaining cellular structure and function. Several signaling molecules are involved in regulating Ca2+ levels in cells and perturbation of calcium signaling processes is implicated in several neurodegenerative and neurologic conditions. Manganese [Mn] is a metal which is essential for basic physiological functions. However, overexposure to Mn from environmental contamination and workplace hazards is a global concern. Mn overexposure leads to its accumulation in several human organs particularly the brain. Mn accumulation in the brain results in a manganism, a Parkinsonian-like syndrome. Additionally, Mn is a risk factor for several neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. Mn neurotoxicity also affects several neurotransmitter systems including dopaminergic, cholinergic and GABAergic. The mechanisms of Mn neurotoxicity are still being elucidated. AIM The review will highlight a potential role for calcium signaling molecules in the mechanisms of Mn neurotoxicity. CONCLUSION Ca2+ regulation influences the neurodegenerative process and there is possible role for perturbed calcium signaling in Mn neurotoxicity. Mechanisms implicated in Mn-induced neurodegeneration include oxidative stress, generation of free radicals, and apoptosis. These are influenced by mitochondrial integrity which can be dependent on intracellular Ca2+ homeostasis. Nevertheless, further elucidation of the direct effects of calcium signaling dysfunction and calcium-binding proteins activities in Mn neurotoxicity is required.
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Affiliation(s)
- Omamuyovwi M Ijomone
- The Neuro- Lab, Department of Human Anatomy, Federal University of Technology Akure, Ondo, Nigeria.
| | - Oritoke M Aluko
- Department of Physiology, Federal University of Technology Akure, Ondo, Nigeria
| | - Comfort O A Okoh
- The Neuro- Lab, Department of Human Anatomy, Federal University of Technology Akure, Ondo, Nigeria
| | - Airton Cunha Martins
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States.
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Andreoni A, Davis CM, Tian L. Measuring brain chemistry using genetically encoded fluorescent sensors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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Subach OM, Barykina NV, Anokhin KV, Piatkevich KD, Subach FV. Near-Infrared Genetically Encoded Positive Calcium Indicator Based on GAF-FP Bacterial Phytochrome. Int J Mol Sci 2019; 20:ijms20143488. [PMID: 31315229 PMCID: PMC6678319 DOI: 10.3390/ijms20143488] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 02/01/2023] Open
Abstract
A variety of genetically encoded calcium indicators are currently available for visualization of calcium dynamics in cultured cells and in vivo. Only one of them, called NIR-GECO1, exhibits fluorescence in the near-infrared region of the spectrum. NIR-GECO1 is engineered based on the near-infrared fluorescent protein mIFP derived from bacterial phytochromes. However, NIR-GECO1 has an inverted response to calcium ions and its excitation spectrum is not optimal for the commonly used 640 nm lasers. Using small near-infrared bacterial phytochrome GAF-FP and calmodulin/M13-peptide pair, we developed a near-infrared calcium indicator called GAF-CaMP2. In vitro, GAF-CaMP2 showed a positive response of 78% and high affinity (Kd of 466 nM) to the calcium ions. It had excitation and emission maxima at 642 and 674 nm, respectively. GAF-CaMP2 had a 2.0-fold lower brightness, 5.5-fold faster maturation and lower pH stability compared to GAF-FP in vitro. GAF-CaMP2 showed 2.9-fold higher photostability than smURFP protein. The GAF-CaMP2 fusion with sfGFP demonstrated a ratiometric response with a dynamic range of 169% when expressed in the cytosol of mammalian cells in culture. Finally, we successfully applied the ratiometric version of GAF-CaMP2 for the simultaneous visualization of calcium transients in three organelles of mammalian cells using four-color fluorescence microscopy.
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Affiliation(s)
- Oksana M Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | | | - Konstantin V Anokhin
- P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia
- Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Fedor V Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia.
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Advances in Engineering and Application of Optogenetic Indicators for Neuroscience. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9030562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Our ability to investigate the brain is limited by available technologies that can record biological processes in vivo with suitable spatiotemporal resolution. Advances in optogenetics now enable optical recording and perturbation of central physiological processes within the intact brains of model organisms. By monitoring key signaling molecules noninvasively, we can better appreciate how information is processed and integrated within intact circuits. In this review, we describe recent efforts engineering genetically-encoded fluorescence indicators to monitor neuronal activity. We summarize recent advances of sensors for calcium, potassium, voltage, and select neurotransmitters, focusing on their molecular design, properties, and current limitations. We also highlight impressive applications of these sensors in neuroscience research. We adopt the view that advances in sensor engineering will yield enduring insights on systems neuroscience. Neuroscientists are eager to adopt suitable tools for imaging neural activity in vivo, making this a golden age for engineering optogenetic indicators.
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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15
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NTnC-like genetically encoded calcium indicator with a positive and enhanced response and fast kinetics. Sci Rep 2018; 8:15233. [PMID: 30323302 PMCID: PMC6189086 DOI: 10.1038/s41598-018-33613-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/03/2018] [Indexed: 12/16/2022] Open
Abstract
The NTnC genetically encoded calcium indicator has an advantageous design because of its smaller size, GFP-like N- and C-terminal ends and two-fold reduced number of calcium binding sites compared with widely used indicators from the GCaMP family. However, NTnC has an inverted and modest calcium response and a low temporal resolution. By replacing the mNeonGreen fluorescent part in NTnC with EYFP, we engineered an NTnC-like indicator, referred to as YTnC, that had a positive and substantially improved calcium response and faster kinetics. YTnC had a 3-fold higher calcium response and 13.6-fold lower brightness than NTnC in vitro. According to stopped-flow experiments performed in vitro, YTnC had 4-fold faster calcium-dissociation kinetics than NTnC. In HeLa cells, YTnC exhibited a 3.3-fold lower brightness and 4.9-fold increased response to calcium transients than NTnC. The spontaneous activity of neuronal cultures induced a 3.6-fold larger ΔF/F response of YTnC than previously shown for NTnC. On patched neurons, YTnC had a 2.6-fold lower ΔF/F than GCaMP6s. YTnC successfully visualized calcium transients in neurons in the cortex of anesthetized mice and the hippocampus of awake mice using single- and two-photon microscopy. Moreover, YTnC outperformed GCaMP6s in the mitochondria and endoplasmic reticulum of cultured HeLa and neuronal cells.
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