1
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Zhao S, Xiong Y, Sunnapu R, Zhang Y, Tian X, Ai HW. Bioluminescence Imaging of Potassium Ion Using a Sensory Luciferin and an Engineered Luciferase. J Am Chem Soc 2024; 146:13406-13416. [PMID: 38698549 PMCID: PMC11100015 DOI: 10.1021/jacs.4c02473] [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: 02/19/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024]
Abstract
Bioluminescent indicators are power tools for studying dynamic biological processes. In this study, we present the generation of novel bioluminescent indicators by modifying the luciferin molecule with an analyte-binding moiety. Specifically, we have successfully developed the first bioluminescent indicator for potassium ions (K+), which are critical electrolytes in biological systems. Our approach involved the design and synthesis of a K+-binding luciferin named potassiorin. Additionally, we engineered a luciferase enzyme called BRIPO (bioluminescent red indicator for potassium) to work synergistically with potassiorin, resulting in optimized K+-dependent bioluminescence responses. Through extensive validation in cell lines, primary neurons, and live mice, we demonstrated the efficacy of this new tool for detecting K+. Our research demonstrates an innovative concept of incorporating sensory moieties into luciferins to modulate luciferase activity. This approach has great potential for developing a wide range of bioluminescent indicators, advancing bioluminescence imaging (BLI), and enabling the study of various analytes in biological systems.
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Affiliation(s)
- Shengyu Zhao
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ying Xiong
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Ranganayakulu Sunnapu
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Yiyu Zhang
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Xiaodong Tian
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Hui-wang Ai
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Center
for Membrane and Cell Physiology, University
of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
- The
UVA Comprehensive Cancer Center, University
of Virginia, Charlottesville, Virginia 22908, United States
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2
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Tian X, Zhang Y, Ai HW. ATP-Independent Water-Soluble Luciferins Enable Non-Invasive High-Speed Video-Rate Bioluminescence Imaging of Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591933. [PMID: 38746394 PMCID: PMC11092570 DOI: 10.1101/2024.04.30.591933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
NanoLuc luciferase and its derivatives are attractive bioluminescent reporters recognized for their efficient photon production and ATP independence. However, utilizing them for in vivo imaging poses notable challenges. Low substrate solubility has been a prominent problem, limiting in vivo brightness, while substrate instability hampers consistent results and handling. To address these issues, we developed a range of caged PEGylated luciferins with improved stability and water solubility of up to 25 mM, resulting in substantial bioluminescence increases in mouse models. This advancement has created the brightest and most sensitive luciferase-luciferin combination, enabling high-speed video-rate imaging of freely moving mice with brain-expressed luciferase. Furthermore, we developed a bioluminescent Ca 2+ indicator with exceptional sensitivity to physiological Ca 2+ changes and paired it with a new substrate to showcase non-invasive, video-rate imaging of Ca 2+ activity in a defined brain region in awake mice. These innovative substrates and the Ca 2+ indicator are poised to become invaluable resources for biological and biomedical fields.
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3
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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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4
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Zhao S, Xiong Y, Sunnapu R, Zhang Y, Tian X, Ai HW. Bioluminescence Imaging of Potassium Ion Using a Sensory Luciferin and an Engineered Luciferase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.581057. [PMID: 38559024 PMCID: PMC10980066 DOI: 10.1101/2024.03.13.581057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bioluminescent indicators are power tools for studying dynamic biological processes. In this study, we present the generation of novel bioluminescent indicators by modifying the luciferin molecule with an analyte-binding moiety. Specifically, we have successfully developed the first bioluminescent indicator for potassium ions (K+), which are critical electrolytes in biological systems. Our approach involved the design and synthesis of a K+-binding luciferin named potassiorin. Additionally, we engineered a luciferase enzyme called BRIPO (bioluminescent red indicator for potassium) to work synergistically with potassiorin, resulting in optimized K+-dependent bioluminescence responses. Through extensive validation in cell lines, primary neurons, and live mice, we demonstrated the efficacy of this new tool for detecting K+. Our research demonstrates an innovative concept of incorporating sensory moieties into luciferins to modulate luciferase activity. This approach has great potential for developing a wide range of bioluminescent indicators, advancing bioluminescence imaging (BLI), and enabling the study of various analytes in biological systems.
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Affiliation(s)
- Shengyu Zhao
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Ying Xiong
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Ranganayakulu Sunnapu
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Yiyu Zhang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Xiaodong Tian
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Hui-Wang Ai
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia 22908, USA
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5
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Valiente-Gabioud AA, Garteizgogeascoa Suñer I, Idziak A, Fabritius A, Basquin J, Angibaud J, Nägerl UV, Singh SP, Griesbeck O. Fluorescent sensors for imaging of interstitial calcium. Nat Commun 2023; 14:6220. [PMID: 37798285 PMCID: PMC10556026 DOI: 10.1038/s41467-023-41928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Inés Garteizgogeascoa Suñer
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Agata Idziak
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Arne Fabritius
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Julie Angibaud
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - U Valentin Nägerl
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Sumeet Pal Singh
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Oliver Griesbeck
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany.
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6
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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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7
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Valiente-Gabioud AA, Fabritius A, Griesbeck O. Probing the interstitial calcium compartment. J Physiol 2023; 601:4217-4226. [PMID: 36073135 DOI: 10.1113/jp279510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Calcium in interstitial fluids is a crucial ion pool for entry into cells through a plethora of calcium-permeable channels. It is also sensed actively by dedicated receptors. While the mechanisms of global calcium homeostasis and regulation in body fluids appear well understood, more efforts and new technology are needed to elucidate local calcium handling in the small and relatively isolated interstitial spaces between cells. Here we review current methodology for monitoring interstitial calcium and highlight the potential of new approaches for its study. In particular, new generations of high-performance low-affinity genetically encoded calcium indicators could allow imaging of calcium in relatively inaccessible intercellular structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
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8
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Petersen ED, Lapan AP, Castellanos Franco EA, Fillion AJ, Crespo EL, Lambert GG, Grady CJ, Zanca AT, Orcutt R, Hochgeschwender U, Shaner NC, Gilad AA. Bioluminescent Genetically Encoded Glutamate Indicators for Molecular Imaging of Neuronal Activity. ACS Synth Biol 2023; 12:2301-2309. [PMID: 37450884 PMCID: PMC10443529 DOI: 10.1021/acssynbio.2c00687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Indexed: 07/18/2023]
Abstract
Genetically encoded optical sensors and advancements in microscopy instrumentation and techniques have revolutionized the scientific toolbox available for probing complex biological processes such as release of specific neurotransmitters. Most genetically encoded optical sensors currently used are based on fluorescence and have been highly successful tools for single-cell imaging in superficial brain regions. However, there remains a need to develop new tools for reporting neuronal activity in vivo within deeper structures without the need for hardware such as lenses or fibers to be implanted within the brain. Our approach to this problem is to replace the fluorescent elements of the existing biosensors with bioluminescent elements. This eliminates the need of external light sources to illuminate the sensor, thus allowing deeper brain regions to be imaged noninvasively. Here, we report the development of the first genetically encoded neurotransmitter indicators based on bioluminescent light emission. These probes were optimized by high-throughput screening of linker libraries. The selected probes exhibit robust changes in light output in response to the extracellular presence of the excitatory neurotransmitter glutamate. We expect this new approach to neurotransmitter indicator design to enable the engineering of specific bioluminescent probes for multiple additional neurotransmitters in the future, ultimately allowing neuroscientists to monitor activity associated with a specific neurotransmitter as it relates to behavior in a variety of neuronal and psychiatric disorders, among many other applications.
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Affiliation(s)
- Eric D. Petersen
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Alexandra P. Lapan
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | | | - Adam J. Fillion
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Emmanuel L. Crespo
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Gerard G. Lambert
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Connor J. Grady
- Department
of Biomedical Engineering, Michigan State
University, East Lansing, Michigan 48824, United States
| | - Albertina T. Zanca
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Richard Orcutt
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Ute Hochgeschwender
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Nathan C. Shaner
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Assaf A. Gilad
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Radiology, Michigan State University, East Lansing, Michigan 48824, United States
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9
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Jiang T, Song J, Zhang Y. Coelenterazine-Type Bioluminescence-Induced Optical Probes for Sensing and Controlling Biological Processes. Int J Mol Sci 2023; 24:ijms24065074. [PMID: 36982148 PMCID: PMC10049153 DOI: 10.3390/ijms24065074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Bioluminescence-based probes have long been used to quantify and visualize biological processes in vitro and in vivo. Over the past years, we have witnessed the trend of bioluminescence-driven optogenetic systems. Typically, bioluminescence emitted from coelenterazine-type luciferin–luciferase reactions activate light-sensitive proteins, which induce downstream events. The development of coelenterazine-type bioluminescence-induced photosensory domain-based probes has been applied in the imaging, sensing, and control of cellular activities, signaling pathways, and synthetic genetic circuits in vitro and in vivo. This strategy can not only shed light on the mechanisms of diseases, but also promote interrelated therapy development. Here, this review provides an overview of these optical probes for sensing and controlling biological processes, highlights their applications and optimizations, and discusses the possible future directions.
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Affiliation(s)
- Tianyu Jiang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- Correspondence: (T.J.); (Y.Z.)
| | - Jingwen Song
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Correspondence: (T.J.); (Y.Z.)
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10
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An optimized bioluminescent substrate for non-invasive imaging in the brain. Nat Chem Biol 2023; 19:731-739. [PMID: 36759751 DOI: 10.1038/s41589-023-01265-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
Bioluminescence imaging (BLI) allows non-invasive visualization of cells and biochemical events in vivo and thus has become an indispensable technique in biomedical research. However, BLI in the central nervous system remains challenging because luciferases show relatively poor performance in the brain with existing substrates. Here, we report the discovery of a NanoLuc substrate with improved brain performance, cephalofurimazine (CFz). CFz paired with Antares luciferase produces greater than 20-fold more signal from the brain than the standard combination of D-luciferin with firefly luciferase. At standard doses, Antares-CFz matches AkaLuc-AkaLumine/TokeOni in brightness, while occasional higher dosing of CFz can be performed to obtain threefold more signal. CFz should allow the growing number of NanoLuc-based indicators to be applied to the brain with high sensitivity. Using CFz, we achieve video-rate non-invasive imaging of Antares in brains of freely moving mice and demonstrate non-invasive calcium imaging of sensory-evoked activity in genetically defined neurons.
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11
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Gräwe A, Merkx M. Bioluminescence Goes Dark: Boosting the Performance of Bioluminescent Sensor Proteins Using Complementation Inhibitors. ACS Sens 2022; 7:3800-3808. [PMID: 36450135 PMCID: PMC9791688 DOI: 10.1021/acssensors.2c01726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Bioluminescent sensor proteins have recently gained popularity in both basic research and point-of-care diagnostics. Sensor proteins based on intramolecular complementation of split NanoLuc are particularly attractive because their intrinsic modular design enables for systematic tuning of sensor properties. Here we show how the sensitivity of these sensors can be enhanced by the introduction of catalytically inactive variants of the small SmBiT subunit (DarkBiTs) as intramolecular inhibitors. Starting from previously developed bioluminescent antibody sensor proteins (LUMABS), we developed single component, biomolecular switches with a strongly reduced background signal for the detection of three clinically relevant antibodies, anti-HIV1-p17, cetuximab (CTX), and an RSV neutralizing antibody (101F). These new dark-LUMABS sensors showed 5-13-fold increases in sensitivity which translated into lower limits of detection. The use of DarkBiTs as competitive intramolecular inhibitor domains is not limited to the LUMABS sensor family and might be used to boost the performance of other bioluminescent sensor proteins based on split luciferase complementation.
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12
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Tian X, Zhang Y, Li X, Xiong Y, Wu T, Ai HW. A luciferase prosubstrate and a red bioluminescent calcium indicator for imaging neuronal activity in mice. Nat Commun 2022; 13:3967. [PMID: 35803917 PMCID: PMC9270435 DOI: 10.1038/s41467-022-31673-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
Although fluorescent indicators have been broadly utilized for monitoring bioactivities, fluorescence imaging, when applied to mammals, is limited to superficial targets or requires invasive surgical procedures. Thus, there is emerging interest in developing bioluminescent indicators for noninvasive mammalian imaging. Bioluminescence imaging (BLI) of neuronal activity is highly desired but hindered by insufficient photons needed to digitalize fast brain activities. In this work, we develop a luciferase prosubstrate deliverable at an increased dose and activated in vivo by nonspecific esterase. We further engineer a bright, bioluminescent indicator with robust responsiveness to calcium ions (Ca2+) and appreciable emission above 600 nm. Integration of these advantageous components enables the imaging of the activity of neuronal ensembles in awake mice minimally invasively with excellent signal-to-background and subsecond temporal resolution. This study thus establishes a paradigm for studying brain function in health and disease.
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Affiliation(s)
- Xiaodong Tian
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Yiyu Zhang
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Xinyu Li
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA ,grid.411643.50000 0004 1761 0411Present Address: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ying Xiong
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Tianchen Wu
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Hui-Wang Ai
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XThe UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908 USA
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13
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Zubi YS, Seki K, Li Y, Hunt AC, Liu B, Roux B, Jewett MC, Lewis JC. Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches. Nat Commun 2022; 13:1864. [PMID: 35387988 PMCID: PMC8987029 DOI: 10.1038/s41467-022-29239-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.
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Affiliation(s)
- Yasmine S Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrew C Hunt
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bingqing Liu
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
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14
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Mertes N, Busch M, Huppertz MC, Hacker CN, Wilhelm J, Gürth CM, Kühn S, Hiblot J, Koch B, Johnsson K. Fluorescent and Bioluminescent Calcium Indicators with Tuneable Colors and Affinities. J Am Chem Soc 2022; 144:6928-6935. [PMID: 35380808 PMCID: PMC9026248 DOI: 10.1021/jacs.2c01465] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We introduce a family
of bright, rhodamine-based calcium indicators
with tuneable affinities and colors. The indicators can be specifically
localized to different cellular compartments and are compatible with
both fluorescence and bioluminescence readouts through conjugation
to HaloTag fusion proteins. Importantly, their increase in fluorescence
upon localization enables no-wash live-cell imaging, which greatly
facilitates their use in biological assays. Applications as fluorescent
indicators in rat hippocampal neurons include the detection of single
action potentials and of calcium fluxes in the endoplasmic reticulum.
Applications as bioluminescent indicators include the recording of
the pharmacological modulation of nuclear calcium in high-throughput
compatible assays. The versatility and remarkable ease of use of these
indicators make them powerful tools for bioimaging and bioassays.
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Affiliation(s)
- Nicole Mertes
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marvin Busch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Christina Nicole Hacker
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Wilhelm
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara-Marie Gürth
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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15
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Yang J, Johnson CH. Bioluminescent Sensors for Ca ++ Flux Imaging and the Introduction of a New Intensity-Based Ca ++ Sensor. Front Bioeng Biotechnol 2021; 9:773353. [PMID: 34778237 PMCID: PMC8578923 DOI: 10.3389/fbioe.2021.773353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Sensitive detection of biological events is a goal for the design and characterization of sensors that can be used in vitro and in vivo. One important second messenger is Ca++ which has been a focus of using genetically encoded Ca++ indicators (GECIs) within living cells or intact organisms in vivo. An ideal GECI would exhibit high signal intensity, excellent signal-to-noise ratio (SNR), rapid kinetics, a large dynamic range within relevant physiological conditions, and red-shifted emission. Most available GECIs are based on fluorescence, but bioluminescent GECIs have potential advantages in terms of avoiding tissue autofluorescence, phototoxicity, photobleaching, and spectral overlap, as well as enhancing SNR. Here, we summarize current progress in the development of bioluminescent GECIs and introduce a new and previously unpublished biosensor. Because these biosensors require a substrate, we also describe the pros and cons of various substrates used with these sensors. The novel GECI that is introduced here is called CalBiT, and it is a Ca++ indicator based on the functional complementation of NanoBiT which shows a high dynamic change in response to Ca++ fluxes. Here, we use CalBiT for the detection of Ca++ fluctuations in cultured cells, including its ability for real-time imaging in living cells.
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Affiliation(s)
- Jie Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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16
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Tran Q, Osabe K, Entani T, Nagai T. A novel petal up-regulated PhXTH7 promoter analysis in Petunia hybrida by using bioluminescence reporter gene. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:197-204. [PMID: 34393598 PMCID: PMC8329265 DOI: 10.5511/plantbiotechnology.21.0130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/30/2021] [Indexed: 06/13/2023]
Abstract
Flower opening is an important phenomenon in plant that indicates the readiness of the flower for pollination leading to petal expansion and pigmentation. This phenomenon has great impact on crop yield, which makes researches of its mechanism attractive for both plant physiology study and agriculture. Gene promoters directing the expression in petal during the petal cell wall modification and expansion when flower opens could be a convenient tool to analyze or monitor gene expression targeting this event. However, there are no reports of isolated gene promoters that can direct gene expression in petal or petal limb during the rapid cell wall dynamics when the flower opens. Xyloglucan endotransglucosylase/hydrolase 7 (XTH7), a cell wall modifying enzyme, was reported having up-regulated gene expression in the petal of Arabidopsis thaliana and Petunia hybrida. In this study, we fused a 1,904 bp length P. hybrida XTH7 promoter with a gene encoding a bright bioluminescent protein (Green enhanced Nano-lantern) to report gene expression and observed petal up-regulated bioluminescence activity by means of a consumer-grade camera. More importantly, this novel promoter demonstrated up-regulated activity in the petal limb of P. hybrida matured flower during flower opening. P. hybrida XTH7 promoter would be a useful tool for flowering study, especially for petal expansion research during flower opening.
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Affiliation(s)
- Quang Tran
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Osabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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17
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Cao M, Wang J, Wang Y, Wang X, Li J, Chen J, Hu B, Hu D. Two cobalt(II) and copper(II) complexes with 2,4,5‐tri(4‐pyridyl)‐imidazole and 5‐hydroxyisophthalic acid as turn‐on luminescence sensors for Mg
2+
, Ca
2+
and SCN
−
ions. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202000328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Meng‐Ge Cao
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Jun‐Jie Wang
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Yu Wang
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Xin‐Fang Wang
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Ji‐Xiang Li
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Jing‐Xia Chen
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Bing‐Qing Hu
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
| | - Dou‐Dou Hu
- College of Chemistry and Chemical Engineering, and Anyang Key Laboratory of New Functional Complex Materials Anyang Normol University Anyang Henan 455000 China
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18
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Li ES, Saha MS. Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology. Biomolecules 2021; 11:343. [PMID: 33668387 PMCID: PMC7996158 DOI: 10.3390/biom11030343] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/16/2022] Open
Abstract
Since the 1970s, the emergence and expansion of novel methods for calcium ion (Ca2+) detection have found diverse applications in vitro and in vivo across a series of model animal systems. Matched with advances in fluorescence imaging techniques, the improvements in the functional range and stability of various calcium indicators have significantly enhanced more accurate study of intracellular Ca2+ dynamics and its effects on cell signaling, growth, differentiation, and regulation. Nonetheless, the current limitations broadly presented by organic calcium dyes, genetically encoded calcium indicators, and calcium-responsive nanoparticles suggest a potential path toward more rapid optimization by taking advantage of a synthetic biology approach. This engineering-oriented discipline applies principles of modularity and standardization to redesign and interrogate endogenous biological systems. This review will elucidate how novel synthetic biology technologies constructed for eukaryotic systems can offer a promising toolkit for interfacing with calcium signaling and overcoming barriers in order to accelerate the process of Ca2+ detection optimization.
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Affiliation(s)
| | - Margaret S. Saha
- Department of Biology, College of William and Mary, Williamsburg, VA 23185, USA;
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19
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Baek K, Ji K, Peng W, Liyanaarachchi SM, Dodani SC. The design and evolution of fluorescent protein-based sensors for monoatomic ions in biology. Protein Eng Des Sel 2021; 34:gzab023. [PMID: 34581820 PMCID: PMC8477612 DOI: 10.1093/protein/gzab023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Living cells rely on a finely tuned symphony of inorganic ion gradients composed of both cations and anions. This delicate balance is maintained by biological receptors all acting in concert to selectively recognize and position ions for homeostasis. These dynamic processes can be intercepted and visualized with optical microscopy at the organismal, tissue, cellular and subcellular levels using fluorescent protein-based biosensors. Since the first report of such tool for calcium (Ca2+) in 1997, outstanding biological questions and innovations in protein engineering along with associated fields have driven the development of new biosensors for Ca2+ and beyond. In this Review, we summarize a workflow that can be used to generate fluorescent protein-based biosensors to study monoatomic ions in biology. To showcase the scope of this approach, we highlight recent advances reported for Ca2+ biosensors and in detail discuss representative case studies of biosensors reported in the last four years for potassium (K+), magnesium (Mg2+), copper (Cu2+/+), lanthanide (Ln3+) and chloride (Cl-) ions.
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Affiliation(s)
- Kiheon Baek
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Ke Ji
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Weicheng Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sureshee M Liyanaarachchi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
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20
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Nguyen LP, Nguyen HT, Yong HJ, Reyes-Alcaraz A, Lee YN, Park HK, Na YH, Lee CS, Ham BJ, Seong JY, Hwang JI. Establishment of a NanoBiT-Based Cytosolic Ca 2+ Sensor by Optimizing Calmodulin-Binding Motif and Protein Expression Levels. Mol Cells 2020; 43:909-920. [PMID: 33162399 PMCID: PMC7700839 DOI: 10.14348/molcells.2020.0144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Cytosolic Ca2+ levels ([Ca2+]c) change dynamically in response to inducers, repressors, and physiological conditions, and aberrant [Ca2+]c concentration regulation is associated with cancer, heart failure, and diabetes. Therefore, [Ca2+]c is considered as a good indicator of physiological and pathological cellular responses, and is a crucial biomarker for drug discovery. A genetically encoded calcium indicator (GECI) was recently developed to measure [Ca2+]c in single cells and animal models. GECI have some advantages over chemically synthesized indicators, although they also have some drawbacks such as poor signal-to-noise ratio (SNR), low positive signal, delayed response, artifactual responses due to protein overexpression, and expensive detection equipment. Here, we developed an indicator based on interactions between Ca2+-loaded calmodulin and target proteins, and generated an innovative GECI sensor using split nano-luciferase (Nluc) fragments to detect changes in [Ca2+]c. Stimulation-dependent luciferase activities were optimized by combining large and small subunits of Nluc binary technology (NanoBiT, LgBiT:SmBiT) fusion proteins and regulating the receptor expression levels. We constructed the binary [Ca2+]c sensors using a multicistronic expression system in a single vector linked via the internal ribosome entry site (IRES), and examined the detection efficiencies. Promoter optimization studies indicated that promoter-dependent protein expression levels were crucial to optimize SNR and sensitivity. This novel [Ca2+]c assay has high SNR and sensitivity, is easy to use, suitable for high-throughput assays, and may be useful to detect [Ca2+]c in single cells and animal models.
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Affiliation(s)
- Lan Phuong Nguyen
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Huong Thi Nguyen
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hyo Jeong Yong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | | | - Yoo-Na Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hee-Kyung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Yun Hee Na
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Cheol Soon Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University College of Medicine, Seoul 02841, Korea
| | - Jae Young Seong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Jong-Ik Hwang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
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21
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Mizui Y, Eguchi M, Tanaka M, Ikeda Y, Yoshimura H, Ozawa T, Citterio D, Hiruta Y. Long-term single cell bioluminescence imaging with C-3 position protected coelenterazine analogues. Org Biomol Chem 2020; 19:579-586. [PMID: 33140803 DOI: 10.1039/d0ob02020f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bioluminescence is a powerful imaging modality for monitoring biological phenomena both in vitro and in vivo. Bioluminescence imagin (BLI) is becoming a seamless imaging technology covering the range from cells to organs of small animals. Long-term imaging at the single cell level would lead to a true understanding of the dynamics of life phenomena. This work presents a long-term single cell bioluminescence imaging technology accomplished with C-3 position protected furimazines (FMZs), a CTZ analogues, which generate intense blue emission when paired with a highly stable engineered luciferase, Nanoluc. Four types of FMZs protected at the C-3 position have been synthesized. The type and steric bulkiness of the protection group strongly contributed to storage stability and the kinetics of the bioluminescence reactions of the analogues in human living cells. In particular, two developed FMZ analogues resulted in significantly longer bioluminescence emission with higher S/N ratio than FMZ at single cell level. Long-term bioluminescence single cell imaging technology with the developed FMZ analogues will lead to seamless imaging in the range from cells to organs of small animals.
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Affiliation(s)
- Yuki Mizui
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan.
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22
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Love AC, Prescher JA. Seeing (and Using) the Light: Recent Developments in Bioluminescence Technology. Cell Chem Biol 2020; 27:904-920. [PMID: 32795417 PMCID: PMC7472846 DOI: 10.1016/j.chembiol.2020.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023]
Abstract
Bioluminescence has long been used to image biological processes in vivo. This technology features luciferase enzymes and luciferin small molecules that produce visible light. Bioluminescent photons can be detected in tissues and live organisms, enabling sensitive and noninvasive readouts on physiological function. Traditional applications have focused on tracking cells and gene expression patterns, but new probes are pushing the frontiers of what can be visualized. The past few years have also seen the merger of bioluminescence with optogenetic platforms. Luciferase-luciferin reactions can drive light-activatable proteins, ultimately triggering signal transduction and other downstream events. This review highlights these and other recent advances in bioluminescence technology, with an emphasis on tool development. We showcase how new luciferins and engineered luciferases are expanding the scope of optical imaging. We also highlight how bioluminescent systems are being leveraged not just for sensing-but also controlling-biological processes.
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Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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23
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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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24
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Edwardraja S, Guo Z, Whitfield J, Lantadilla IR, Johnston WA, Walden P, Vickers CE, Alexandrov K. Caged Activators of Artificial Allosteric Protein Biosensors. ACS Synth Biol 2020; 9:1306-1314. [PMID: 32339455 DOI: 10.1021/acssynbio.9b00500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ability of proteins to interconvert unrelated biochemical inputs and outputs underlays most energy and information processing in biology. A common conversion mechanism involves a conformational change of a protein receptor in response to a ligand binding or a covalent modification, leading to allosteric activity modulation of the effector domain. Designing such systems rationally is a central goal of synthetic biology and protein engineering. A two-component sensory system based on the scaffolding of modules in the presence of an analyte is one of the most generalizable biosensor architectures. An inherent problem of such systems is dependence of the response on the absolute and relative concentrations of the components. Here we use the example of two-component sensory systems based on calmodulin-operated synthetic switches to analyze and address this issue. We constructed "caged" versions of the activating domain thereby creating a thermodynamic barrier for spontaneous activation of the system. We demonstrate that the caged biosensor architectures could operate at concentrations spanning 3 orders of magnitude and are applicable to electrochemical, luminescent, and fluorescent two-component biosensors. We analyzed the activation kinetics of the caged biosensors and determined that the core allosteric switch is likely to be the rate limiting component of the system. These findings provide guidance for predictable engineering of robust sensory systems with inputs and outputs of choice.
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Affiliation(s)
- Selvakumar Edwardraja
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Jason Whitfield
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | | | - Wayne A. Johnston
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
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Hossain MN, Ishida R, Hattori M, Matsuda T, Nagai T. Bioluminescent Ratiometric Indicator for Analysis of Water Hardness in Household Water. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3164. [PMID: 32498467 PMCID: PMC7308811 DOI: 10.3390/s20113164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Water hardness (WH) is a useful parameter for testing household water, such as drinking, cooking, and washing water. Many countries around the world use pipeline water in their houses, but there is a need to monitor the WH because hard water has a negative impact on appliances. Currently, WH is often measured using chemical dye-based WH indicators, and these techniques require expensive equipment, and trained personnel. Therefore, a low-cost and simple measurement method has been desired. Here, we report LOTUS-W, which consists of a luciferase, Nanoluc, a yellow fluorescent protein Venus, and a Ca2+/Mg2+ detection domain of human centrin 3. The binding of Ca2+/Mg2+ to this indicator changes the conformation of human centrin 3, and induces bioluminescence resonance energy transfer (BRET) from Nanoluc to Venus, which changes its emission spectrum about 140%. The dissociation constants of LOTUS-W for Ca2+/Mg2+ are approximately several mM, making it suitable for measuring WH in the household water. With this indicator in combination with a smartphone, we have demonstrated that it is possible to evaluate WH easily and quickly. This novel indicator has the potential to be used for measuring not only household water but also water used in the food industry, etc.
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Affiliation(s)
- Md Nadim Hossain
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; (M.N.H.); (R.I.); (M.H.); (T.M.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Ryuichi Ishida
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; (M.N.H.); (R.I.); (M.H.); (T.M.)
| | - Mitsuru Hattori
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; (M.N.H.); (R.I.); (M.H.); (T.M.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Tomoki Matsuda
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; (M.N.H.); (R.I.); (M.H.); (T.M.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; (M.N.H.); (R.I.); (M.H.); (T.M.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
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Recent advances in the use of genetically encodable optical tools to elicit and monitor signaling events. Curr Opin Cell Biol 2020; 63:114-124. [PMID: 32058267 DOI: 10.1016/j.ceb.2020.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023]
Abstract
Cells rely on a complex network of spatiotemporally regulated signaling activities to effectively transduce information from extracellular cues to intracellular machinery. To probe this activity architecture, researchers have developed an extensive molecular tool kit of fluorescent biosensors and optogenetic actuators capable of monitoring and manipulating various signaling activities with high spatiotemporal precision. The goal of this review is to provide readers with an overview of basic concepts and recent advances in the development and application of genetically encodable biosensors and optogenetic tools for understanding signaling activity.
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Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells. Int J Mol Sci 2019; 20:ijms20225784. [PMID: 31744242 PMCID: PMC6887983 DOI: 10.3390/ijms20225784] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022] Open
Abstract
Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.
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