1
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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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2
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Yu L, Liu Z, Xu W, Jin K, Liu J, Zhu X, Zhang Y, Wu Y. Towards overcoming obstacles of type II photodynamic therapy: Endogenous production of light, photosensitizer, and oxygen. Acta Pharm Sin B 2024; 14:1111-1131. [PMID: 38486983 PMCID: PMC10935104 DOI: 10.1016/j.apsb.2023.11.007] [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: 07/04/2023] [Revised: 10/20/2023] [Accepted: 10/28/2023] [Indexed: 03/17/2024] Open
Abstract
Conventional photodynamic therapy (PDT) approaches face challenges including limited light penetration, low uptake of photosensitizers by tumors, and lack of oxygen in tumor microenvironments. One promising solution is to internally generate light, photosensitizers, and oxygen. This can be accomplished through endogenous production, such as using bioluminescence as an endogenous light source, synthesizing genetically encodable photosensitizers in situ, and modifying cells genetically to express catalase enzymes. Furthermore, these strategies have been reinforced by the recent rapid advancements in synthetic biology. In this review, we summarize and discuss the approaches to overcome PDT obstacles by means of endogenous production of excitation light, photosensitizers, and oxygen. We envision that as synthetic biology advances, genetically engineered cells could act as precise and targeted "living factories" to produce PDT components, leading to enhanced performance of PDT.
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Affiliation(s)
- Lin Yu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
- School of Medicine, Shanghai University, Shanghai 200433, China
| | - Zhen Liu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
| | - Wei Xu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
| | - Kai Jin
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
| | - Jinliang Liu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
| | - Xiaohui Zhu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
| | - Yong Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Yihan Wu
- Department of Chemical and Environmental Engineering, Shanghai University, Shanghai 200433, China
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3
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To TL, Li X, Shu X. Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters. Viruses 2023; 15:2005. [PMID: 37896782 PMCID: PMC10612051 DOI: 10.3390/v15102005] [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: 09/06/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related diseases. Fluorescence microscopy plays a vital role in virus imaging, offering high spatiotemporal resolution, sensitivity, and spectroscopic versatility. In this opinion piece, we first highlight two recent techniques, SunTag and StayGold, for the in situ imaging of viral RNA translation and viral assembly. Next, we discuss a new class of genetically encoded fluorogenic protease reporters, such as FlipGFP, which can be customized to monitor SARS-CoV-2's main (Mpro) or papain-like (PLpro) protease activity. These assays have proven effective in identifying potential antivirals through high-throughput screening, making fluorogenic viral protease reporters a promising platform for viral disease diagnostics and therapeutics.
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Affiliation(s)
| | - Xiaoquan Li
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
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4
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Konrad KR, Gao S, Zurbriggen MD, Nagel G. Optogenetic Methods in Plant Biology. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:313-339. [PMID: 37216203 DOI: 10.1146/annurev-arplant-071122-094840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.
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Affiliation(s)
- Kai R Konrad
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany;
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany;
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
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5
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Fine spectral tuning of a flavin-binding fluorescent protein for multicolor imaging. J Biol Chem 2023; 299:102977. [PMID: 36738792 PMCID: PMC10023982 DOI: 10.1016/j.jbc.2023.102977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Flavin-binding fluorescent proteins are promising genetically encoded tags for microscopy. However, spectral properties of their chromophores (riboflavin, flavin mononucleotide, and flavin adenine dinucleotide) are notoriously similar even between different protein families, which limits applications of flavoproteins in multicolor imaging. Here, we present a palette of 22 finely tuned fluorescent tags based on the thermostable LOV domain from Chloroflexus aggregans. We performed site saturation mutagenesis of three amino acid positions in the flavin-binding pocket, including the photoactive cysteine, to obtain variants with fluorescence emission maxima uniformly covering the wavelength range from 486 to 512 nm. We demonstrate three-color imaging based on spectral separation and two-color fluorescence lifetime imaging of bacteria, as well as two-color imaging of mammalian cells (HEK293T), using the proteins from the palette. These results highlight the possibility of fine spectral tuning of flavoproteins and pave the way for further applications of flavin-binding fluorescent proteins in fluorescence microscopy.
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6
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Upconversion nanoparticle-based optogenetic nanosystem for photodynamic therapy and cascade gene therapy. Acta Biomater 2023; 157:538-550. [PMID: 36494007 DOI: 10.1016/j.actbio.2022.12.002] [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: 09/05/2022] [Revised: 11/26/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Most photosensitizer molecules used for the photodynamic therapy (PDT) are chemically-synthesized organic photosensitizer dyes which show several limitations such as unsatisfactory cell uptake, weak selectivity and off-target phototoxicity. Recently, genetically-encoded photosensitizers have attracted increasing attentions which provide the targeted cell elimination with single-cell precision. However, their applications are mainly limited by the shallow tissue penetration depth of the excitation light and the low cell apoptosis ratio. Herein, we developed a feasible upconversion nanoparticle (UCNP)-based optogenetic nanosystem with three-in-one functional integration: bio-imaging, NIR-triggered PDT and cascade gene therapy. Firstly, the mitochondria-targeted genetically-encoded photosensitizer was constructed and transfected into cancer cells. Then, the functional upconversion nanoprobe was constructed with the mitochondria targetability and then the siRNA was loaded on the surface of UCNPs via the reactive oxygen species (ROSs) sensitive chemical bond. After the transfection and incubation, both of the upconversion nanoprobe and the genetically-encoded photosensitizer were accumulated in the mitochondria of cancer cells. Under the NIR irradiation, the emission of UCNPs could excite the expressed protein photosensitizer to generate ROSs which then stimulated the release of siRNAs in a controllable manner, achieving PDT and cascade gene therapy. Since the generation of ROSs and the release of siRNA occurred in the mitochondria in-situ, the mitochondria-mediated cell apoptosis signal pathway would be activated to induce cell apoptosis and subsequently inhibit tumor growth. To the best of our knowledge, this is the first report about NIR laser-activated, organelle-localized genetically-encoded photosensitizers developed for cascade therapy, which will widen the application of optogenetic tools in the tumor therapy. STATEMENT OF SIGNIFICANCE: The application of genetically-encoded photosensitizers in photodynamic therapy (PDT) is mainly limited by the shallow tissue penetration depth of the excitation light and unsatisfactory therapeutic performance. In this experiment, we developed an upconversion nanoparticles-based optogenetic nanosystem to enhance the PDT and cascade gene therapy for malignant tumors. The expressed genetically-encoded photosensitizers were accumulated in the mitochondria, which were activated in situ by the upconversion nanoprobe. Besides, the photogenerated reactive oxygen species (ROSs) stimulated the release of siRNAs in a controllable manner. To the best of our knowledge, this is the first report about NIR laser-activated, genetically-encoded photosensitizers developed for organelle-localized controllable cascade therapy. We hope this work can accelerate the application of genetically-encoded photosensitizers in the tumor therapy.
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7
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Bitzenhofer NL, Hilgers F, Bosio GN, Torra J, Casini G, Beinlich FRM, Knieps-Grünhagen E, Gordeliy V, Jaeger KE, Nonell S, Krauss U, Gensch T, Drepper T. Development and Characterization of Flavin-Binding Fluorescent Proteins, Part II: Advanced Characterization. Methods Mol Biol 2023; 2564:143-183. [PMID: 36107341 DOI: 10.1007/978-1-0716-2667-2_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs), a class of small fluorescent proteins derived from light-oxygen-voltage (LOV) domains, bind ubiquitous endogenous flavins as chromophores. Due to their unique properties, they can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents methodologies for in-depth characterization of the biochemical, spectroscopic, photophysical, and photochemical properties of FbFPs.
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Affiliation(s)
- Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Gabriela N Bosio
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Giorgia Casini
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Felix R M Beinlich
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Esther Knieps-Grünhagen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Gordeliy
- Institute of Bio-and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain.
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.
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8
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Fan H, Barnes C, Hwang H, Zhang K, Yang J. Precise modulation of embryonic development through optogenetics. Genesis 2022; 60:e23505. [PMID: 36478118 PMCID: PMC9847014 DOI: 10.1002/dvg.23505] [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: 09/06/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed enormous progress in optogenetics, which uses photo-sensitive proteins to control signal transduction in live cells and animals. The ever-increasing amount of optogenetic tools, however, could overwhelm the selection of appropriate optogenetic strategies. In this work, we summarize recent progress in this emerging field and highlight the application of opsin-free optogenetics in studying embryonic development, focusing on new insights gained into optical induction of morphogenesis, cell polarity, cell fate determination, tissue differentiation, neuronal regeneration, synaptic plasticity, and removal of cells during development.
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Affiliation(s)
- Huaxun Fan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin Barnes
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
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9
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Utsumi MK, Akahoshi T, Oka K, Hotta K. MiniSOG2-mediated Specific Photoablation of Motor Neurons in Ascidian Embryos. Bio Protoc 2022; 12:e4537. [PMID: 36353720 PMCID: PMC9606450 DOI: 10.21769/bioprotoc.4537] [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: 04/29/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/29/2022] Open
Abstract
When understanding the neuronal function of a specific neural circuit, single-cell level photoablation of a targeted cell is one of the useful experimental approaches. This protocol describes a method to photoablate specific motor neurons via the mini singlet oxygen generator (miniSOG2), a light-oxygen-voltage (LOV)-based optogenetic tool used for ablating targeted cells in arbitrary areas. MiniSOG2 could induce the cell death pathway by generating reactive oxygen species (ROS) upon blue light illumination. Photoablation of a specific cell using the miniSOG2 was performed to show that, in Ciona intestinalis type A ( Ciona robusta) , a single pair of motor neurons, MN2/A10.64, is necessary to drive their tail muscle contraction. The membrane targeted miniSOG2 combined with neuron-specific promoter (pSP-Neurog::miniSOG2-CAAX) was electroplated into the Ciona egg and transiently expressed at specific neurons of the embryo. MN2 labeled with pSP-Neurog:mCherry-CAAX was irradiated using a 440-nm laser from the lateral side for 10 min to ablate its neural function. The behavior of the embryo before and after the irradiation was recorded with a high-speed camera. Graphical abstract.
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Affiliation(s)
- Madoka K. Utsumi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
| | - Taichi Akahoshi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
,
Waseda Research Institute for Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
,
Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
,
*For correspondence:
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10
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Li Y, Cui ZJ. Photodynamic Activation of the Cholecystokinin 1 Receptor with Tagged Genetically Encoded Protein Photosensitizers: Optimizing the Tagging Patterns. Photochem Photobiol 2022; 98:1215-1228. [PMID: 35211987 DOI: 10.1111/php.13611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/20/2022] [Indexed: 02/05/2023]
Abstract
Cholecystokinin 1 receptor (CCK1R) is activated photodynamically. For this to happen in situ, genetically encoded protein photosensitizers (GEPP) may be tagged to natively expressed CCK1R, but how to best tag GEPP has not been examined. Therefore, GEPP (miniSOG or KillerRed) was tagged to CCK1R and light-driven photodynamic CCK1R activation was monitored by Fura-2 fluorescent calcium imaging, to screen for optimized tagging patterns. Blue light-emitting diode irradiation of CHO-K1 cells expressing miniSOG fused to N- or C-terminus of CCK1R was found to both trigger persistent calcium oscillations-a hallmark of permanent photodynamic CCK1R activation. Photodynamic CCK1R activation was accomplished also with miniSOG fused to N-terminus of CCK1R via linker (GlySerGly)4 or 8 , but not linker (GSG)12 or an internal ribosomal entry site insert. KillerRed fused to N- or C-terminus of CCK1R after white light irradiation resulted in similar activation of in-frame CCK1R. Photodynamic CCK1R activation in miniSOG-CCK1R-CHO-K1 cells was blocked by singlet oxygen (1 O2 ) quencher uric acid or Trolox C, corroborating the role of 1 O2 as the reactive intermediate. It is concluded that photodynamic CCK1R activation can be achieved either with direct GEPP fusion to CCK1R or fusion via a short linker, fusion via long linkers might serve as the internal control.
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Affiliation(s)
- Yuan Li
- Institute of Cell Biology, Beijing Normal University, Beijing, China
| | - Zong Jie Cui
- Institute of Cell Biology, Beijing Normal University, Beijing, China
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11
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Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Nat Commun 2022; 13:4906. [PMID: 35987950 PMCID: PMC9392063 DOI: 10.1038/s41467-022-32689-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/11/2022] [Indexed: 12/18/2022] Open
Abstract
AbstractEnzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.
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12
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Abstract
Optogenetic actuators enable highly precise spatiotemporal interrogation of biological processes at levels ranging from the subcellular to cells, circuits and behaving organisms. Although their application in neuroscience has traditionally focused on the control of spiking activity at the somatodendritic level, the scope of optogenetic modulators for direct manipulation of presynaptic functions is growing. Presynaptically localized opsins combined with light stimulation at the terminals allow light-mediated neurotransmitter release, presynaptic inhibition, induction of synaptic plasticity and specific manipulation of individual components of the presynaptic machinery. Here, we describe presynaptic applications of optogenetic tools in the context of the unique cell biology of axonal terminals, discuss their potential shortcomings and outline future directions for this rapidly developing research area.
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13
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Sang L, Yang L, Ge Q, Xie S, Zhou T, Lin A. Subcellular distribution, localization, and function of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1729. [PMID: 35413151 DOI: 10.1002/wrna.1729] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Lingjie Sang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luojia Yang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aifu Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Yang YHC, Briant LJB, Raab CA, Mullapudi ST, Maischein HM, Kawakami K, Stainier DYR. Innervation modulates the functional connectivity between pancreatic endocrine cells. eLife 2022; 11:64526. [PMID: 35373736 PMCID: PMC9007585 DOI: 10.7554/elife.64526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/03/2022] [Indexed: 11/20/2022] Open
Abstract
The importance of pancreatic endocrine cell activity modulation by autonomic innervation has been debated. To investigate this question, we established an in vivo imaging model that also allows chronic and acute neuromodulation with genetic and optogenetic tools. Using the GCaMP6s biosensor together with endocrine cell fluorescent reporters, we imaged calcium dynamics simultaneously in multiple pancreatic islet cell types in live animals in control states and upon changes in innervation. We find that by 4 days post fertilization in zebrafish, a stage when islet architecture is reminiscent of that in adult rodents, prominent activity coupling between beta cells is present in basal glucose conditions. Furthermore, we show that both chronic and acute loss of nerve activity result in diminished beta–beta and alpha–beta activity coupling. Pancreatic nerves are in contact with all islet cell types, but predominantly with beta and delta cells. Surprisingly, a subset of delta cells with detectable peri-islet neural activity coupling had significantly higher homotypic coupling with other delta cells suggesting that some delta cells receive innervation that coordinates their output. Overall, these data show that innervation plays a vital role in the maintenance of homotypic and heterotypic cellular connectivity in pancreatic islets, a process critical for islet function.
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Affiliation(s)
- Yu Hsuan Carol Yang
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Christopher A Raab
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sri Teja Mullapudi
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hans-Martin Maischein
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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15
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Akahoshi T, Utsumi MK, Oonuma K, Murakami M, Horie T, Kusakabe TG, Oka K, Hotta K. A single motor neuron determines the rhythm of early motor behavior in Ciona. SCIENCE ADVANCES 2021; 7:eabl6053. [PMID: 34890229 PMCID: PMC8664258 DOI: 10.1126/sciadv.abl6053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/21/2021] [Indexed: 05/25/2023]
Abstract
Recent work in tunicate supports the similarity between the motor circuits of vertebrates and basal deuterostome lineages. To understand how the rhythmic activity in motor circuits is acquired during development of protochordate Ciona, we investigated the coordination of the motor response by identifying a single pair of oscillatory motor neurons (MN2/A10.64). The MN2 neurons had Ca2+ oscillation with an ~80-s interval that was cell autonomous even in a dissociated single cell. The Ca2+ oscillation of MN2 coincided with the early tail flick (ETF). The spikes of the membrane potential in MN2 gradually correlated with the rhythm of ipsilateral muscle contractions in ETFs. The optogenetic experiments indicated that MN2 is a necessary and sufficient component of ETFs. These results indicate that MN2 is indispensable for the early spontaneous rhythmic motor behavior of Ciona. Our findings shed light on the understanding of development and evolution of chordate rhythmical locomotion.
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Affiliation(s)
- Taichi Akahoshi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
| | - Madoka K. Utsumi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
| | - Kouhei Oonuma
- Institute for Integrative Neurobiology and Department of Biology, Konan University, Kobe 658-8501, Japan
| | - Makoto Murakami
- Institute for Integrative Neurobiology and Department of Biology, Konan University, Kobe 658-8501, Japan
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shimoda 415-0025, Japan
| | - Takehiro G. Kusakabe
- Institute for Integrative Neurobiology and Department of Biology, Konan University, Kobe 658-8501, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
| | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku, Yokohama 223-8522, Japan
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16
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Diaz D, Vidal X, Sunna A, Care A. Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:7977-7986. [PMID: 33586952 DOI: 10.1021/acsami.0c21141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as "nanoreactors" for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision are lacking. We report the construction of a light-responsive encapsulin nanoreactor for "on demand" production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-singlet oxygen generator (miniSOG), a biological photosensitizer that is activated by blue light to generate ROS, primarily singlet oxygen (1O2). We established that the nanocompartments stably encased miniSOG and in response to blue light were able to mediate the photoconversion of molecular oxygen into ROS. Using an in vitro model of lung cancer, we showed that ROS generated by the nanoreactor triggered photosensitized oxidation reactions which exerted a toxic effect on tumor cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Xavier Vidal
- Fraunhofer Institut für Angewandte Festkörperphysik (IAF), Tullastrasse 72, 79108 Freiburg, Germany
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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17
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Genetically Encoded Photosensitizer for Destruction of Protein or Cell Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:265-279. [PMID: 33398819 DOI: 10.1007/978-981-15-8763-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There are several paths when excited molecules return to the ground state. In the case of fluorescent molecules, the dominant path is fluorescence emission that is greatly contributing to bioimaging. Meanwhile, photosensitizers transfer electron or energy from chromophore to the surrounding molecules, including molecular oxygen. Generated reactive oxygen species has potency to attack other molecules by oxidation. In this chapter, we introduce the chromophore-assisted light inactivation (CALI) method using a photosensitizer to inactivate proteins in a spatiotemporal manner and development of CALI tools, which is useful for investigation of protein functions and dynamics, by inactivation of the target molecules. Moreover, photosensitizers with high efficiency make it possible optogenetic control of cell ablation in living organisms and photodynamic therapy. Further development of photosensitizers with different excitation wavelengths will contribute to the investigation of multiple proteins or cell functions through inactivation in the different positions and timings.
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18
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Das S, Tiwari M, Mondal D, Sahoo BR, Tiwari DK. Growing tool-kit of photosensitizers for clinical and non-clinical applications. J Mater Chem B 2020; 8:10897-10940. [PMID: 33165483 DOI: 10.1039/d0tb02085k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosensitizers are photosensitive molecules utilized in clinical and non-clinical applications by taking advantage of light-mediated reactive oxygen generation, which triggers local and systemic cellular toxicity. Photosensitizers are used for diverse biological applications such as spatio-temporal inactivation of a protein in a living system by chromophore-assisted light inactivation, localized cell photoablation, photodynamic and immuno-photodynamic therapy, and correlative light-electron microscopy imaging. Substantial efforts have been made to develop several genetically encoded, chemically synthesized, and nanotechnologically driven photosensitizers for successful implementation in redox biology applications. Genetically encoded photosensitizers (GEPS) or reactive oxygen species (ROS) generating proteins have the advantage of using them in the living system since they can be manipulated by genetic engineering with a variety of target-specific genes for the precise spatio-temporal control of ROS generation. The GEPS variety is limited but is expanding with a variety of newly emerging GEPS proteins. Apart from GEPS, a large variety of chemically- and nanotechnologically-empowered photosensitizers have been developed with a major focus on photodynamic therapy-based cancer treatment alone or in combination with pre-existing treatment methods. Recently, immuno-photodynamic therapy has emerged as an effective cancer treatment method using smartly designed photosensitizers to initiate and engage the patient's immune system so as to empower the photosensitizing effect. In this review, we have discussed various types of photosensitizers, their clinical and non-clinical applications, and implementation toward intelligent efficacy, ROS efficiency, and target specificity in biological systems.
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Affiliation(s)
- Suman Das
- Department of Biotechnology, Faculty of Life Sciences and Environment, Goa University, Taleigao Plateau, Goa 403206, India.
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19
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Gorbachev DA, Staroverov DB, Lukyanov KA, Sarkisyan KS. Genetically Encoded Red Photosensitizers with Enhanced Phototoxicity. Int J Mol Sci 2020; 21:E8800. [PMID: 33233801 PMCID: PMC7709005 DOI: 10.3390/ijms21228800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Genetically encoded photosensitizers are increasingly used as optogenetic tools to control cell fate or trigger intracellular processes. A monomeric red fluorescent protein called SuperNova has been recently developed, however, it demonstrates suboptimal characteristics in most phototoxicity-based applications. Here, we applied directed evolution to this protein and identified SuperNova2, a protein with S10R substitution that results in enhanced brightness, chromophore maturation and phototoxicity in bacterial and mammalian cell cultures.
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Affiliation(s)
- Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Dmitry B Staroverov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
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20
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Li Y, Cui ZJ. Photodynamic Activation of Cholecystokinin 1 Receptor with Different Genetically Encoded Protein Photosensitizers and from Varied Subcellular Sites. Biomolecules 2020; 10:biom10101423. [PMID: 33050050 PMCID: PMC7601527 DOI: 10.3390/biom10101423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Cholecystokinin 1 receptor (CCK1R) is activated by singlet oxygen (1O2) generated in photodynamic action with sulphonated aluminum phthalocyanine (SALPC) or genetically encoded protein photosensitizer (GEPP) KillerRed or mini singlet oxygen generator (miniSOG). A large number of GEPP with varied 1O2 quantum yields have appeared recently; therefore, in the present work, the efficacy of different GEPP to photodynamically activate CCK1R was examined, as monitored by Fura-2 calcium imaging. KillerRed, miniSOG, miniSOG2, singlet oxygen protein photosensitizer (SOPP), flavin-binding fluorescent protein from Methylobacterium radiotolerans with point mutation C71G (Mr4511C71G), and flavin-binding fluorescent protein from Dinoroseobacter shibae (DsFbFP) were expressed at the plasma membrane (PM) in AR4-2J cells, which express endogenous CCK1R. Light irradiation (KillerRed: white light 85.3 mW‧cm-2, 4' and all others: LED 450 nm, 85 mW·cm-2, 1.5') of GEPPPM-expressing AR4-2J was found to all trigger persistent calcium oscillations, a hallmark of permanent photodynamic CCK1R activation; DsFbFP was the least effective, due to poor expression. miniSOG was targeted to PM, mitochondria (MT) or lysosomes (LS) in AR4-2J in parallel experiments; LED light irradiation was found to all induce persistent calcium oscillations. In miniSOGPM-AR4-2J cells, light emitting diode (LED) light irradiation-induced calcium oscillations were readily inhibited by CCK1R antagonist devazepide 2 nM; miniSOGMT-AR4-2J cells were less susceptible, but miniSOGLS-AR4-2J cells were not inhibited. In conclusion, different GEPPPM could all photodynamically activate CCK1R. Intracellular GEPP photodynamic action may prove particularly suited to study intracellular GPCR.
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21
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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22
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [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: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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23
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Mruk K, Ciepla P, Piza PA, Alnaqib MA, Chen JK. Targeted cell ablation in zebrafish using optogenetic transcriptional control. Development 2020; 147:dev183640. [PMID: 32414936 PMCID: PMC7328002 DOI: 10.1242/dev.183640] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
Cell ablation is a powerful method for elucidating the contributions of individual cell populations to embryonic development and tissue regeneration. Targeted cell loss in whole organisms has been typically achieved through expression of a cytotoxic or prodrug-activating gene product in the cell type of interest. This approach depends on the availability of tissue-specific promoters, and it does not allow further spatial selectivity within the promoter-defined region(s). To address this limitation, we have used the light-inducible GAVPO transactivator in combination with two genetically encoded cell-ablation technologies: the nitroreductase/nitrofuran system and a cytotoxic variant of the M2 ion channel. Our studies establish ablative methods that provide the tissue specificity afforded by cis-regulatory elements and the conditionality of optogenetics. Our studies also demonstrate differences between the nitroreductase and M2 systems that influence their efficacies for specific applications. Using this integrative approach, we have ablated cells in zebrafish embryos with both spatial and temporal control.
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Affiliation(s)
- Karen Mruk
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- School of Pharmacy, University of Wyoming, Laramie, WY 82071, USA
| | - Paulina Ciepla
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick A Piza
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mohammad A Alnaqib
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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24
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Abstract
Drosophila melanogaster has historically been a workhorse model organism for studying developmental biology. In addition, Drosophila is an excellent model for studying how damaged tissues and organs can regenerate. Recently, new precision approaches that enable both highly targeted injury and genetic manipulation have accelerated progress in this field. Here, we highlight these techniques and review examples of recently discovered mechanisms that regulate regeneration in Drosophila larval and adult tissues. We also discuss how, by applying these powerful approaches, studies of Drosophila can continue to guide the future of regeneration research.
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Affiliation(s)
- Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Erez Cohen
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Rachel Smith-Bolton
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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25
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Kakanj P, Eming SA, Partridge L, Leptin M. Long-term in vivo imaging of Drosophila larvae. Nat Protoc 2020; 15:1158-1187. [DOI: 10.1038/s41596-019-0282-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
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26
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Zhang Y, Zhang W, Zeng K, Ao Y, Wang M, Yu Z, Qi F, Yu W, Mao H, Tao L, Zhang C, Tan TTY, Yang X, Pu K, Gao S. Upconversion Nanoparticles-Based Multiplex Protein Activation to Neuron Ablation for Locomotion Regulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906797. [PMID: 32003923 DOI: 10.1002/smll.201906797] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/06/2020] [Indexed: 05/24/2023]
Abstract
The optogenetic neuron ablation approach enables noninvasive remote decoding of specific neuron function within a complex living organism in high spatiotemporal resolution. However, it suffers from shallow tissue penetration of visible light with low ablation efficiency. This study reports a upconversion nanoparticle (UCNP)-based multiplex proteins activation tool to ablate deep-tissue neurons for locomotion modulation. By optimizing the dopant contents and nanoarchitecure, over 300-fold enhancement of blue (450-470 nm) and red (590-610 nm) emissions from UCNPs is achieved upon 808 nm irradiation. Such emissions simultaneously activate mini singlet oxygen generator and Chrimson, leading to boosted near infrared (NIR) light-induced neuronal ablation efficiency due to the synergism between singlet oxygen generation and intracellular Ca2+ elevation. The loss of neurons severely inhibits reverse locomotion, revealing the instructive role of neurons in controlling motor activity. The deep penetrance NIR light makes the current system feasible for in vivo deep-tissue neuron elimination. The results not only provide a rapidly adoptable platform to efficient photoablate single- and multiple-cells, but also define the neural circuits underlying behavior, with potential for development of remote therapy in diseases.
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Affiliation(s)
- Yan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Wanmei Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Kanghua Zeng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yanxiao Ao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Mengdie Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, P. R. China
| | - Zhongzheng Yu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Fukang Qi
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Weiwei Yu
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Heng Mao
- LMAM, School of Mathematical Sciences, Peking University, Beijing, 100871, P. R. China
| | - Louis Tao
- Center for Quantitative Biology, Peking University, Beijing, 100871, P. R. China
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Timothy Thatt Yang Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Xiangliang Yang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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27
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Kim S, Shin J, Oh H, Ahn S, Kim N, Heo WD. An inducible system for in vitro and in vivo Fas activation using FKBP-FRB-rapamycin complex. Biochem Biophys Res Commun 2019; 523:473-480. [PMID: 31882118 DOI: 10.1016/j.bbrc.2019.12.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/15/2019] [Indexed: 11/16/2022]
Abstract
The inducible activation system is valuable for investigating spatiotemporal roles of molecules. A chemically inducible activation system for Fas (CD95/APO-1), which works efficiently to induce apoptosis and leads non-apoptotic pathways, has not yet been developed. Here, we engineered a rapamycin-induced dimerization system of Fas consisting of FKBP and FRB proteins. Treatment of rapamycin specifically induces cellular apoptosis. In neurons and cells with high c-FLIP expression, rapamycin-induced Fas activation triggered the activation of the non-apoptotic pathway components instead of cell death. Intracranial delivery of the system could be utilized to induce apoptosis of tumor cells upon rapamycin treatment. Our results demonstrate a novel inducible Fas activation system which operates with high efficiency and temporal precision in vitro and in vivo promising a potential therapeutic strategy.
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Affiliation(s)
- Seokhwi Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jongpil Shin
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Hyunsik Oh
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Sangphil Ahn
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Nury Kim
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea; Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, Republic of Korea; KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea.
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28
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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29
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Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
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Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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30
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Liu F, Dai S, Feng D, Peng X, Qin Z, Kearns AC, Huang W, Chen Y, Ergün S, Wang H, Rappaport J, Bryda EC, Chandrasekhar A, Aktas B, Hu H, Chang SL, Gao B, Qin X. Versatile cell ablation tools and their applications to study loss of cell functions. Cell Mol Life Sci 2019; 76:4725-4743. [PMID: 31359086 PMCID: PMC6858955 DOI: 10.1007/s00018-019-03243-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022]
Abstract
Targeted cell ablation is a powerful approach for studying the role of specific cell populations in a variety of organotypic functions, including cell differentiation, and organ generation and regeneration. Emerging tools for permanently or conditionally ablating targeted cell populations and transiently inhibiting neuronal activities exhibit a diversity of application and utility. Each tool has distinct features, and none can be universally applied to study different cell types in various tissue compartments. Although these tools have been developed for over 30 years, they require additional improvement. Currently, there is no consensus on how to select the tools to answer the specific scientific questions of interest. Selecting the appropriate cell ablation technique to study the function of a targeted cell population is less straightforward than selecting the method to study a gene's functions. In this review, we discuss the features of the various tools for targeted cell ablation and provide recommendations for optimal application of specific approaches.
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Affiliation(s)
- Fengming Liu
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Shen Dai
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Dechun Feng
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiao Peng
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Zhongnan Qin
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Alison C Kearns
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Wenfei Huang
- Institute of NeuroImmune Pharmacology, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Yong Chen
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Key Lab for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, 261053, Weifang, People's Republic of China
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius-Maximillan University, 97070, Wurzburg, Germany
| | - Hong Wang
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Jay Rappaport
- Division of Pathology, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Elizabeth C Bryda
- Rat Resource and Research Center, University of Missouri, 4011 Discovery Drive, Columbia, MO, 65201, USA
| | - Anand Chandrasekhar
- Division of Biological Sciences, 340D Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, USA
| | - Bertal Aktas
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Hongzhen Hu
- Department of Anesthesiology, Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuebin Qin
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA.
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA.
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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31
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Wang P, Tang W, Li Z, Zou Z, Zhou Y, Li R, Xiong T, Wang J, Zou P. Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling. Nat Chem Biol 2019; 15:1110-1119. [PMID: 31591565 DOI: 10.1038/s41589-019-0368-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/19/2019] [Indexed: 12/20/2022]
Abstract
RNA molecules are highly compartmentalized in eukaryotic cells, with their localizations intimately linked to their functions. Despite the importance of RNA targeting, our current knowledge of the spatial organization of the transcriptome has been limited by a lack of analytical tools. In this study, we develop a chemical biology approach to label RNAs in live cells with high spatial specificity. Our method, called CAP-seq, capitalizes on light-activated, proximity-dependent photo-oxidation of RNA nucleobases, which could be subsequently enriched via affinity purification and identified by high-throughput sequencing. Using this technique, we investigate the local transcriptomes that are proximal to various subcellular compartments, including the endoplasmic reticulum and mitochondria. We discover that messenger RNAs encoding for ribosomal proteins and oxidative phosphorylation pathway proteins are highly enriched at the outer mitochondrial membrane. Due to its specificity and ease of use, CAP-seq is a generally applicable technique to investigate the spatial transcriptome in many biological systems.
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Affiliation(s)
- Pengchong Wang
- School of Life Sciences, Tsinghua University, Beijing, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Wei Tang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Zeyao Li
- School of Life Sciences, Tsinghua University, Beijing, China.,Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
| | - Zhongyu Zou
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Ying Zhou
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Ran Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Tianyu Xiong
- Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China. .,Chinese Institute for Brain Research, Beijing, China.
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China. .,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China. .,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China. .,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China. .,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
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32
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Shilovskiy IP, Dyneva ME, Kurbacheva OM, Kudlay DA, Khaitov MR. The Role of Interleukin-37 in the Pathogenesis of Allergic Diseases. Acta Naturae 2019; 11:54-64. [PMID: 31993235 PMCID: PMC6977961 DOI: 10.32607/20758251-2019-11-4-54-64] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
Cytokines of the interleukin-1 (IL-1) family play an important role in the realization of the protective functions of innate immunity and are the key mediators involved in the pathogenesis of a wide range of diseases, including various manifestations of allergy. The IL-1 family includes more than 11 members. However, the functions of many of them remain to be elucidated. Recently, new members of the IL-1 family have been discovered. In 2000, several independent research groups reported the discovery of a new interleukin of this family, which was named IL-37, or IL-1F7 (according to the new nomenclature). IL-37 was assigned to the IL-1 family based on its structural similarity with other members of this family. The study of its biological properties showed that its activity changes in inflammatory diseases, such as rheumatoid arthritis, psoriasis, as well as allergic diseases (allergic rhinitis, bronchial asthma, and atopic dermatitis). However, unlike most members of the IL-1 family, IL-37 acts as a negative regulator of inflammation. Activation of IL-37 suppresses inflammation, resulting in the suppression of inflammatory cytokines and chemokines, which in turn prevents infiltration of pro-inflammatory cells, mainly eosinophils and neutrophils. The exact molecular and cellular mechanisms of the anti-inflammatory effect of IL-37 in the development of allergic diseases (AD) have not been fully studied. This review summarizes and analyzes the accumulated experimental data on the role of IL-37 in the pathogenesis of AD, such as allergic rhinitis, bronchial asthma, and atopic dermatitis.
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Affiliation(s)
- I. P. Shilovskiy
- National Research Center – Institute of Immunology Federal Medical-Biological Agency of Russia, Moscow, 115522 Russia
| | - M. E. Dyneva
- National Research Center – Institute of Immunology Federal Medical-Biological Agency of Russia, Moscow, 115522 Russia
| | - O. M. Kurbacheva
- National Research Center – Institute of Immunology Federal Medical-Biological Agency of Russia, Moscow, 115522 Russia
| | - D. A. Kudlay
- National Research Center – Institute of Immunology Federal Medical-Biological Agency of Russia, Moscow, 115522 Russia
| | - M. R. Khaitov
- National Research Center – Institute of Immunology Federal Medical-Biological Agency of Russia, Moscow, 115522 Russia
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33
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Shilova ON, Deyev SM. DARPins: Promising Scaffolds for Theranostics. Acta Naturae 2019; 11:42-53. [PMID: 31993234 PMCID: PMC6977956 DOI: 10.32607/20758251-2019-11-4-42-53] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022] Open
Abstract
Monoclonal antibodies are the classical basis for targeted therapy, but the development of alternative binding proteins has made it possible to use non-immunoglobulin proteins as targeting modules. The advantages of DARPins, scaffold proteins based on ankyrin repeats, over antibodies are as follows: small size, stability over a wide range of temperatures and pH values, low aggregation tendency, and ease of production in heterologous expression systems. The differences in the structure of the paratope of DARPin and antibodies broaden the spectrum of target molecules, while the ease of creating hybrid fusion proteins allows one to obtain bispecific and multivalent constructs. In this article, we summarize recent data on the development of therapeutic and imaging compounds based on DARPins.
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Affiliation(s)
- O. N. Shilova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
| | - S. M. Deyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
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34
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Xiong Y, Tian X, Ai HW. Molecular Tools to Generate Reactive Oxygen Species in Biological Systems. Bioconjug Chem 2019; 30:1297-1303. [PMID: 30986044 DOI: 10.1021/acs.bioconjchem.9b00191] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Reactive oxygen species (ROS) not only are byproducts of aerobic respiration, but also play vital roles in metabolism regulation and signal transductions. It is important to understand the functions of ROS in biological systems. In addition, scientists have made use of ROS to kill bacteria and tumors through a process known as photodynamic therapy (PDT). This paper provides a concise review of current molecular tools that can generate ROS in biological systems via either nongenetic or genetically encoded way. Challenges and perspectives are further discussed with the hope of broadening the applications of ROS generators in research and clinical settings.
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Affiliation(s)
- Ying Xiong
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Xiaodong Tian
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
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35
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Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A. Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Sci Rep 2019; 9:2428. [PMID: 30787421 PMCID: PMC6382843 DOI: 10.1038/s41598-019-38955-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 11/15/2022] Open
Abstract
miniSOG is the first flavin-binding protein that has been developed with the specific aim of serving as a genetically-encodable light-induced source of singlet oxygen (1O2). We have determined its 1.17 Å resolution structure, which has allowed us to investigate its mechanism of photosensitization using an integrated approach combining spectroscopic and structural methods. Our results provide a structural framework to explain the ability of miniSOG to produce 1O2 as a competition between oxygen- and protein quenching of its triplet state. In addition, a third excited-state decay pathway has been identified that is pivotal for the performance of miniSOG as 1O2 photosensitizer, namely the photo-induced transformation of flavin mononucleotide (FMN) into lumichrome, which increases the accessibility of oxygen to the flavin FMN chromophore and makes protein quenching less favourable. The combination of the two effects explains the increase in the 1O2 quantum yield by one order of magnitude upon exposure to blue light. Besides, we have identified several surface electron-rich residues that are progressively photo-oxidized, further contributing to facilitate the production of 1O2. Our results help reconcile the apparent poor level of 1O2 generation by miniSOG and its excellent performance in correlative light and electron microscopy experiments.
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Affiliation(s)
- Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain
| | - Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, F-38043, Grenoble, France
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience), Ciudad Universitaria de Cantoblanco, C/Faraday 9, 28049, Madrid, Spain.,Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC-IMDEA), Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, 94158-9001, United States.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California, 94158-9001, United States
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain.
| | | | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France. .,European Synchrotron Radiation Facility, F-38043, Grenoble, France.
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36
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Trewin AJ, Berry BJ, Wei AY, Bahr LL, Foster TH, Wojtovich AP. Light-induced oxidant production by fluorescent proteins. Free Radic Biol Med 2018; 128:157-164. [PMID: 29425690 PMCID: PMC6078816 DOI: 10.1016/j.freeradbiomed.2018.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/22/2018] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
Abstract
Oxidants play an important role in the cell and are involved in many redox processes. Oxidant concentrations are maintained through coordinated production and removal systems. The dysregulation of oxidant homeostasis is a hallmark of many disease pathologies. The local oxidant microdomain is crucial for the initiation of many redox signaling events; however, methods to control oxidant product are limited. Some fluorescent proteins, including GFP, TagRFP, KillerRed, miniSOG, and their derivatives, generate oxidants in response to light. These genetically-encoded photosensitizers produce singlet oxygen and superoxide upon illumination and offer spatial and temporal control over oxidant production. In this review, we will examine the photosensitization properties of fluorescent proteins and their application to redox biology. Emerging concepts of selective oxidant species production via photosensitization and the impact of light on biological systems are discussed.
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Affiliation(s)
- Adam J Trewin
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester 14642, United States
| | - Brandon J Berry
- University of Rochester Medical Center, Department of Pharmacology and Physiology, Rochester 14642, United States
| | - Alicia Y Wei
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester 14642, United States
| | - Laura L Bahr
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester 14642, United States
| | - Thomas H Foster
- University of Rochester Medical Center, Department of Imaging Sciences, Rochester 14642, United States
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester 14642, United States; University of Rochester Medical Center, Department of Pharmacology and Physiology, Rochester 14642, United States.
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37
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An optogenetic toolbox of LOV-based photosensitizers for light-driven killing of bacteria. Sci Rep 2018; 8:15021. [PMID: 30301917 PMCID: PMC6177443 DOI: 10.1038/s41598-018-33291-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 09/26/2018] [Indexed: 01/04/2023] Open
Abstract
Flavin-binding fluorescent proteins (FPs) are genetically encoded in vivo reporters, which are derived from microbial and plant LOV photoreceptors. In this study, we comparatively analyzed ROS formation and light-driven antimicrobial efficacy of eleven LOV-based FPs. In particular, we determined singlet oxygen (1O2) quantum yields and superoxide photosensitization activities via spectroscopic assays and performed cell toxicity experiments in E. coli. Besides miniSOG and SOPP, which have been engineered to generate 1O2, all of the other tested flavoproteins were able to produce singlet oxygen and/or hydrogen peroxide but exhibited remarkable differences in ROS selectivity and yield. Accordingly, most LOV-FPs are potent photosensitizers, which can be used for light-controlled killing of bacteria. Furthermore, the two variants Pp2FbFP and DsFbFP M49I, exhibiting preferential photosensitization of singlet oxygen or singlet oxygen and superoxide, respectively, were shown to be new tools for studying specific ROS-induced cell signaling processes. The tested LOV-FPs thus further expand the toolbox of optogenetic sensitizers usable for a broad spectrum of microbiological and biomedical applications.
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38
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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39
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Riani YD, Matsuda T, Takemoto K, Nagai T. Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation. BMC Biol 2018; 16:50. [PMID: 29712573 PMCID: PMC5928576 DOI: 10.1186/s12915-018-0514-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/06/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Photosensitizing fluorescent proteins, which generate reactive oxygen species (ROS) upon light irradiation, are useful for spatiotemporal protein inactivation and cell ablation. They give us clues about protein function, intracellular signaling pathways and intercellular interactions. Since ROS generation of a photosensitizer is specifically controlled by certain excitation wavelengths, utilizing colour variants of photosensitizing protein would allow multi-spatiotemporal control of inactivation. To expand the colour palette of photosensitizing protein, here we developed SuperNova Green from its red predecessor, SuperNova. RESULTS SuperNova Green is able to produce ROS spatiotemporally upon blue light irradiation. Based on protein characterization, SuperNova Green produces insignificant amounts of singlet oxygen and predominantly produces superoxide and its derivatives. We utilized SuperNova Green to specifically inactivate the pleckstrin homology domain of phospholipase C-δ1 and to ablate cancer cells in vitro. As a proof of concept for multi-spatiotemporal control of inactivation, we demonstrate that SuperNova Green can be used with its red variant, SuperNova, to perform independent protein inactivation or cell ablation studies in a spatiotemporal manner by selective light irradiation. CONCLUSION Development of SuperNova Green has expanded the photosensitizing protein toolbox to optogenetically control protein inactivation and cell ablation.
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Affiliation(s)
- Yemima Dani Riani
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tomoki Matsuda
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan
| | - Kiwamu Takemoto
- Graduate School of Medicine, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, 236-0027, Japan
| | - Takeharu Nagai
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan. .,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan.
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40
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Rodríguez-Pulido A, Torra J, Mejías SH, Cortajarena AL, Ruiz-González R, Nonell S, Flors C. Fluorescent Flavoprotein Heterodimers: Combining Photostability with Singlet Oxygen Generation. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201800002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alberto Rodríguez-Pulido
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and; Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC); C/ Faraday 9 28049 Madrid Spain
| | - Joaquim Torra
- Institut Químic de Sarrià; Universitat Ramon Llull; Via Augusta 390 08017 Barcelona Spain
| | - Sara H. Mejías
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and; Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC); C/ Faraday 9 28049 Madrid Spain
| | - Aitziber L. Cortajarena
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and; Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC); C/ Faraday 9 28049 Madrid Spain
- CIC biomaGUNE; Parque Tecnológico de San Sebastián; Paseo de Miramón 182 20014 Donostia-San Sebastián Spain
- Ikerbasque, Basque Foundation for Science; Mª Díaz de Haro 3 48013 Bilbao Spain
| | - Rubén Ruiz-González
- Institut Químic de Sarrià; Universitat Ramon Llull; Via Augusta 390 08017 Barcelona Spain
| | - Santi Nonell
- Institut Químic de Sarrià; Universitat Ramon Llull; Via Augusta 390 08017 Barcelona Spain
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and; Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC); C/ Faraday 9 28049 Madrid Spain
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Barnett ME, Baran TM, Foster TH, Wojtovich AP. Quantification of light-induced miniSOG superoxide production using the selective marker, 2-hydroxyethidium. Free Radic Biol Med 2018; 116:134-140. [PMID: 29353158 PMCID: PMC5815924 DOI: 10.1016/j.freeradbiomed.2018.01.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/31/2022]
Abstract
Genetically-encoded photosensitizers produce reactive oxygen species (ROS) in response to light. Transgenic expression of fusion proteins can target the photosensitizers to specific cell regions and permit the spatial and temporal control of ROS production. These ROS-generating proteins (RGPs) are widely used for cell ablation, mutagenesis and chromophore-assisted light inactivation of target proteins. However, the species produced by RGPs are unclear due to indirect measures with confounding interpretations. Recently, the RGP mini "Singlet Oxygen Generator" (miniSOG) was engineered from Arabidopsis thaliana phototropin 2. While miniSOG produces singlet oxygen (1O2), the contribution of superoxide (O2•-) to miniSOG-generated ROS remains unclear. We measured the light-dependent O2•- production of purified miniSOG using HPLC separation of dihydroethidium (DHE) oxidation products. We demonstrate that DHE is insensitive to 1O2 and establish that DHE is a suitable indicator to measure O2•- production in a system that produces both 1O2 and O2•-. We report that miniSOG produces both 1O2 and O2•-, as can its free chromophore, flavin mononucleotide. miniSOG produced O2•- at a rate of ~4.0µmol O2•-/min/µmol photosensitizer for an excitation fluence rate of 5.9mW/mm2 at 470 ± 20nm, and the rate remained consistent across fluences (light doses). Overall, the contribution of O2•- to miniSOG phenotypes should be considered.
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Affiliation(s)
- Miriam E Barnett
- University of Rochester Medical Center, Department of Pharmacology and Physiology, Rochester 14642, United States
| | - Timothy M Baran
- University of Rochester Medical Center, Department of Imaging Sciences, Rochester 14642, United States
| | - Thomas H Foster
- University of Rochester Medical Center, Department of Imaging Sciences, Rochester 14642, United States
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Pharmacology and Physiology, Rochester 14642, United States; University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester 14642. United States.
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Westberg M, Bregnhøj M, Etzerodt M, Ogilby PR. No Photon Wasted: An Efficient and Selective Singlet Oxygen Photosensitizing Protein. J Phys Chem B 2017; 121:9366-9371. [PMID: 28892628 DOI: 10.1021/acs.jpcb.7b07831] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Optogenetics has been, and will continue to be, a boon to mechanistic studies of cellular processes. Genetically encodable proteins that sensitize the production of reactive oxygen species (ROS) are expected to play an increasingly important role, particularly in elucidating mechanisms of temporally and spatially dependent cell signaling. However, a substantial challenge in developing such photosensitizing proteins has been to funnel the optical excitation energy into the initial selective production of only one ROS. Singlet molecular oxygen, O2(a1Δg), is a ROS known to have a wide range of effects on cell function. Nevertheless, mechanistic details of singlet oxygen's behavior in a cell are lacking. On the basis of the rational optimization of a LOV-derived flavoprotein, we now report the development and photophysical characterization of a protein-encased photosensitizer that efficiently and selectively produces singlet oxygen at the expense of other ROS, especially ROS that derive from photoinduced electron transfer reactions. These results set the stage for a plethora of new experiments to elucidate ROS-mediated events in cells.
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Affiliation(s)
- Michael Westberg
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University , DK-8000 Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
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43
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Engineering a light-activated caspase-3 for precise ablation of neurons in vivo. Proc Natl Acad Sci U S A 2017; 114:E8174-E8183. [PMID: 28893998 DOI: 10.1073/pnas.1705064114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circuitry of the brain is characterized by cell heterogeneity, sprawling cellular anatomy, and astonishingly complex patterns of connectivity. Determining how complex neural circuits control behavior is a major challenge that is often approached using surgical, chemical, or transgenic approaches to ablate neurons. However, all these approaches suffer from a lack of precise spatial and temporal control. This drawback would be overcome if cellular ablation could be controlled with light. Cells are naturally and cleanly ablated through apoptosis due to the terminal activation of caspases. Here, we describe the engineering of a light-activated human caspase-3 (Caspase-LOV) by exploiting its natural spring-loaded activation mechanism through rational insertion of the light-sensitive LOV2 domain that expands upon illumination. We apply the light-activated caspase (Caspase-LOV) to study neurodegeneration in larval and adult Drosophila Using the tissue-specific expression system (UAS)-GAL4, we express Caspase-LOV specifically in three neuronal cell types: retinal, sensory, and motor neurons. Illumination of whole flies or specific tissues containing Caspase-LOV-induced cell death and allowed us to follow the time course and sequence of neurodegenerative events. For example, we find that global synchronous activation of caspase-3 drives degeneration with a different time-course and extent in sensory versus motor neurons. We believe the Caspase-LOV tool we engineered will have many other uses for neurobiologists and others for specific temporal and spatial ablation of cells in complex organisms.
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44
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Illuminating developmental biology through photochemistry. Nat Chem Biol 2017; 13:587-598. [PMID: 28514427 DOI: 10.1038/nchembio.2369] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/22/2017] [Indexed: 01/06/2023]
Abstract
Developmental biology has been continually shaped by technological advances, evolving from a descriptive science into one immersed in molecular and cellular mechanisms. Most recently, genome sequencing and 'omics' profiling have provided developmental biologists with a wealth of genetic and biochemical information; however, fully translating this knowledge into functional understanding will require new experimental capabilities. Photoactivatable probes have emerged as particularly valuable tools for investigating developmental mechanisms, as they can enable rapid, specific manipulations of DNA, RNA, proteins, and cells with spatiotemporal precision. In this Perspective, we describe optochemical and optogenetic systems that have been applied in multicellular organisms, insights gained through the use of these probes, and their current limitations. We also suggest how chemical biologists can expand the reach of photoactivatable technologies and bring new depth to our understanding of organismal development.
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45
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Westberg M, Bregnhøj M, Etzerodt M, Ogilby PR. Temperature Sensitive Singlet Oxygen Photosensitization by LOV-Derived Fluorescent Flavoproteins. J Phys Chem B 2017; 121:2561-2574. [PMID: 28257211 DOI: 10.1021/acs.jpcb.7b00561] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Optogenetic sensitizers that selectively produce a given reactive oxygen species (ROS) constitute a promising tool for studying cell signaling processes with high levels of spatiotemporal control. However, to harness the full potential of this tool for live cell studies, the photophysics of currently available systems need to be explored further and optimized. Of particular interest in this regard, are the flavoproteins miniSOG and SOPP, both of which (1) contain the chromophore flavin mononucleotide, FMN, in a LOV-derived protein enclosure, and (2) photosensitize the production of singlet oxygen, O2(a1Δg). Here we present an extensive experimental study of the singlet and triplet state photophysics of FMN in SOPP and miniSOG over a physiologically relevant temperature range. Although changes in temperature only affect the singlet excited state photophysics slightly, the processes that influence the deactivation of the triplet excited state are more sensitive to temperature. Most notably, for both proteins, the rate constant for quenching of 3FMN by ground state oxygen, O2(X3Σg-), increases ∼10-fold upon increasing the temperature from 10 to 43 °C, while the oxygen-independent channels of triplet state deactivation are less affected. As a consequence, this increase in temperature results in higher yields of O2(a1Δg) formation for both SOPP and miniSOG. We also show that the quantum yields of O2(a1Δg) production by both miniSOG and SOPP are mainly limited by the fraction of FMN triplet states quenched by O2(X3Σg-). The results presented herein provide a much-needed quantitative framework that will facilitate the future development of optogenetic ROS sensitizers.
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Affiliation(s)
- Michael Westberg
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University , DK-8000 Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
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Jiang HN, Li Y, Cui ZJ. Photodynamic Physiology-Photonanomanipulations in Cellular Physiology with Protein Photosensitizers. Front Physiol 2017; 8:191. [PMID: 28421000 PMCID: PMC5378799 DOI: 10.3389/fphys.2017.00191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/14/2017] [Indexed: 02/05/2023] Open
Abstract
Singlet oxygen generated in a type II photodynamic action, due to its limited lifetime (1 μs) and reactive distance (<10 nm), could regulate live cell function nanoscopically. The genetically-encoded protein photosensitizers (engineered fluorescent proteins such as KillerRed, TagRFP, and flavin-binding proteins such as miniSOG, Pp2FbFPL30M) could be expressed in a cell type- and/or subcellular organelle-specific manner for targeted protein photo-oxidative activation/desensitization. The newly emerged active illumination technique provides an additional level of specificity. Typical examples of photodynamic activation include permanent activation of G protein-coupled receptor CCK1 and photodynamic activation of ionic channel TRPA1. Protein photosensitizers have been used to photodynamically modulate major cellular functions (such as neurotransmitter release and gene transcription) and animal behavior. Protein photosensitizers are increasingly used in photon-driven nanomanipulation in cell physiology research.
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