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Matsuda T, Sakai S, Okazaki KI, Nagai T. Improvement of the Green-Red Förster Resonance Energy Transfer-Based Ca 2+ Indicator by Using the Green Fluorescent Protein, Gamillus, with a Trans Chromophore as the Donor. ACS Sens 2024; 9:1743-1748. [PMID: 38515268 PMCID: PMC11059083 DOI: 10.1021/acssensors.3c02398] [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: 11/11/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
To monitor the Ca2+ dynamics in cells, various genetically encoded Ca2+ indicators (GECIs) based on Förster resonance energy transfer (FRET) between fluorescent proteins are widely used for live imaging. Conventionally, cyan and yellow fluorescent proteins have been often used as FRET pairs. Meanwhile, bathochromically shifted indicators with green and red fluorescent protein pairs have various advantages, such as low toxicity and autofluorescence in cells. However, it remains difficult to develop them with a similar level of dynamic range as cyan and yellow fluorescent protein pairs. To improve this, we used Gamillus, which has a unique trans-configuration chromophore, as a green fluorescent protein. Based on one of the best high-dynamic-range GECIs, Twitch-NR, we developed a GECI with 1.5-times higher dynamic range (253%), Twitch-GmRR, using RRvT as a red fluorescent protein. Twitch-GmRR had high brightness and photostability and was successfully applied for imaging the Ca2+ dynamics in live cells. Our results suggest that Gamillus with trans-type chromophores contributes to improving the dynamic range of GECIs. Therefore, selection of the cis-trans isomer of the chromophore may be a fundamental approach to improve the dynamic range of green-red FRET indicators, unlimited by GECIs.
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Affiliation(s)
- Tomoki Matsuda
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shinya Sakai
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kei-ichi Okazaki
- Research
Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate
Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Takeharu Nagai
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [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] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Parkkinen I, Their A, Asghar MY, Sree S, Jokitalo E, Airavaara M. Pharmacological Regulation of Endoplasmic Reticulum Structure and Calcium Dynamics: Importance for Neurodegenerative Diseases. Pharmacol Rev 2023; 75:959-978. [PMID: 37127349 DOI: 10.1124/pharmrev.122.000701] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 05/03/2023] Open
Abstract
The endoplasmic reticulum (ER) is the largest organelle of the cell, composed of a continuous network of sheets and tubules, and is involved in protein, calcium (Ca2+), and lipid homeostasis. In neurons, the ER extends throughout the cell, both somal and axodendritic compartments, and is highly important for neuronal functions. A third of the proteome of a cell, secreted and membrane-bound proteins, are processed within the ER lumen and most of these proteins are vital for neuronal activity. The brain itself is high in lipid content, and many structural lipids are produced, in part, by the ER. Cholesterol and steroid synthesis are strictly regulated in the ER of the blood-brain barrier protected brain cells. The high Ca2+ level in the ER lumen and low cytosolic concentration is needed for Ca2+-based intracellular signaling, for synaptic signaling and Ca2+ waves, and for preparing proteins for correct folding in the presence of high Ca2+ concentrations to cope with the high concentrations of extracellular milieu. Particularly, ER Ca2+ is controlled in axodendritic areas for proper neurito- and synaptogenesis and synaptic plasticity and remodeling. In this review, we cover the physiologic functions of the neuronal ER and discuss it in context of common neurodegenerative diseases, focusing on pharmacological regulation of ER Ca2+ Furthermore, we postulate that heterogeneity of the ER, its protein folding capacity, and ensuring Ca2+ regulation are crucial factors for the aging and selective vulnerability of neurons in various neurodegenerative diseases. SIGNIFICANCE STATEMENT: Endoplasmic reticulum (ER) Ca2+ regulators are promising therapeutic targets for degenerative diseases for which efficacious drug therapies do not exist. The use of pharmacological probes targeting maintenance and restoration of ER Ca2+ can provide restoration of protein homeostasis (e.g., folding of complex plasma membrane signaling receptors) and slow down the degeneration process of neurons.
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Affiliation(s)
- Ilmari Parkkinen
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
| | - Anna Their
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
| | - Muhammad Yasir Asghar
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
| | - Sreesha Sree
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
| | - Mikko Airavaara
- Neuroscience Center (I.P., A.T., M.A.), Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy (I.P., M.A.), Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (M.Y.A., S.S., E.J.), and Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Sciences (E.J.), University of Helsinki, Helsinki, Finland
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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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Gohil K, Wu SY, Takahashi-Yamashiro K, Shen Y, Campbell RE. Biosensor Optimization Using a Förster Resonance Energy Transfer Pair Based on mScarlet Red Fluorescent Protein and an mScarlet-Derived Green Fluorescent Protein. ACS Sens 2023; 8:587-597. [PMID: 36693235 DOI: 10.1021/acssensors.2c01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are indispensable tools for monitoring biochemical changes in cells. Green and red fluorescent protein-based FRET pairs offer advantages over the classically employed cyan and yellow fluorescent protein pairs, such as better spectral separation, lower phototoxicity, and less autofluorescence. Here, we describe the development of an mScarlet-derived green fluorescent protein (designated as mWatermelon) and its use as a FRET donor to the red fluorescent protein mScarlet-I as a FRET acceptor. We tested the functionality of this FRET pair by engineering biosensors for the detection of protease activity, Ca2+, and K+. Furthermore, we described a strategy to enhance the FRET efficiency of these biosensors by modulating the intramolecular association between mWatermelon and mScarlet-I.
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Affiliation(s)
- Khyati Gohil
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.,Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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Bong AHL, Hua T, So CL, Peters AA, Robitaille M, Tan YY, Roberts-Thomson SJ, Monteith GR. AKT Regulation of ORAI1-Mediated Calcium Influx in Breast Cancer Cells. Cancers (Basel) 2022; 14:cancers14194794. [PMID: 36230716 PMCID: PMC9562175 DOI: 10.3390/cancers14194794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary A remodeling in calcium homeostasis and the protein kinase AKT signaling pathway often promotes tumorigenic traits in cancer cells. Changes in calcium signaling can be mediated through altered expression or activity of calcium channels and pumps, which constitute a class of targetable therapeutic targets. Currently, the interplay between the two signaling pathways in breast cancer cells is unclear. A better understanding of the association between calcium and AKT signaling, and the molecular players involved may identify novel therapeutic strategies for breast cancers with abnormal AKT signaling. Using fluorescence calcium imaging and gene silencing/knockout techniques, we showed that increased AKT activation results in increased calcium entry, and that this is mediated through ORAI1 calcium channels. Future studies exploring therapeutic strategies to target PTEN-deficient or hyperactivated AKT cancers should consider this novel correlation between AKT activation and ORAI1-mediated calcium influx. Abstract Although breast cancer cells often exhibit both abnormal AKT signaling and calcium signaling, the association between these two pathways is unclear. Using a combination of pharmacological tools, siRNA and CRISPR/Cas9 gene silencing techniques, we investigated the association between PTEN, AKT phosphorylation and calcium signaling in a basal breast cancer cell line. We found that siRNA-mediated PTEN silencing promotes AKT phosphorylation and calcium influx in MDA-MB-231 cells. This increase in AKT phosphorylation and calcium influx was phenocopied by the pharmacological AKT activator, SC79. The increased calcium influx associated with SC79 is inhibited by silencing AKT2, but not AKT1. This increase in calcium influx is suppressed when the store-operated calcium channel, ORAI1 is silenced. The results from this study open a novel avenue for therapeutic targeting of cancer cells with increased AKT activation. Given the association between ORAI1 and breast cancer, ORAI1 is a possible therapeutic target in cancers with abnormal AKT signaling.
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Affiliation(s)
- Alice Hui Li Bong
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Trinh Hua
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Choon Leng So
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Amelia A. Peters
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Mélanie Robitaille
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Yin Yi Tan
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | | | - Gregory R. Monteith
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
- Mater Research, Translational Research Institute, The University of Queensland, Brisbane, QLD 4101, Australia
- Correspondence:
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Beck C, Gong Y. Engineering rhodopsins' activation spectra using a FRET-based approach. Biophys J 2022; 121:1765-1776. [PMID: 35331688 PMCID: PMC9117881 DOI: 10.1016/j.bpj.2022.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 03/18/2022] [Indexed: 11/16/2022] Open
Abstract
In the past decade, optogenetics has become a nearly ubiquitous tool in neuroscience because it enables researchers to manipulate neural activity with high temporal resolution and genetic specificity. Rational engineering of optogenetic tools has produced channelrhodopsins with a wide range of kinetics and photocurrent magnitude. Genome mining for previously unidentified species of rhodopsin has uncovered optogenetic tools with diverse spectral sensitivities. However, rational engineering of a rhodopsin has thus far been unable to re-engineer spectral sensitivity while preserving full photocurrent. Here, we developed and characterized ChroME-mTFP, a rhodopsin-fluorescent protein fusion that drives photocurrent through Förster resonance energy transfer (FRET). This FRET-opsin mechanism artificially broadened the activation spectrum of the blue-green-light-activated rhodopsin ChroME by approximately 50 nm, driving higher photocurrent at blue-shifted excitation wavelengths without sacrificing kinetics. The excitation spectra's increase at short wavelengths enabled us to optogenetically excite neurons at lower excitation powers with shorter wavelengths of light. Increasing this rhodopsin's sensitivity to shorter, bluer wavelengths pushes it toward dual-channel, crosstalk-free optogenetic stimulation and imaging with green-light-activated sensors. However, this iteration of FRET-opsin suffers from some imaging-light-induced photocurrent crosstalk from green or yellow light due to maintained, low-efficiency excitation at longer wavelengths.
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Affiliation(s)
- Connor Beck
- Department of Biomedical Engineering, Duke University, Durham, North Carolina.
| | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina.
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