1
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Vlasova AD, Bukhalovich SM, Bagaeva DF, Polyakova AP, Ilyinsky NS, Nesterov SV, Tsybrov FM, Bogorodskiy AO, Zinovev EV, Mikhailov AE, Vlasov AV, Kuklin AI, Borshchevskiy VI, Bamberg E, Uversky VN, Gordeliy VI. Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling. Chem Soc Rev 2024; 53:3327-3349. [PMID: 38391026 DOI: 10.1039/d3cs00699a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in optogenetic control of intracellular metabolism and signaling via precise manipulations of organelle ion gradients using light. This new optogenetic field expands the opportunities for basic and medical studies of cancer, cardiovascular, and metabolic disorders, providing more detailed and accurate control of cell physiology. This review summarizes recent advances in studies of the cellular metabolic processes and signaling mediated by optogenetic tools targeting mitochondria, endoplasmic reticulum (ER), lysosomes, and synaptic vesicles. Finally, we discuss perspectives of such an optogenetic approach in both fundamental and applied research.
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Affiliation(s)
- Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei M Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Diana F Bagaeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Aleksandra P Polyakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor M Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France.
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2
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Mumford TR, Rae D, Brackhahn E, Idris A, Gonzalez-Martinez D, Pal AA, Chung MC, Guan J, Rhoades E, Bugaj LJ. Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. Cell Syst 2024; 15:166-179.e7. [PMID: 38335954 PMCID: PMC10947474 DOI: 10.1016/j.cels.2024.01.005] [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: 08/22/2022] [Revised: 11/06/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Protein clustering plays numerous roles in cell physiology and disease. However, protein oligomers can be difficult to detect because they are often too small to appear as puncta in conventional fluorescence microscopy. Here, we describe a fluorescent reporter strategy that detects protein clusters with high sensitivity called CluMPS (clusters magnified by phase separation). A CluMPS reporter detects and visually amplifies even small clusters of a binding partner, generating large, quantifiable fluorescence condensates. We use computational modeling and optogenetic clustering to demonstrate that CluMPS can detect small oligomers and behaves rationally according to key system parameters. CluMPS detected small aggregates of pathological proteins where the corresponding GFP fusions appeared diffuse. CluMPS also detected and tracked clusters of unmodified and tagged endogenous proteins, and orthogonal CluMPS probes could be multiplexed in cells. CluMPS provides a powerful yet straightforward approach to observe higher-order protein assembly in its native cellular context. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Thomas R Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diarmid Rae
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Brackhahn
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abbas Idris
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Chung
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - Juan Guan
- Department of Physics, University of Florida, Gainesville, FL 32611, USA; Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Wurz AI, Zheng KS, Hughes RM. Optogenetic Regulation of EphA1 RTK Activation and Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579139. [PMID: 38370612 PMCID: PMC10871282 DOI: 10.1101/2024.02.06.579139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Eph receptors are ubiquitous class of transmembrane receptors that mediate cell-cell communication, proliferation, differentiation, and migration. EphA1 receptors specifically play an important role in angiogenesis, fetal development, and cancer progression; however, studies of this receptor can be challenging as its ligand, ephrinA1, binds and activates several EphA receptors simultaneously. Optogenetic strategies could be applied to circumvent this requirement for ligand activation and enable selective activation of the EphA1 subtype. In this work, we designed and tested several iterations of an optogenetic EphA1 - Cryptochrome 2 (Cry2) fusion, investigating their capacity to mimic EphA1-dependent signaling in response to light activation. We then characterized the key cell signaling target of MAPK phosphorylation activated in response to light stimulation. The optogenetic regulation of Eph receptor RTK signaling without the need for external stimulus promises to be an effective means of controlling individual Eph receptor-mediated activities and creates a path forward for the identification of new Eph-dependent functions.
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Affiliation(s)
- Anna I. Wurz
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Kevin S. Zheng
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Robert M. Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
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4
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Huang Dennis Z, Benman W, Dong L, Bugaj LJ. Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust. J Mol Biol 2024; 436:168452. [PMID: 38246410 DOI: 10.1016/j.jmb.2024.168452] [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: 09/05/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Protein clustering is a powerful form of optogenetic control, yet remarkably few proteins are known to oligomerize with light. Recently, the photoreceptor BcLOV4 was found to form protein clusters in mammalian cells in response to blue light, although clustering coincided with its translocation to the plasma membrane, potentially constraining its application as an optogenetic clustering module. Herein we identify key amino acids that couple BcLOV4 clustering to membrane binding, allowing us to engineer a variant that clusters in the cytoplasm and does not associate with the membrane in response to blue light. This variant-called BcLOVclust-clustered over many cycles with substantially faster clustering and de-clustering kinetics compared to the widely used optogenetic clustering protein Cry2. The magnitude of clustering could be strengthened by appending an intrinsically disordered region from the fused in sarcoma (FUS) protein, or by selecting the appropriate fluorescent protein to which it was fused. Like wt BcLOV4, BcLOVclust activity was sensitive to temperature: light-induced clusters spontaneously dissolved at a rate that increased with temperature despite constant illumination. At low temperatures, BcLOVclust and Cry2 could be multiplexed in the same cells, allowing light control of independent protein condensates. BcLOVclust could also be applied to control signaling proteins and stress granules in mammalian cells. While its usage is currently best suited in cells and organisms that can be cultured below ∼30 °C, a deeper understanding of BcLOVclust thermal response will further enable its use at physiological mammalian temperatures.
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Affiliation(s)
- Zikang Huang Dennis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liang Dong
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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Chen Y, Jiang W, Wang J, Ma X, Wu D, Liu L, Ji M, Qu X, Liu C, Liu H, Qin X, Xiang Y. Conditional knockout of ITGB4 in bronchial epithelial cells directs bronchopulmonary dysplasia. J Cell Mol Med 2023; 27:3760-3772. [PMID: 37698050 PMCID: PMC10718146 DOI: 10.1111/jcmm.17948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023] Open
Abstract
Neonatal respiratory system disease is closely associated with embryonic lung development. Our group found that integrin β4 (ITGB4) is downregulated in the airway epithelium of asthma patients. Asthma is the most common chronic respiratory illness in childhood. Therefore, we suspect whether the deletion of ITGB4 would affect fetal lung development. In this study, we characterized the role of ITGB4 deficiency in bronchopulmonary dysplasia (BPD). ITGB4 was conditionally knocked out in CCSP-rtTA, Tet-O-Cre and ITGB4f/f triple transgenic mice. Lung tissues at different developmental stages were collected for experimental detection and transcriptome sequencing. The effects of ITGB4 deficiency on lung branching morphogenesis were observed by fetal mouse lung explant culture. Deleting ITGB4 from the airway epithelial cells results in enlargement of alveolar airspaces, inhibition of branching, the abnormal structure of epithelium cells and the impairment of cilia growth during lung development. Scanning electron microscopy showed that the airway epithelial cilia of the β4ccsp.cre group appear to be sparse, shortened and lodging. Lung-development-relevant factors such as SftpC and SOX2 significantly decreased both mRNA and protein levels. KEGG pathway analysis indicated that multiple ontogenesis-regulating-relevant pathways converge to FAK. Accordingly, ITGB4 deletion decreased phospho-FAK, phospho-GSK3β and SOX2 levels, and the correspondingly contrary consequence was detected after treatment with GSK3β agonist (wortmannin). Airway branching defect of β4ccsp.cre mice lung explants was also partly recovered after wortmannin treatment. Airway epithelial-specific deletion of ITGB4 contributes to lung developmental defect, which could be achieved through the FAK/GSK3β/SOX2 signal pathway.
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Affiliation(s)
- Yu Chen
- School of Basic MedicineCentral South UniversityChangshaChina
- Department of Medical Laboratory, School of MedicineHunan Normal UniversityChangshaChina
| | - Wang Jiang
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Jin‐Mei Wang
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Xiao‐Di Ma
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Di Wu
- School of Basic MedicineCentral South UniversityChangshaChina
- School of MedicineFoshan UniversityFoshanChina
| | - Le‐Xin Liu
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Ming Ji
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Xiang‐Ping Qu
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Chi Liu
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Hui‐Jun Liu
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Xiao‐Qun Qin
- School of Basic MedicineCentral South UniversityChangshaChina
| | - Yang Xiang
- School of Basic MedicineCentral South UniversityChangshaChina
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6
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Marcus DJ, Bruchas MR. Optical Approaches for Investigating Neuromodulation and G Protein-Coupled Receptor Signaling. Pharmacol Rev 2023; 75:1119-1139. [PMID: 37429736 PMCID: PMC10595021 DOI: 10.1124/pharmrev.122.000584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 07/12/2023] Open
Abstract
Despite the fact that roughly 40% of all US Food and Drug Administration (FDA)-approved pharmacological therapeutics target G protein-coupled receptors (GPCRs), there remains a gap in our understanding of the physiologic and functional role of these receptors at the systems level. Although heterologous expression systems and in vitro assays have revealed a tremendous amount about GPCR signaling cascades, how these cascades interact across cell types, tissues, and organ systems remains obscure. Classic behavioral pharmacology experiments lack both the temporal and spatial resolution to resolve these long-standing issues. Over the past half century, there has been a concerted effort toward the development of optical tools for understanding GPCR signaling. From initial ligand uncaging approaches to more recent development of optogenetic techniques, these strategies have allowed researchers to probe longstanding questions in GPCR pharmacology both in vivo and in vitro. These tools have been employed across biologic systems and have allowed for interrogation of everything from specific intramolecular events to pharmacology at the systems level in a spatiotemporally specific manner. In this review, we present a historical perspective on the motivation behind and development of a variety of optical toolkits that have been generated to probe GPCR signaling. Here we highlight how these tools have been used in vivo to uncover the functional role of distinct populations of GPCRs and their signaling cascades at a systems level. SIGNIFICANCE STATEMENT: G protein-coupled receptors (GPCRs) remain one of the most targeted classes of proteins for pharmaceutical intervention, yet we still have a limited understanding of how their unique signaling cascades effect physiology and behavior at the systems level. In this review, we discuss a vast array of optical techniques that have been devised to probe GPCR signaling both in vitro and in vivo.
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Affiliation(s)
- David J Marcus
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
| | - Michael R Bruchas
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
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7
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Huang Z, Benman W, Dong L, Bugaj LJ. Rapid optogenetic clustering of a cytoplasmic BcLOV4 variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557726. [PMID: 37745456 PMCID: PMC10515924 DOI: 10.1101/2023.09.14.557726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein clustering is a powerful form of optogenetic control, yet there is currently only one protein -Cry2-whose light-induced clustering has been harnessed for these purposes. Recently, the photoreceptor BcLOV4 was found to form protein clusters in mammalian cells in response to blue light, although clustering coincided with its translocation to the plasma membrane, potentially constraining its application as an optogenetic clustering module. Herein we identify key amino acids that couple clustering to membrane binding, allowing us to engineer a variant of BcLOV4 that clusters in the cytoplasm and does not associate with the membrane in response to blue light. This variant, BcLOVclust, clustered over many cycles with dramatically faster clustering and de-clustering kinetics compared to Cry2. The magnitude of BcLOVclust clustering could be strengthened by appending an intrinsically disordered region from the fused in sarcoma (FUS) protein, or by optimizing the fluorescent protein to which it was fused. BcLOVclust retained the temperature sensitivity of BcLOV4 such that light induced clustering was transient, and the rate of spontaneous declustering increased with temperature. At low temperatures, BcLOVclust and Cry2 could be multiplexed in the same cells, allowing light control of independent protein condensates. BcLOVclust could also be applied to control signaling proteins and stress granules in mammalian cells. Thus BcLOVclust provides an alternative to Cry2 for optogenetic clustering and a method for multiplexed clustering. While its usage is currently suited for organisms that can be cultured below ~30 °C, a deeper understanding of BcLOVclust thermal response will further enable its use at physiological mammalian temperatures.
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Affiliation(s)
- Zikang Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Liang Dong
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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8
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Pal AA, Benman W, Mumford TR, Huang Z, Chow BY, Bugaj LJ. Optogenetic clustering and membrane translocation of the BcLOV4 photoreceptor. Proc Natl Acad Sci U S A 2023; 120:e2221615120. [PMID: 37527339 PMCID: PMC10410727 DOI: 10.1073/pnas.2221615120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/25/2023] [Indexed: 08/03/2023] Open
Abstract
Optogenetic tools respond to light through one of a small number of behaviors including allosteric changes, dimerization, clustering, or membrane translocation. Here, we describe a new class of optogenetic actuator that simultaneously clusters and translocates to the plasma membrane in response to blue light. We demonstrate that dual translocation and clustering of the BcLOV4 photoreceptor can be harnessed for novel single-component optogenetic tools, including for control of the entire family of epidermal growth factor receptor (ErbB1-4) tyrosine kinases. We further find that clustering and membrane translocation are mechanistically linked. Stronger clustering increased the magnitude of translocation and downstream signaling, increased sensitivity to light by ~threefold-to-fourfold, and decreased the expression levels needed for strong signal activation. Thus light-induced clustering of BcLOV4 provides a strategy to generate a new class of optogenetic tools and to enhance existing ones.
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Affiliation(s)
- Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Thomas R. Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Zikang Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Brian Y. Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA19104
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA19104
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9
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Sánchez MF, Tampé R. Ligand-independent receptor clustering modulates transmembrane signaling: a new paradigm. Trends Biochem Sci 2023; 48:156-171. [PMID: 36115755 DOI: 10.1016/j.tibs.2022.08.002] [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: 05/23/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 01/25/2023]
Abstract
Cell-surface receptors mediate communication between cells and their environment. Lateral membrane organization and dynamic receptor cluster formation are fundamental in signal transduction and cell signaling. However, it is not yet fully understood how receptor clustering modulates a wide variety of physiologically relevant processes. Recent growing evidence indicates that biological responses triggered by membrane receptors can be modulated even in the absence of the natural receptor ligand. We review the most recent findings on how ligand-independent receptor clustering can regulate transmembrane signaling. We discuss the latest technologies to control receptor assembly, such as DNA nanotechnology, optogenetics, and optochemistry, focusing on the biological relevance and unraveling of ligand-independent signaling.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany.
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10
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Vettkötter D, Schneider M, Goulden BD, Dill H, Liewald J, Zeiler S, Guldan J, Ateş YA, Watanabe S, Gottschalk A. Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles. Nat Commun 2022; 13:7827. [PMID: 36535932 PMCID: PMC9763335 DOI: 10.1038/s41467-022-35324-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Acutely silencing specific neurons informs about their functional roles in circuits and behavior. Existing optogenetic silencers include ion pumps, channels, metabotropic receptors, and tools that damage the neurotransmitter release machinery. While the former hyperpolarize the cell, alter ionic gradients or cellular biochemistry, the latter allow only slow recovery, requiring de novo synthesis. Thus, tools combining fast activation and reversibility are needed. Here, we use light-evoked homo-oligomerization of cryptochrome CRY2 to silence synaptic transmission, by clustering synaptic vesicles (SVs). We benchmark this tool, optoSynC, in Caenorhabditis elegans, zebrafish, and murine hippocampal neurons. optoSynC clusters SVs, observable by electron microscopy. Locomotion silencing occurs with tauon ~7.2 s and recovers with tauoff ~6.5 min after light-off. optoSynC can inhibit exocytosis for several hours, at very low light intensities, does not affect ion currents, biochemistry or synaptic proteins, and may further allow manipulating different SV pools and the transfer of SVs between them.
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Affiliation(s)
- Dennis Vettkötter
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany
| | - Martin Schneider
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany
- Max Planck Institute for Neurobiology, D-82152, Martinsried, Germany
| | - Brady D Goulden
- Department of Cell Biology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Holger Dill
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany
| | - Jana Liewald
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany
| | - Sandra Zeiler
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany
| | - Julia Guldan
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Master Program Interdisciplinary Neurosciences, Department of Biological Sciences, Goethe University, Frankfurt, Germany
| | - Yilmaz Arda Ateş
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany
- Master Program Interdisciplinary Neurosciences, Department of Biological Sciences, Goethe University, Frankfurt, Germany
| | - Shigeki Watanabe
- Department of Cell Biology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438, Frankfurt, Germany.
- Institute of Biophysical Chemistry, Goethe University, D-60438, Frankfurt, Germany.
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11
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Philippi M, Richter CP, Kappen M, Watrinet I, Miao Y, Runge M, Jorde L, Korneev S, Holtmannspötter M, Kurre R, Holthuis JCM, Garcia KC, Plückthun A, Steinhart M, Piehler J, You C. Biofunctional Nanodot Arrays in Living Cells Uncover Synergistic Co-Condensation of Wnt Signalodroplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203723. [PMID: 36266931 DOI: 10.1002/smll.202203723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Qualitative and quantitative analysis of transient signaling platforms in the plasma membrane has remained a key experimental challenge. Here, biofunctional nanodot arrays (bNDAs) are developed to spatially control dimerization and clustering of cell surface receptors at the nanoscale. High-contrast bNDAs with spot diameters of ≈300 nm are obtained by capillary nanostamping of bovine serum albumin bioconjugates, which are subsequently biofunctionalized by reaction with tandem anti-green fluorescence protein (GFP) clamp fusions. Spatially controlled assembly of active Wnt signalosomes is achieved at the nanoscale in the plasma membrane of live cells by capturing the co-receptor Lrp6 into bNDAs via an extracellular GFP tag. Strikingly, co-recruitment is observed of co-receptor Frizzled-8 as well as the cytosolic scaffold proteins Axin-1 and Disheveled-2 into Lrp6 nanodots in the absence of ligand. Density variation and the high dynamics of effector proteins uncover highly cooperative liquid-liquid phase separation (LLPS)-driven assembly of Wnt "signalodroplets" at the plasma membrane, pinpointing the synergistic effects of LLPS for Wnt signaling amplification. These insights highlight the potential of bNDAs for systematically interrogating nanoscale signaling platforms and condensation at the plasma membrane of live cells.
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Affiliation(s)
- Michael Philippi
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Christian P Richter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Marie Kappen
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Isabelle Watrinet
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mercedes Runge
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Lara Jorde
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Sergej Korneev
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Joost C M Holthuis
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, Zurich, 8057, Switzerland
| | - Martin Steinhart
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Changjiang You
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
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12
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Tang WC, Liu YT, Yeh CH, Lu CH, Tu CH, Lin YL, Lin YC, Hsu TL, Gao L, Chang SW, Chen P, Chen BC. Optogenetic manipulation of cell migration with high spatiotemporal resolution using lattice lightsheet microscopy. Commun Biol 2022; 5:879. [PMID: 36028551 PMCID: PMC9418249 DOI: 10.1038/s42003-022-03835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Lattice lightsheet microscopy (LLSM) featuring three-dimensional recording is improved to manipulate cellular behavior with subcellular resolution through optogenetic activation (optoLLSM). A position-controllable Bessel beam as a stimulation source is integrated into the LLSM to achieve spatiotemporal photoactivation by changing the spatial light modulator (SLM) patterns. Unlike the point-scanning in a confocal microscope, the lattice beams are capable of wide-field optical sectioning for optogenetic activation along the Bessel beam path.We show that the energy power required for optogenetic activations is lower than 1 nW (or 24 mWcm-2) for time-lapses of CRY2olig clustering proteins, and membrane ruffling can be induced at different locations within a cell with subcellular resolution through light-triggered recruitment of phosphoinositide 3-kinase. Moreover, with the epidermal growth factor receptor (EGFR) fused with CRY2olig, we are able to demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable cellular damages. Using a Bessel beam as a simulation source allows the use of lattice lightsheet microscopy for spatiotemporal control of photoactivation, illustrated by the control of cellular migration behavior.
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Affiliation(s)
- Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Han Yeh
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiao-Hui Tu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Liang Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Physics, Academia Sinica, Taipei, 11529, Taiwan.
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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13
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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14
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Chen Z, Biswas KH, Groves AJT. Patterned Substrate of Mobile and Immobile Ligands to Probe EphA2 Receptor Clustering. Bio Protoc 2022; 12:e4434. [PMID: 35799902 PMCID: PMC9243512 DOI: 10.21769/bioprotoc.4434] [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: 01/31/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 12/29/2022] Open
Abstract
A multitude of membrane-localized receptors are utilized by cells to integrate both biochemical and physical signals from their microenvironment. The clustering of membrane receptors is widely presumed to have functional consequences for subsequent signal transduction. However, it is experimentally challenging to selectively manipulate receptor clustering without altering other biochemical aspects of the cellular system. Here, we describe a method to fabricate multicomponent, ligand-functionalized microarrays, for spatially segregated and simultaneous monitoring of receptor activation and signaling in individual living cells. While existing micropatterning techniques allow for the display of fixed ligands, this protocol uniquely allows for functionalization of both mobile membrane corrals and immobile polymers with selective ligands, as well as microscopic monitoring of cognate receptor activation at the cell membrane interface. This protocol has been developed to study the effects of clustering on EphA2 signaling transduction. It is potentially applicable to multiple cell signaling systems, or microbe/host interactions. Graphical abstract: A side-by-side comparison of clustered or non-clustered EphA2 receptor signaling in a single cell.
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Affiliation(s)
- Zhongwen Chen
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
,
*For correspondence:
| | - Kabir H. Biswas
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - And Jay T. Groves
- Department of Chemistry, University of California, Berkeley, California, USA
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15
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Miura Y, Senoo A, Doura T, Kiyonaka S. Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches. RSC Chem Biol 2022; 3:269-287. [PMID: 35359495 PMCID: PMC8905536 DOI: 10.1039/d1cb00195g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Cell surface receptors transmit extracellular information into cells. Spatiotemporal regulation of receptor signaling is crucial for cellular functions, and dysregulation of signaling causes various diseases. Thus, it is highly desired to control receptor functions with high spatial and/or temporal resolution. Conventionally, genetic engineering or chemical ligands have been used to control receptor functions in cells. As the alternative, chemogenetics has been proposed, in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. The engineered receptor dissects the function of one receptor member among a highly homologous receptor family in a cell-specific manner. Notably, some chemogenetic strategies have been used to reveal the receptor signaling of target cells in living animals. In this review, we summarize the developing chemogenetic methods of transmembrane receptors for cell-specific regulation of receptor signaling. We also discuss the prospects of chemogenetics for clinical applications.
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Affiliation(s)
- Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akinobu Senoo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
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16
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Crossman SH, Janovjak H. Light-activated receptor tyrosine kinases: Designs and applications. Curr Opin Pharmacol 2022; 63:102197. [PMID: 35245796 DOI: 10.1016/j.coph.2022.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
Receptor tyrosine kinases (RTKs) are a large and essential membrane receptor family. The molecular mechanisms and physiological consequences of RTK activation depend on, for example, ligand identity, subcellular localization, and developmental or disease stage. In the past few years, genetically-encoded light-activated RTKs (Opto-RTKs) have been developed to dissect these complexities by providing reversible and spatio-temporal control over cell signaling. These methods have very recently matured to include highly-sensitive multi-color actuators. The new ability to regulate RTK activity with high precision has been recently harnessed to gain mechanistic insights in subcellular, tissue, and animal models. Because of their sophisticated engineering, Opto-RTKs may only mirror some aspects of natural activation mechanisms but nevertheless offer unique opportunities to study RTK signaling and physiology.
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Affiliation(s)
- Samuel H Crossman
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia.
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17
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Zhu D, Johnson HJ, Chen J, Schaffer DV. Optogenetic Application to Investigating Cell Behavior and Neurological Disease. Front Cell Neurosci 2022; 16:811493. [PMID: 35273478 PMCID: PMC8902366 DOI: 10.3389/fncel.2022.811493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cells reside in a dynamic microenvironment that presents them with regulatory signals that vary in time, space, and amplitude. The cell, in turn, interprets these signals and accordingly initiates downstream processes including cell proliferation, differentiation, migration, and self-organization. Conventional approaches to perturb and investigate signaling pathways (e.g., agonist/antagonist addition, overexpression, silencing, knockouts) are often binary perturbations that do not offer precise control over signaling levels, and/or provide limited spatial or temporal control. In contrast, optogenetics leverages light-sensitive proteins to control cellular signaling dynamics and target gene expression and, by virtue of precise hardware control over illumination, offers the capacity to interrogate how spatiotemporally varying signals modulate gene regulatory networks and cellular behaviors. Recent studies have employed various optogenetic systems in stem cell, embryonic, and somatic cell patterning studies, which have addressed fundamental questions of how cell-cell communication, subcellular protein localization, and signal integration affect cell fate. Other efforts have explored how alteration of signaling dynamics may contribute to neurological diseases and have in the process created physiologically relevant models that could inform new therapeutic strategies. In this review, we focus on emerging applications within the expanding field of optogenetics to study gene regulation, cell signaling, neurodevelopment, and neurological disorders, and we comment on current limitations and future directions for the growth of the field.
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Affiliation(s)
- Danqing Zhu
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - Hunter J. Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, United States
- Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Jun Chen
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - David V. Schaffer
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David V. Schaffer
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18
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Shen Y, Luchetti A, Fernandes G, Do Heo W, Silva AJ. The emergence of molecular systems neuroscience. Mol Brain 2022; 15:7. [PMID: 34983613 PMCID: PMC8728933 DOI: 10.1186/s13041-021-00885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.
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Affiliation(s)
- Yang Shen
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Alessandro Luchetti
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Giselle Fernandes
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA.
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19
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Huang P, Zhao Z, Duan L. Optogenetic activation of intracellular signaling based on light-inducible protein-protein homo-interactions. Neural Regen Res 2022; 17:25-30. [PMID: 34100422 PMCID: PMC8451544 DOI: 10.4103/1673-5374.314293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dynamic protein-protein interactions are essential for proper cell functioning. Homo-interaction events—physical interactions between the same type of proteins—represent a pivotal subset of protein-protein interactions that are widely exploited in activating intracellular signaling pathways. Capacities of modulating protein-protein interactions with spatial and temporal resolution are greatly desired to decipher the dynamic nature of signal transduction mechanisms. The emerging optogenetic technology, based on genetically encoded light-sensitive proteins, provides promising opportunities to dissect the highly complex signaling networks with unmatched specificity and spatiotemporal precision. Here we review recent achievements in the development of optogenetic tools enabling light-inducible protein-protein homo-interactions and their applications in optical activation of signaling pathways.
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Affiliation(s)
- Peiyuan Huang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
| | - Zhihao Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
| | - Liting Duan
- Department of Biomedical Engineering; Shun Hing Institute of Advanced Engineering (SHIAE), The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
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20
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Chen Z, Oh D, Biswas KH, Zaidel-Bar R, Groves JT. Probing the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility. eLife 2021; 10:67379. [PMID: 34414885 PMCID: PMC8397371 DOI: 10.7554/elife.67379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
Clustering of ligand:receptor complexes on the cell membrane is widely presumed to have functional consequences for subsequent signal transduction. However, it is experimentally challenging to selectively manipulate receptor clustering without altering other biochemical aspects of the cellular system. Here, we develop a microfabrication strategy to produce substrates displaying mobile and immobile ligands that are separated by roughly 1 µm, and thus experience an identical cytoplasmic signaling state, enabling precision comparison of downstream signaling reactions. Applying this approach to characterize the ephrinA1:EphA2 signaling system reveals that EphA2 clustering enhances both receptor phosphorylation and downstream signaling activity. Single-molecule imaging clearly resolves increased molecular binding dwell times at EphA2 clusters for both Grb2:SOS and NCK:N-WASP signaling modules. This type of intracellular comparison enables a substantially higher degree of quantitative analysis than is possible when comparisons must be made between different cells and essentially eliminates the effects of cellular response to ligand manipulation.
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Affiliation(s)
- Zhongwen Chen
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Dongmyung Oh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, United States.,Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Kabir Hassan Biswas
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
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21
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Yadav V, Tolwinski N, Saunders TE. Spatiotemporal sensitivity of mesoderm specification to FGFR signalling in the Drosophila embryo. Sci Rep 2021; 11:14091. [PMID: 34238963 PMCID: PMC8266908 DOI: 10.1038/s41598-021-93512-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Development of the Drosophila embryonic mesoderm is controlled through both internal and external inputs to the mesoderm. One such factor is Heartless (Htl), a Fibroblast Growth Factor Receptor (FGFR) expressed in the mesoderm. Although Htl has been extensively studied, the dynamics of its action are poorly understood after the initial phases of mesoderm formation and spreading. To begin to address this challenge, we have developed an optogenetic version of the FGFR Heartless in Drosophila (Opto-htl). Opto-htl enables us to activate the FGFR pathway in selective spatial (~ 35 μm section from one of the lateral sides of the embryo) and temporal domains (ranging from 40 min to 14 h) during embryogenesis. Importantly, the effects can be tuned by the intensity of light-activation, making this approach significantly more flexible than other genetic approaches. We performed controlled perturbations to the FGFR pathway to define the contribution of Htl signalling to the formation of the developing embryonic heart and somatic muscles. We find a direct correlation between Htl signalling dosage and number of Tinman-positive heart cells specified. Opto-htl activation favours the specification of Tinman positive cardioblasts and eliminates Eve-positive DA1 muscles. This effect is seen to increase progressively with increasing light intensity. Therefore, fine tuning of phenotypic responses to varied Htl signalling dosage can be achieved more conveniently than with other genetic approaches. Overall, Opto-htl is a powerful new tool for dissecting the role of FGFR signalling during development.
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Affiliation(s)
- V. Yadav
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - N. Tolwinski
- grid.4280.e0000 0001 2180 6431Yale-NUS, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - T. E. Saunders
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cell Biology, A*Star, Singapore, Singapore ,grid.7372.10000 0000 8809 1613Warwick Medical School, University of Warwick, Coventry, UK
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22
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Lim WK, Kaur P, Huang H, Jo RS, Ramamoorthy A, Ng LF, Suresh J, Maisha FI, Mathuru AS, Tolwinski NS. Optogenetic approaches for understanding homeostatic and degenerative processes in Drosophila. Cell Mol Life Sci 2021; 78:5865-5880. [PMID: 34232330 PMCID: PMC8260576 DOI: 10.1007/s00018-021-03836-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/22/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022]
Abstract
Many organs and tissues have an intrinsic ability to regenerate from a dedicated, tissue-specific stem cell pool. As organisms age, the process of self-regulation or homeostasis begins to slow down with fewer stem cells available for tissue repair. Tissues become more fragile and organs less efficient. This slowdown of homeostatic processes leads to the development of cellular and neurodegenerative diseases. In this review, we highlight the recent use and future potential of optogenetic approaches to study homeostasis. Optogenetics uses photosensitive molecules and genetic engineering to modulate cellular activity in vivo, allowing precise experiments with spatiotemporal control. We look at applications of this technology for understanding the mechanisms governing homeostasis and degeneration as applied to widely used model organisms, such as Drosophila melanogaster, where other common tools are less effective or unavailable.
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Affiliation(s)
- Wen Kin Lim
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Prameet Kaur
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Huanyan Huang
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | | | - Li Fang Ng
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Jahnavi Suresh
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | - Ajay S Mathuru
- Science Division, Yale-NUS College, Singapore, Singapore
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23
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Repina NA, McClave T, Johnson HJ, Bao X, Kane RS, Schaffer DV. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics. Cell Rep 2021; 31:107737. [PMID: 32521262 PMCID: PMC9357365 DOI: 10.1016/j.celrep.2020.107737] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 10/31/2022] Open
Abstract
Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics affect cell behavior. Here, we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). By patterning human embryonic stem cell (hESC) cultures with varying light intensities, LAVA devices enabled dose-responsive control of optoWnt activation and Brachyury expression. Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models the embryonic presentation of Wnt signals in vitro. LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.
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Affiliation(s)
- Nicole A Repina
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas McClave
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hunter J Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoping Bao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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24
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Kramer MM, Lataster L, Weber W, Radziwill G. Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways. Int J Mol Sci 2021; 22:5300. [PMID: 34069904 PMCID: PMC8157557 DOI: 10.3390/ijms22105300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events.
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Affiliation(s)
- Markus M. Kramer
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Levin Lataster
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
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25
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Ruijgrok PV, Ghosh RP, Zemsky S, Nakamura M, Gong R, Ning L, Chen R, Vachharajani VT, Chu AE, Anand N, Eguchi RR, Huang PS, Lin MZ, Alushin GM, Liphardt JT, Bryant Z. Optical control of fast and processive engineered myosins in vitro and in living cells. Nat Chem Biol 2021; 17:540-548. [PMID: 33603247 PMCID: PMC10807509 DOI: 10.1038/s41589-021-00740-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
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Affiliation(s)
- Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Robert Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Vipul T Vachharajani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Alexander E Chu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Namrata Anand
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Gregory M Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Bio-X Institute, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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26
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Mahuron KM, Moreau JM, Glasgow JE, Boda DP, Pauli ML, Gouirand V, Panjabi L, Grewal R, Luber JM, Mathur AN, Feldman RM, Shifrut E, Mehta P, Lowe MM, Alvarado MD, Marson A, Singer M, Wells J, Jupp R, Daud AI, Rosenblum MD. Layilin augments integrin activation to promote antitumor immunity. J Exp Med 2021; 217:151858. [PMID: 32539073 PMCID: PMC7478725 DOI: 10.1084/jem.20192080] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/03/2020] [Accepted: 04/10/2020] [Indexed: 12/15/2022] Open
Abstract
Tumor-infiltrating CD8+ T cells mediate antitumor immune responses. However, the mechanisms by which T cells remain poised to kill cancer cells despite expressing high levels of inhibitory receptors are unknown. Here, we report that layilin, a C-type lectin domain-containing membrane glycoprotein, is selectively expressed on highly activated, clonally expanded, but phenotypically exhausted CD8+ T cells in human melanoma. Lineage-specific deletion of layilin on murine CD8+ T cells reduced their accumulation in tumors and increased tumor growth in vivo. Congruently, gene editing of LAYN in human CD8+ T cells reduced direct tumor cell killing ex vivo. On a molecular level, layilin colocalized with integrin αLβ2 (LFA-1) on T cells, and cross-linking layilin promoted the activated state of this integrin. Accordingly, LAYN deletion resulted in attenuated LFA-1-dependent cellular adhesion. Collectively, our results identify layilin as part of a molecular pathway in which exhausted or "dysfunctional" CD8+ T cells enhance cellular adhesiveness to maintain their cytotoxic potential.
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Affiliation(s)
- Kelly M Mahuron
- Department of Surgery, University of California, San Francisco, San Francisco, CA
| | - Joshua M Moreau
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Devi P Boda
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Mariela L Pauli
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Victoire Gouirand
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Luv Panjabi
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Robby Grewal
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Jacob M Luber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Anubhav N Mathur
- Department of Dermatology, University of California, San Francisco, San Francisco, CA.,T-REX Bio, Burlingame, CA
| | | | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Pooja Mehta
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Margaret M Lowe
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Michael D Alvarado
- Department of Surgery, University of California, San Francisco, San Francisco, CA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Meromit Singer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA.,Department of Immunology, Harvard Medical School, Boston, MA.,Dana-Farber Cancer Institute, Boston, MA
| | - Jim Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | | | - Adil I Daud
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Michael D Rosenblum
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
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27
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Christie JM, Zurbriggen MD. Optogenetics in plants. THE NEW PHYTOLOGIST 2021; 229:3108-3115. [PMID: 33064858 DOI: 10.1111/nph.17008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
The last two decades have witnessed the emergence of optogenetics; a field that has given researchers the ability to use light to control biological processes at high spatiotemporal and quantitative resolutions, in a reversible manner with minimal side-effects. Optogenetics has revolutionized the neurosciences, increased our understanding of cellular signalling and metabolic networks and resulted in variety of applications in biotechnology and biomedicine. However, implementing optogenetics in plants has been less straightforward, given their dependency on light for their life cycle. Here, we highlight some of the widely used technologies in microorganisms and animal systems derived from plant photoreceptor proteins and discuss strategies recently implemented to overcome the challenges for using optogenetics in plants.
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Affiliation(s)
- John M Christie
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Duesseldorf, Duesseldorf, 40225, Germany
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28
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Shaaya M, Fauser J, Karginov AV. Optogenetics: The Art of Illuminating Complex Signaling Pathways. Physiology (Bethesda) 2021; 36:52-60. [PMID: 33325819 DOI: 10.1152/physiol.00022.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dissection of cell signaling requires tools that can mimic spatiotemporal dynamics of individual pathways in living cells. Optogenetic methods enable manipulation of signaling processes with precise timing and local control. In this review, we describe recent optogenetic approaches for regulation of cell signaling, highlight their advantages and limitations, and discuss examples of their application.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois.,University of Illinois Cancer Center, The University of Illinois at Chicago, Chicago, Illinois
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29
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Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
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Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
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30
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Leopold AV, Verkhusha VV. Light control of RTK activity: from technology development to translational research. Chem Sci 2020; 11:10019-10034. [PMID: 33209247 PMCID: PMC7654314 DOI: 10.1039/d0sc03570j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/30/2020] [Indexed: 12/11/2022] Open
Abstract
Inhibition of receptor tyrosine kinases (RTKs) by small molecule inhibitors and monoclonal antibodies is used to treat cancer. Conversely, activation of RTKs with their ligands, including growth factors and insulin, is used to treat diabetes and neurodegeneration. However, conventional therapies that rely on injection of RTK inhibitors or activators do not provide spatiotemporal control over RTK signaling, which results in diminished efficiency and side effects. Recently, a number of optogenetic and optochemical approaches have been developed that allow RTK inhibition or activation in cells and in vivo with light. Light irradiation can control RTK signaling non-invasively, in a dosed manner, with high spatio-temporal precision, and without the side effects of conventional treatments. Here we provide an update on the current state of the art of optogenetic and optochemical RTK technologies and the prospects of their use in translational studies and therapy.
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Affiliation(s)
- Anna V Leopold
- Medicum , Faculty of Medicine , University of Helsinki , Helsinki 00290 , Finland
| | - Vladislav V Verkhusha
- Medicum , Faculty of Medicine , University of Helsinki , Helsinki 00290 , Finland
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center , Albert Einstein College of Medicine , Bronx , NY 10461 , USA .
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31
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Wittmann T, Dema A, van Haren J. Lights, cytoskeleton, action: Optogenetic control of cell dynamics. Curr Opin Cell Biol 2020; 66:1-10. [PMID: 32371345 PMCID: PMC7577957 DOI: 10.1016/j.ceb.2020.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/29/2023]
Abstract
Cell biology is moving from observing molecules to controlling them in real time, a critical step towards a mechanistic understanding of how cells work. Initially developed from light-gated ion channels to control neuron activity, optogenetics now describes any genetically encoded protein system designed to accomplish specific light-mediated tasks. Recent photosensitive switches use many ingenious designs that bring spatial and temporal control within reach for almost any protein or pathway of interest. This next generation optogenetics includes light-controlled protein-protein interactions and shape-shifting photosensors, which in combination with live microscopy enable acute modulation and analysis of dynamic protein functions in living cells. We provide a brief overview of various types of optogenetic switches. We then discuss how diverse approaches have been used to control cytoskeleton dynamics with light through Rho GTPase signaling, microtubule and actin assembly, mitotic spindle positioning and intracellular transport and highlight advantages and limitations of different experimental strategies.
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Affiliation(s)
- Torsten Wittmann
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Alessandro Dema
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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32
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Mukherjee A, Sudrik C, Hu Y, Arha M, Stathos M, Baek J, Schaffer DV, Kane RS. CL6mN: Rationally Designed Optogenetic Photoswitches with Tunable Dissociation Dynamics. ACS Synth Biol 2020; 9:2274-2281. [PMID: 32794731 DOI: 10.1021/acssynbio.0c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of optogenetics uses genetically encoded photoswitches to modulate biological phenomena with high spatiotemporal resolution. We report a set of rationally designed optogenetic photoswitches that use the photolyase homology region of A. thaliana cryptochrome 2 (Cry2PHR) as a building block and exhibit highly efficient and tunable clustering in a blue-light dependent manner. CL6mN (Cry2-mCherry-LRP6c with N mutated PPPAP motifs) proteins were designed by mutating and/or truncating five crucial PPP(S/T)P motifs near the C-terminus of the optogenetic Wnt activator Cry2-mCherry-LRP6c, thus eliminating its Wnt activity. Light-induced CL6mN clusters have significantly greater dissociation half-lives than clusters of wild-type Cry2PHR. Moreover, the dissociation half-lives can be tuned by varying the number of PPPAP motifs, with the half-life increasing as much as 6-fold for a variant with five motifs (CL6m5) relative to Cry2PHR. Finally, we demonstrate the compatibility of CL6mN with previously reported Cry2-based photoswitches by optogenetically activating RhoA in mammalian cells.
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Affiliation(s)
- Abhirup Mukherjee
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chaitanya Sudrik
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yuge Hu
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Manish Arha
- Centre for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mark Stathos
- Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jieung Baek
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ravi S Kane
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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33
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Wong M, Gilmour D. Getting back on track: exploiting canalization to uncover the mechanisms of developmental robustness. Curr Opin Genet Dev 2020; 63:53-60. [DOI: 10.1016/j.gde.2020.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/09/2020] [Indexed: 02/08/2023]
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34
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Kainrath S, Janovjak H. Design and Application of Light-Regulated Receptor Tyrosine Kinases. Methods Mol Biol 2020; 2173:233-246. [PMID: 32651922 DOI: 10.1007/978-1-0716-0755-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware.
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Affiliation(s)
- Stephanie Kainrath
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.,Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Clayton, VIC, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia. .,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Clayton, VIC, Australia.
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35
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Construction of Light-Activated Neurotrophin Receptors Using the Improved Light-Induced Dimerizer (iLID). J Mol Biol 2020; 432:3739-3748. [PMID: 32335036 PMCID: PMC9879133 DOI: 10.1016/j.jmb.2020.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Receptor tyrosine kinases (RTKs) play crucial roles in human health, and their misregulation is implicated in disorders ranging from neurodegenerative diseases to cancers. The highly conserved mechanism of activation of RTKs makes them especially appealing candidates for control via optogenetic dimerization methods. This work offers a strategy for using the improved light-induced dimer (iLID) system with a constructed tandem dimer of its binding partner nano (tdnano) to build light-activatable versions of RTKs. In the absence of light, the iLID-RTK is cytosolic, monomeric, and inactive. Under blue light, the iLID + tdnano system recruits two copies of iLID-RTK to tdnano, dimerizing, and activating the RTK. We demonstrate that iLID opto-iTrkA and opto-iTrkB are capable of reproducing downstream ERK and Akt signaling only in the presence of tdnano. We further show with our opto-iTrkA that the system is compatible with multi-day and population-level activation of TrkA in PC12 cells. By leveraging genetic targeting of tdnano, we achieve RTK activation at a specific subcellular location even with whole-cell illumination, allowing us to confidently probe the impact of context on signaling outcome.
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36
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Ma L, Wang X, Guan Z, Wang L, Wang Y, Zheng L, Gong Z, Shen C, Wang J, Zhang D, Liu Z, Yin P. Structural insights into BIC-mediated inactivation of Arabidopsis cryptochrome 2. Nat Struct Mol Biol 2020; 27:472-479. [PMID: 32398826 DOI: 10.1038/s41594-020-0410-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/09/2020] [Indexed: 02/04/2023]
Abstract
Cryptochromes (CRYs) are blue-light receptors in plants that harbor FAD as a cofactor and regulate various physiological responses. Photoactivated CRYs undergo oligomerization, which increases the binding affinity to downstream signaling partners. Despite decades of research on the activation of CRYs, little is known about how they are inactivated. Binding of blue-light inhibitors of cryptochromes (BICs) to CRY2 suppresses its photoactivation, but the underlying mechanism remains unknown. Here, we report crystal structures of CRY2N (CRY2 PHR domain) and the BIC2-CRY2N complex with resolutions of 2.7 and 2.5 Å, respectively. In the BIC2-CRY2N complex, BIC2 exhibits an extremely extended structure that sinuously winds around CRY2N. In this way, BIC2 not only restrains the transfer of electrons and protons from CRY2 to FAD during photoreduction but also interacts with the CRY2 oligomer to return it to the monomer form. Uncovering the mechanism of CRY2 inactivation lays a solid foundation for the investigation of cryptochrome protein function.
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Affiliation(s)
- Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yidong Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Le Zheng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Zhou Gong
- Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Cuicui Shen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.
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37
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An Optogenetic Method to Study Signal Transduction in Intestinal Stem Cell Homeostasis. J Mol Biol 2020; 432:3159-3176. [DOI: 10.1016/j.jmb.2020.03.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
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38
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Lim CH, Kaur P, Teo E, Lam VYM, Zhu F, Kibat C, Gruber J, Mathuru AS, Tolwinski NS. Application of optogenetic Amyloid-β distinguishes between metabolic and physical damages in neurodegeneration. eLife 2020; 9:52589. [PMID: 32228858 PMCID: PMC7145416 DOI: 10.7554/elife.52589] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
The brains of Alzheimer’s disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-β plaques. These plaques are formed by aggregation of polypeptides that are derived from the Amyloid Precursor Protein (APP). Amyloid-β plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the aetiology of Alzheimer’s disease (AD) is subject to debate as the biological effects of soluble and aggregated Amyloid-β peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-β oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-β peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-β oligomers underlie the pathologies of A. We use Drosophila, C. elegans and D. rerio to show that, although both expression and induced oligomerization of Amyloid-β were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-β oligomerization from Amyloid-β expression alone. The physical damage caused by Amyloid-β oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-β oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression. Alzheimer's disease is a progressive condition that damages the brain over time. The cause is not clear, but a toxic molecule called Amyloid-β peptide seems to play a part. It builds up in the brains of people with Alzheimer's disease, forming hard clumps called plaques. Yet, though the plaques are a hallmark of the disease, experimental treatments designed to break them down do not seem to help. This raises the question – do Amyloid-β plaques actually cause Alzheimer's disease? Answering this question is not easy. One way to study the effect of amyloid plaques is to inject clumps of Amyloid-β peptides into model organisms. This triggers Alzheimer's-like brain damage, but it is not clear why. It remains difficult to tell the difference between the damage caused by the injected Amyloid-β peptides and the damage caused by the solid plaques that they form. For this, researchers need a way to trigger plaque formation directly inside animal brains. This would make it possible to test the effects of plaque-targeting treatments, like the drug lithium. Optogenetics is a technique that uses light to control molecules in living animals. Hsien, Kaur et al. have now used this approach to trigger plaque formation by fusing light-sensitive proteins to Amyloid-β peptides in worms, fruit flies and zebrafish. This meant that the peptides clumped together to form plaques whenever the animals were exposed to blue light. This revealed that, while both the Amyloid-β peptides and the plaques caused damage, the plaques were much more toxic. They damaged cell metabolism and caused tissue loss that resembled late Alzheimer's disease in humans. To find out whether it was possible to test Alzheimer's treatments in these animals, Hsien, Kaur et al. treated them with the drug, lithium. This increased their lifespan, reversing some of the damage caused by the plaques. Alzheimer's disease affects more than 46.8 million people worldwide and is the sixth leading cause of death in the USA. But, despite over 50 years of research, there is no cure. This new plaque-formation technique allows researchers to study the effects of amyloid plaques in living animals, providing a new way to test Alzheimer's treatments. This could be of particular help in studies of experimental drugs that aim to reduce plaque formation.
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Affiliation(s)
- Chu Hsien Lim
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Prameet Kaur
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Emelyne Teo
- Science Division, Yale- NUS College, Singapore, Singapore
| | | | - Fangchen Zhu
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Caroline Kibat
- Science Division, Yale- NUS College, Singapore, Singapore.,Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore.,Department of Physiology, YLL School of Medicine, Singapore, Singapore
| | - Jan Gruber
- Science Division, Yale- NUS College, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Ajay S Mathuru
- Science Division, Yale- NUS College, Singapore, Singapore.,Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore.,Department of Physiology, YLL School of Medicine, Singapore, Singapore
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39
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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40
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Zhou R, Han B, Xia C, Zhuang X. Membrane-associated periodic skeleton is a signaling platform for RTK transactivation in neurons. Science 2019; 365:929-934. [PMID: 31467223 PMCID: PMC7063502 DOI: 10.1126/science.aaw5937] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/02/2019] [Indexed: 01/23/2023]
Abstract
Actin, spectrin, and related molecules form a membrane-associated periodic skeleton (MPS) in neurons. The function of the MPS, however, remains poorly understood. Using super-resolution imaging, we observed that G protein-coupled receptors (GPCRs), cell adhesion molecules (CAMs), receptor tyrosine kinases (RTKs), and related signaling molecules were recruited to the MPS in response to extracellular stimuli, resulting in colocalization of these molecules and RTK transactivation by GPCRs and CAMs, giving rise to extracellular signal-regulated kinase (ERK) signaling. Disruption of the MPS prevented such molecular colocalizations and downstream ERK signaling. ERK signaling in turn caused calpain-dependent MPS degradation, providing a negative feedback that modulates signaling strength. These results reveal an important functional role of the MPS and establish it as a dynamically regulated platform for GPCR- and CAM-mediated RTK signaling.
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Affiliation(s)
- Ruobo Zhou
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Boran Han
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chenglong Xia
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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41
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Dietler J, Stabel R, Möglich A. Pulsatile illumination for photobiology and optogenetics. Methods Enzymol 2019; 624:227-248. [PMID: 31370931 DOI: 10.1016/bs.mie.2019.04.005] [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] [Indexed: 12/13/2022]
Abstract
Living organisms exhibit a wide range of intrinsic adaptive responses to incident light. Likewise, in optogenetics, biological systems are tailored to initiate predetermined cellular processes upon light exposure. As genetically encoded, light-gated actuators, sensory photoreceptors are at the heart of these responses in both the natural and engineered scenarios. Upon light absorption, photoreceptors enter a series of generally rapid photochemical reactions leading to population of the light-adapted signaling state of the receptor. Notably, this state persists for a while before thermally reverting to the original dark-adapted resting state. As a corollary, the inactivation of photosensitive biological circuits upon light withdrawal can exhibit substantial inertia. Intermittent illumination of suitable pulse frequency can hence maintain the photoreceptor in its light-adapted state while greatly reducing overall light dose, thereby mitigating adverse side effects. Moreover, several photoreceptor systems may be actuated sequentially with a single light color if they sufficiently differ in their inactivation kinetics. Here, we detail the construction of programmable illumination devices for the rapid and parallelized testing of biological responses to diverse lighting regimes. As the technology is based on open electronics and readily available, inexpensive components, it can be adopted by most laboratories at moderate expenditure. As we exemplify for two use cases, the programmable devices enable the facile interrogation of diverse illumination paradigms and their application in optogenetics and photobiology.
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Affiliation(s)
- Julia Dietler
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Robert Stabel
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany; Research Center for Bio-Macromolecules, Universität Bayreuth, Bayreuth, Germany; Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany; North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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42
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Wang M, He F, Li H, Yang S, Zhang J, Ghosh P, Wang HH, Nie Z. Near-Infrared Light-Activated DNA-Agonist Nanodevice for Nongenetically and Remotely Controlled Cellular Signaling and Behaviors in Live Animals. NANO LETTERS 2019; 19:2603-2613. [PMID: 30907088 PMCID: PMC6530480 DOI: 10.1021/acs.nanolett.9b00421] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Optogenetics provides promising tools for the precise control of receptor-mediated cell behaviors in a spatiotemporal manner. Yet, most photoreceptors require extensive genetic manipulation and respond only to ultraviolet or visible light, which are suboptimal for in vivo applications because they do not penetrate thick tissues. Here we report a novel near-infrared light-activated DNA agonist (NIR-DA) nanodevice for nongenetic manipulation of cell signaling and phenotype in deep tissues. This nanodevice is prepared by conjugating a preinactivated DNA agonist onto the gold nanorods (AuNRs). Upon NIR light treatment, the DNA agonist is released through the localized surface plasmon resonance (LSPR)-based photothermal effect of AuNRs and becomes active. The active DNA agonist dimerizes the DNA-modified chimeric or native receptor tyrosine kinase (RTK) on cell surfaces and activates downstream signal transduction in live cells. Such NIR-DA activation of RTK signaling enables the control of cytoskeletal remodeling, cell polarization, and directional migration. Furthermore, we demonstrate that the NIR-DA system can be used in vivo to mediate RTK signaling and skeletal muscle satellite cell migration and myogenesis, which are critical cellular behaviors in the process of skeletal muscle regeneration. Thus, the NIR-DA system offers a powerful and versatile platform for exogenous modulation of deep tissues for purposes such as regenerative medicine.
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Affiliation(s)
- Miao Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Fang He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Hao Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jinghui Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Pradipta Ghosh
- Department of Medicine, Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0651, USA
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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43
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Photodimerization systems for regulating protein-protein interactions with light. Curr Opin Struct Biol 2019; 57:1-8. [PMID: 30818200 DOI: 10.1016/j.sbi.2019.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/28/2019] [Indexed: 12/17/2022]
Abstract
Optogenetic dimerizers are modular domains that can be utilized in a variety of versatile ways to modulate cellular biochemistry. Because of their modularity, many applications using these tools can be easily transferred to new targets without extensive engineering. While a number of photodimerizer systems are currently available, the field remains nascent, with new optimizations for existing systems and new approaches to regulating biological function continuing to be introduced at a steady pace.
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44
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Mansouri M, Strittmatter T, Fussenegger M. Light-Controlled Mammalian Cells and Their Therapeutic Applications in Synthetic Biology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800952. [PMID: 30643713 PMCID: PMC6325585 DOI: 10.1002/advs.201800952] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Indexed: 05/12/2023]
Abstract
The ability to remote control the expression of therapeutic genes in mammalian cells in order to treat disease is a central goal of synthetic biology-inspired therapeutic strategies. Furthermore, optogenetics, a combination of light and genetic sciences, provides an unprecedented ability to use light for precise control of various cellular activities with high spatiotemporal resolution. Recent work to combine optogenetics and therapeutic synthetic biology has led to the engineering of light-controllable designer cells, whose behavior can be regulated precisely and noninvasively. This Review focuses mainly on non-neural optogenetic systems, which are often used in synthetic biology, and their applications in genetic programing of mammalian cells. Here, a brief overview of the optogenetic tool kit that is available to build light-sensitive mammalian cells is provided. Then, recently developed strategies for the control of designer cells with specific biological functions are summarized. Recent translational applications of optogenetically engineered cells are also highlighted, ranging from in vitro basic research to in vivo light-controlled gene therapy. Finally, current bottlenecks, possible solutions, and future prospects for optogenetics in synthetic biology are discussed.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
- Faculty of ScienceUniversity of BaselMattenstrasse 26CH‐4058BaselSwitzerland
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45
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Ueda Y, Sato M. Cell membrane dynamics induction using optogenetic tools. Biochem Biophys Res Commun 2018; 506:387-393. [DOI: 10.1016/j.bbrc.2017.11.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/13/2017] [Indexed: 10/25/2022]
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46
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Krishnamurthy VV, Zhang K. Chemical physics in living cells — Using light to visualize and control intracellular signal transduction. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vishnu V. Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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47
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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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48
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Ueda Y, Sato M. Induction of Signal Transduction by Using Non-Channelrhodopsin-Type Optogenetic Tools. Chembiochem 2018; 19:1217-1231. [PMID: 29577530 DOI: 10.1002/cbic.201700635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 12/24/2022]
Abstract
Signal transductions are the basis for all cellular functions. Previous studies investigating signal transductions mainly relied on pharmacological inhibition, RNA interference, and constitutive active/dominant negative protein expression systems. However, such studies do not allow the modulation of protein activity with high spatial and temporal precision in cells, tissues, and organs in animals. Recently, non-channelrhodopsin-type optogenetic tools for regulating signal transduction have emerged. These photoswitches address several disadvantages of previous techniques, and allow us to control a variety of signal transductions such as cell membrane dynamics, calcium signaling, lipid signaling, and apoptosis. In this review we summarize recent advances in the development of such photoswitches and in how these optotools are applied to signaling processes.
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Affiliation(s)
- Yoshibumi Ueda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- AMED-PRIME (Japan), Agency for Medical Research and Development, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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49
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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50
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Weddell JC, Imoukhuede PI. Integrative meta-modeling identifies endocytic vesicles, late endosome and the nucleus as the cellular compartments primarily directing RTK signaling. Integr Biol (Camb) 2018; 9:464-484. [PMID: 28436498 DOI: 10.1039/c7ib00011a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, intracellular receptor signaling has been identified as a key component mediating cell responses for various receptor tyrosine kinases (RTKs). However, the extent each endocytic compartment (endocytic vesicle, early endosome, recycling endosome, late endosome, lysosome and nucleus) contributes to receptor signaling has not been quantified. Furthermore, our understanding of endocytosis and receptor signaling is complicated by cell- or receptor-specific endocytosis mechanisms. Therefore, towards understanding the differential endocytic compartment signaling roles, and identifying how to achieve signal transduction control for RTKs, we delineate how endocytosis regulates RTK signaling. We achieve this via a meta-analysis across eight RTKs, integrating computational modeling with experimentally derived cell (compartment volume, trafficking kinetics and pH) and ligand-receptor (ligand/receptor concentration and interaction kinetics) physiology. Our simulations predict the abundance of signaling from eight RTKs, identifying the following hierarchy in RTK signaling: PDGFRβ > IGFR1 > EGFR > PDGFRα > VEGFR1 > VEGFR2 > Tie2 > FGFR1. We find that endocytic vesicles are the primary cell signaling compartment; over 43% of total receptor signaling occurs within the endocytic vesicle compartment for these eight RTKs. Mechanistically, we found that high RTK signaling within endocytic vesicles may be attributed to their low volume (5.3 × 10-19 L) which facilitates an enriched ligand concentration (3.2 μM per ligand molecule within the endocytic vesicle). Under the analyzed physiological conditions, we identified extracellular ligand concentration as the most sensitive parameter to change; hence the most significant one to modify when regulating absolute compartment signaling. We also found that the late endosome and nucleus compartments are important contributors to receptor signaling, where 26% and 18%, respectively, of average receptor signaling occurs across the eight RTKs. Conversely, we found very low membrane-based receptor signaling, exhibiting <1% of the total receptor signaling for these eight RTKs. Moreover, we found that nuclear translocation, mechanistically, requires late endosomal transport; when we blocked receptor trafficking from late endosomes to the nucleus we found a 57% reduction in nuclear translocation. In summary, our research has elucidated the significance of endocytic vesicles, late endosomes and the nucleus in RTK signal propagation.
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Affiliation(s)
- Jared C Weddell
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 W Springfield Ave., 3233 Digital Computer Laboratory, Urbana, IL 61801, USA.
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