1
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Aguida B, Babo J, Baouz S, Jourdan N, Procopio M, El-Esawi MA, Engle D, Mills S, Wenkel S, Huck A, Berg-Sørensen K, Kampranis SC, Link J, Ahmad M. 'Seeing' the electromagnetic spectrum: spotlight on the cryptochrome photocycle. FRONTIERS IN PLANT SCIENCE 2024; 15:1340304. [PMID: 38495372 PMCID: PMC10940379 DOI: 10.3389/fpls.2024.1340304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/12/2024] [Indexed: 03/19/2024]
Abstract
Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or 'lit' state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or 'resting' state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of 'magneto-genetics' for future applications in synthetic biology and medicine.
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Affiliation(s)
- Blanche Aguida
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Jonathan Babo
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Soria Baouz
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Nathalie Jourdan
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Maria Procopio
- Department of Biophysics, Faculty of Arts and Sciences, Johns Hopkins University, Baltimore, MD, United States
| | | | - Dorothy Engle
- Biology Department, Xavier University, Cincinnati, OH, United States
| | - Stephen Mills
- Chemistry Department, Xavier University, Cincinnati, OH, United States
| | - Stephan Wenkel
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Alexander Huck
- DTU Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Sotirios C. Kampranis
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Justin Link
- Physics and Engineering Department, Cincinnati, OH, United States
| | - Margaret Ahmad
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
- Biology Department, Xavier University, Cincinnati, OH, United States
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2
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Harmer ZP, McClean MN. High-Throughput Optogenetics Experiments in Yeast Using the Automated Platform Lustro. J Vis Exp 2023:10.3791/65686. [PMID: 37590537 PMCID: PMC11085938 DOI: 10.3791/65686] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
Optogenetics offers precise control over cellular behavior by utilizing genetically encoded light-sensitive proteins. However, optimizing these systems to achieve the desired functionality often requires multiple design-build-test cycles, which can be time-consuming and labor-intensive. To address this challenge, we have developed Lustro, a platform that combines light stimulation with laboratory automation, enabling efficient high-throughput screening and characterization of optogenetic systems. Lustro utilizes an automation workstation equipped with an illumination device, a shaking device, and a plate reader. By employing a robotic arm, Lustro automates the movement of a microwell plate between these devices, allowing for the stimulation of optogenetic strains and the measurement of their response. This protocol provides a step-by-step guide on using Lustro to characterize optogenetic systems for gene expression control in the budding yeast Saccharomyces cerevisiae. The protocol covers the setup of Lustro's components, including the integration of the illumination device with the automation workstation. It also provides detailed instructions for programming the illumination device, plate reader, and robot, ensuring smooth operation and data acquisition throughout the experimental process.
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Affiliation(s)
- Zachary P Harmer
- Department of Biomedical Engineering, University of Wisconsin-Madison
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health;
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3
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Harmer Z, McClean MN. Lustro: High-Throughput Optogenetic Experiments Enabled by Automation and a Yeast Optogenetic Toolkit. ACS Synth Biol 2023; 12:1943-1951. [PMID: 37434272 PMCID: PMC10368012 DOI: 10.1021/acssynbio.3c00215] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 07/13/2023]
Abstract
Optogenetic systems use genetically encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light; however, these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae. We expand the yeast optogenetic toolkit to include variants of the cryptochromes and enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to the high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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Affiliation(s)
- Zachary
P. Harmer
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Megan N. McClean
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- University
of Wisconsin Carbone Cancer Center, University
of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States
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4
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Lemma LM, Varghese M, Ross TD, Thomson M, Baskaran A, Dogic Z. Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids. PNAS NEXUS 2023; 2:pgad130. [PMID: 37168671 PMCID: PMC10165807 DOI: 10.1093/pnasnexus/pgad130] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
- Department of Physics, University of California, Santa Barbara, 93106 CA, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
| | - Tyler D Ross
- Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E California Blvd. Pasadena, 91125 CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, 91125 CA, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
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5
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Gao TT, Oh T, Mehta K, Huang YA, Camp T, Fan H, Han JW, Barnes CM, Zhang K. The clinical potential of optogenetic interrogation of pathogenesis. Clin Transl Med 2023; 13:e1243. [PMID: 37132114 PMCID: PMC10154842 DOI: 10.1002/ctm2.1243] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Opsin-based optogenetics has emerged as a powerful biomedical tool using light to control protein conformation. Such capacity has been initially demonstrated to control ion flow across the cell membrane, enabling precise control of action potential in excitable cells such as neurons or muscle cells. Further advancement in optogenetics incorporates a greater variety of photoactivatable proteins and results in flexible control of biological processes, such as gene expression and signal transduction, with commonly employed light sources such as LEDs or lasers in optical microscopy. Blessed by the precise genetic targeting specificity and superior spatiotemporal resolution, optogenetics offers new biological insights into physiological and pathological mechanisms underlying health and diseases. Recently, its clinical potential has started to be capitalized, particularly for blindness treatment, due to the convenient light delivery into the eye. AIMS AND METHODS This work summarizes the progress of current clinical trials and provides a brief overview of basic structures and photophysics of commonly used photoactivable proteins. We highlight recent achievements such as optogenetic control of the chimeric antigen receptor, CRISPR-Cas system, gene expression, and organelle dynamics. We discuss conceptual innovation and technical challenges faced by current optogenetic research. CONCLUSION In doing so, we provide a framework that showcases ever-growing applications of optogenetics in biomedical research and may inform novel precise medicine strategies based on this enabling technology.
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Affiliation(s)
- Tianyu Terry Gao
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Teak‐Jung Oh
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Kritika Mehta
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Yu‐En Andrew Huang
- University of Illinois at Urbana‐ChampaignCenter for Biophysics and Quantitative BiologyUrbanaIllinoisUSA
| | - Tyler Camp
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Huaxun Fan
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Jeong Won Han
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Collin Michael Barnes
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Kai Zhang
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
- University of Illinois at Urbana‐ChampaignCenter for Biophysics and Quantitative BiologyUrbanaIllinoisUSA
- Cancer Center at IllinoisUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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6
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Harmer ZP, McClean MN. Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536078. [PMID: 37066312 PMCID: PMC10104134 DOI: 10.1101/2023.04.07.536078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Optogenetic systems use genetically-encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light, however these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae . We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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7
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Di Iorio D, Bergmann J, Higashi SL, Hoffmann A, Wegner SV. A disordered tether to iLID improves photoswitchable protein patterning on model membranes. Chem Commun (Camb) 2023; 59:4380-4383. [PMID: 36946614 DOI: 10.1039/d3cc00709j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Reversible protein patterning on model membranes is important to reproduce spatiotemporal protein dynamics in vitro. An engineered version of iLID, disiLID, with a disordered domain as a membrane tether improves the recruitment of Nano under blue light and the reversibility in the dark, which enables protein patterning on membranes with higher spatiotemporal precision.
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Affiliation(s)
- Daniele Di Iorio
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Johanna Bergmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Sayuri L Higashi
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Arne Hoffmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
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8
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Jang J, Tang K, Youn J, McDonald S, Beyer HM, Zurbriggen MD, Uppalapati M, Woolley GA. Engineering of bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL)s. Nat Methods 2023; 20:432-441. [PMID: 36823330 DOI: 10.1038/s41592-023-01764-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 12/21/2022] [Indexed: 02/25/2023]
Abstract
Optogenetic tools for controlling protein-protein interactions (PPIs) have been developed from a small number of photosensory modules that respond to a limited selection of wavelengths. Cyanobacteriochrome (CBCR) GAF domain variants respond to an unmatched array of colors; however, their natural molecular mechanisms of action cannot easily be exploited for optogenetic control of PPIs. Here we developed bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL)s by engineering synthetic light-dependent interactors for a red/green GAF domain. The systematic approach enables the future engineering of the broad chromatic palette of CBCRs for optogenetics use. BICYCLs are among the smallest optogenetic tools for controlling PPIs and enable either green-ON/red-OFF (BICYCL-Red) or red-ON/green-OFF (BICYCL-Green) control with up to 800-fold state selectivity. The access to green wavelengths creates new opportunities for multiplexing with existing tools. We demonstrate the utility of BICYCLs for controlling protein subcellular localization and transcriptional processes in mammalian cells and for multiplexing with existing blue-light tools.
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Affiliation(s)
- Jaewan Jang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kun Tang
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jeffrey Youn
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany. .,CEPLAS - Cluster of Excellence on Plant Science, Düsseldorf, Germany.
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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9
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Nagasaki SC, Fukuda TD, Yamada M, Suzuki YIII, Kakutani R, Guy AT, Imayoshi I. Enhancement of Vivid-based photo-activatable Gal4 transcription factor in mammalian cells. Cell Struct Funct 2023; 48:31-47. [PMID: 36529516 PMCID: PMC10721950 DOI: 10.1247/csf.22074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The Gal4/UAS system is a versatile tool to manipulate exogenous gene expression of cells spatially and temporally in many model organisms. Many variations of light-controllable Gal4/UAS system are now available, following the development of photo-activatable (PA) molecular switches and integration of these tools. However, many PA-Gal4 transcription factors have undesired background transcription activities even in dark conditions, and this severely attenuates reliable light-controlled gene expression. Therefore, it is important to develop reliable PA-Gal4 transcription factors with robust light-induced gene expression and limited background activity. By optimization of synthetic PA-Gal4 transcription factors, we have validated configurations of Gal4 DNA biding domain, transcription activation domain and blue light-dependent dimer formation molecule Vivid (VVD), and applied types of transcription activation domains to develop a new PA-Gal4 transcription factor we have named eGAV (enhanced Gal4-VVD transcription factor). Background activity of eGAV in dark conditions was significantly lower than that of hGAVPO, a commonly used PA-Gal4 transcription factor, and maximum light-induced gene expression levels were also improved. Light-controlled gene expression was verified in cultured HEK293T cells with plasmid-transient transfections, and in mouse EpH4 cells with lentivirus vector-mediated transduction. Furthermore, light-controlled eGAV-mediated transcription was confirmed in transfected neural stem cells and progenitors in developing and adult mouse brain and chick spinal cord, and in adult mouse hepatocytes, demonstrating that eGAV can be applied to a wide range of experimental systems and model organisms.Key words: optogenetics, Gal4/UAS system, transcription, gene expression, Vivid.
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Affiliation(s)
- Shinji C. Nagasaki
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori D. Fukuda
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Mayumi Yamada
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Cell Biology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yusuke III Suzuki
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ryo Kakutani
- Laboratory of Cell Biology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Adam T. Guy
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Science Communication, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Itaru Imayoshi
- Laboratory of Brain Development and Regeneration, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Deconstruction of Stem Cells, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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10
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Crellin HA, Buckley CE. Using Optogenetics to Investigate the Shared Mechanisms of Apical-Basal Polarity and Mitosis. Cells Tissues Organs 2023; 213:161-180. [PMID: 36599311 DOI: 10.1159/000528796] [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: 07/25/2022] [Accepted: 12/18/2022] [Indexed: 01/05/2023] Open
Abstract
The initiation of apical-basal (AB) polarity and the process of mitotic cell division are both characterised by the generation of specialised plasma membrane and cortical domains. These are generated using shared mechanisms, such as asymmetric protein accumulation, Rho GTPase signalling, cytoskeletal reorganisation, vesicle trafficking, and asymmetric phosphoinositide distribution. In epithelial tissue, the coordination of AB polarity and mitosis in space and time is important both during initial epithelial development and to maintain tissue integrity and ensure appropriate cell differentiation at later stages. Whilst significant progress has been made in understanding the mechanisms underlying cell division and AB polarity, it has so far been challenging to fully unpick the complex interrelationship between polarity, signalling, morphogenesis, and cell division. However, the recent emergence of optogenetic protein localisation techniques is now allowing researchers to reversibly control protein activation, localisation, and signalling with high spatiotemporal resolution. This has the potential to revolutionise our understanding of how subcellular processes such as AB polarity are integrated with cell behaviours such as mitosis and how these processes impact whole tissue morphogenesis. So far, these techniques have been used to investigate processes such as cleavage furrow ingression, mitotic spindle positioning, and in vivo epithelial morphogenesis. This review describes some of the key shared mechanisms of cell division and AB polarity establishment, how they are coordinated during development and how the advance of optogenetic techniques is furthering this research field.
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Affiliation(s)
- Helena A Crellin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Clare E Buckley
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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11
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Ueda Y, Miura Y, Tomishige N, Sugimoto N, Murase M, Kawamura G, Sasaki N, Ishiwata T, Ozawa T. Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation. Cell Chem Biol 2022; 29:1576-1587.e5. [PMID: 36288730 DOI: 10.1016/j.chembiol.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/26/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Hyperactivation of phosphatidylinositol 3-kinase (PI3K) signaling is a prominent feature in cancer cells. However, the mechanism underlying malignant behaviors in the state remains unknown. Here, we describe a mechanism of cancer drug resistance through the protein synthesis pathway, downstream of PI3K signaling. An optogenetic tool (named PPAP2) controlling PI3K signaling was developed. Melanoma cells stably expressing PPAP2 (A375-PPAP2) acquired resistance to a cancer drug in the hyperactivation state. Proteome analyses revealed that expression of the antiapoptotic factor tumor necrosis factor alpha-induced protein 8 (TNFAIP8) was upregulated. TNFAIP8 upregulation was mediated by protein translation from preexisting mRNA. These results suggest that cancer cells escape death via upregulation of TNFAIP8 expression from preexisting mRNA even though alkylating cancer drugs damage DNA.
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Affiliation(s)
- Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan.
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | | | - Naotoshi Sugimoto
- Department of Physiology, Graduate School of Medical Science, Kanazawa University, Ishikawa, Japan
| | - Megumi Murase
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
| | - Genki Kawamura
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
| | - Norihiko Sasaki
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Toshiyuki Ishiwata
- Division of Aging and Carcinogenesis, Research Team for Geriatric Pathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan.
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12
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Kuznetsov IA, Berlew EE, Glantz ST, Hannanta-Anan P, Chow BY. Computational framework for single-cell spatiotemporal dynamics of optogenetic membrane recruitment. CELL REPORTS METHODS 2022; 2:100245. [PMID: 35880018 PMCID: PMC9308134 DOI: 10.1016/j.crmeth.2022.100245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 10/27/2022]
Abstract
We describe a modular computational framework for analyzing cell-wide spatiotemporal signaling dynamics in single-cell microscopy experiments that accounts for the experiment-specific geometric and diffractive complexities that arise from heterogeneous cell morphologies and optical instrumentation. Inputs are unique cell geometries and protein concentrations derived from confocal stacks and spatiotemporally varying environmental stimuli. After simulating the system with a model of choice, the output is convolved with the microscope point-spread function for direct comparison with the observable image. We experimentally validate this approach in single cells with BcLOV4, an optogenetic membrane recruitment system for versatile control over cell signaling, using a three-dimensional non-linear finite element model with all parameters experimentally derived. The simulations recapitulate observed subcellular and cell-to-cell variability in BcLOV4 signaling, allowing for inter-experimental differences of cellular and instrumentation origins to be elucidated and resolved for improved interpretive robustness. This single-cell approach will enhance optogenetics and spatiotemporally resolved signaling studies.
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Affiliation(s)
- Ivan A. Kuznetsov
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin E. Berlew
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Spencer T. Glantz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pimkhuan Hannanta-Anan
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Brian Y. Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Su Y, Chen X, Wang H, Sun L, Xu Y, Li D. Enhancing cell membrane phase separation for inhibiting cancer metastasis with a stimuli-responsive DNA nanodevice. Chem Sci 2022; 13:6303-6308. [PMID: 35733880 PMCID: PMC9159096 DOI: 10.1039/d2sc00371f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/26/2022] [Indexed: 12/19/2022] Open
Abstract
Phase separation in cell membranes promotes the assembly of transmembrane receptors to initiate signal transduction in response to environmental cues. Many cellular behaviors are manipulated by promoting membrane phase separation through binding to multivalent extracellular ligands. However, available extracellular molecule tools that enable manipulating the clustering of transmembrane receptors in a controllable manner are rare. In the present study, we report a DNA nanodevice that enhances membrane phase separation through the clustering of dynamic lipid rafts. This DNA nanodevice is anchored in the lipid raft region of the cell membrane and initiated by ATP. In a tumor microenvironment, this device could be activated to form a long DNA duplex on the cell membrane, which not only enhances membrane phase separation, but also blocks the interaction between the transmembrane surface adhesion receptor and extracellular matrix, leading to reduced migration. We demonstrate that the ATP-activated DNA nanodevice could inhibit cancer cell migration both in vitro and in vivo. The concept of using DNA to regulate membrane phase separation provides new possibilities for manipulating versatile cell functions through rational design of functional DNA structures.
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Affiliation(s)
- Yingying Su
- School of Chemistry and Molecular Engineering, East China Normal University 200241 Shanghai China
| | - Xiaoqing Chen
- School of Chemistry and Molecular Engineering, East China Normal University 200241 Shanghai China
| | - Hui Wang
- School of Chemistry and Molecular Engineering, East China Normal University 200241 Shanghai China
| | - Lele Sun
- School of Life Science, Shanghai University Shanghai 200444 China
| | - Ying Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine Shanghai 200025 China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University 200241 Shanghai China
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14
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Chen W, Li C, Liang W, Li Y, Zou Z, Xie Y, Liao Y, Yu L, Lin Q, Huang M, Li Z, Zhu X. The Roles of Optogenetics and Technology in Neurobiology: A Review. Front Aging Neurosci 2022; 14:867863. [PMID: 35517048 PMCID: PMC9063564 DOI: 10.3389/fnagi.2022.867863] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 01/07/2023] Open
Abstract
Optogenetic is a technique that combines optics and genetics to control specific neurons. This technique usually uses adenoviruses that encode photosensitive protein. The adenovirus may concentrate in a specific neural region. By shining light on the target nerve region, the photosensitive protein encoded by the adenovirus is controlled. Photosensitive proteins controlled by light can selectively allow ions inside and outside the cell membrane to pass through, resulting in inhibition or activation effects. Due to the high precision and minimally invasive, optogenetics has achieved good results in many fields, especially in the field of neuron functions and neural circuits. Significant advances have also been made in the study of many clinical diseases. This review focuses on the research of optogenetics in the field of neurobiology. These include how to use optogenetics to control nerve cells, study neural circuits, and treat diseases by changing the state of neurons. We hoped that this review will give a comprehensive understanding of the progress of optogenetics in the field of neurobiology.
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Affiliation(s)
- Wenqing Chen
- Department of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
| | - Wanmin Liang
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Yunqi Li
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Zhuoheng Zou
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Yunxuan Xie
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Yangzeng Liao
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Lin Yu
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Qianyi Lin
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Meiying Huang
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
| | - Zesong Li
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Key Laboratory of Genitourinary Tumor, Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
| | - Xiao Zhu
- Department of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Zhu’s Team, Guangdong Medical University, Zhanjiang, China
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15
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Hongdusit A, Liechty ET, Fox JM. Analysis of Three Architectures for Controlling PTP1B with Light. ACS Synth Biol 2022; 11:61-68. [PMID: 34898189 DOI: 10.1021/acssynbio.1c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Photosensory domains are powerful tools for placing proteins under optical control, but their integration into light-sensitive chimeras is often challenging. Many designs require structural iterations, and direct comparisons of alternative approaches are rare. This study uses protein tyrosine phosphatase 1B (PTP1B), an influential regulatory enzyme, to compare three architectures for controlling PTPs with light: a protein fusion, an insertion chimera, and a split construct. All three designs permitted optical control of PTP1B activity in vitro (i.e., kinetic assays of purified enzyme) and in mammalian cells; photoresponses measured under both conditions, while different in magnitude, were linearly correlated. The fusion- and insertion-based architectures exhibited the highest dynamic range and maintained native localization patterns in mammalian cells. A single insertion architecture enabled optical control of both PTP1B and TCPTP, but not SHP2, where the analogous chimera was active but not photoswitchable. Findings suggest that PTPs are highly tolerant of domain insertions and support the use of in vitro screens to evaluate different optogenetic designs.
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Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Evan T. Liechty
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
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16
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Directed evolution approaches for optogenetic tool development. Biochem Soc Trans 2021; 49:2737-2748. [PMID: 34783342 DOI: 10.1042/bst20210700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022]
Abstract
Photoswitchable proteins enable specific molecular events occurring in complex biological settings to be probed in a rapid and reversible fashion. Recent progress in the development of photoswitchable proteins as components of optogenetic tools has been greatly facilitated by directed evolution approaches in vitro, in bacteria, or in yeast. We review these developments and suggest future directions for this rapidly advancing field.
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17
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Ryan A, Hammond GRV, Deiters A. Optical Control of Phosphoinositide Binding: Rapid Activation of Subcellular Protein Translocation and Cell Signaling. ACS Synth Biol 2021; 10:2886-2895. [PMID: 34748306 DOI: 10.1021/acssynbio.1c00328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells utilize protein translocation to specific compartments for spatial and temporal regulation of protein activity, in particular in the context of signaling processes. Protein recognition and binding to various subcellular membranes is mediated by a network of phosphatidylinositol phosphate (PIP) species bearing one or multiple phosphate moieties on the polar inositol head. Here, we report a new, highly efficient method for optical control of protein localization through the site-specific incorporation of a photocaged amino acid for steric and electrostatic disruption of inositol phosphate recognition and binding. We demonstrate general applicability of the approach by photocaging two unrelated proteins, sorting nexin 3 (SNX3) and the pleckstrin homology (PH) domain of phospholipase C delta 1 (PLCδ1), with two distinct PIP binding domains and distinct subcellular localizations. We have established the applicability of this methodology through its application to Son of Sevenless 2 (SOS2), a signaling protein involved in the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) cascade. Upon fusing the photocaged plasma membrane-targeted construct PH-enhanced green fluorescent protein (EGFP), to the catalytic domain of SOS2, we demonstrated light-induced membrane localization of the construct resulting in fast and extensive activation of the ERK signaling pathway in NIH 3T3 cells. This approach can be readily extended to other proteins, with minimal protein engineering, and provides a method for acute optical control of protein translocation with rapid and complete activation.
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Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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18
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Bermudez JG, Deiters A, Good MC. Patterning Microtubule Network Organization Reshapes Cell-Like Compartments. ACS Synth Biol 2021; 10:1338-1350. [PMID: 33988978 DOI: 10.1021/acssynbio.0c00575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.
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Affiliation(s)
- Jessica G. Bermudez
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander Deiters
- Chemistry Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew C. Good
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Cell and Developmental Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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19
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Dietler J, Schubert R, Krafft TGA, Meiler S, Kainrath S, Richter F, Schweimer K, Weyand M, Janovjak H, Möglich A. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J Mol Biol 2021; 433:167107. [PMID: 34146595 DOI: 10.1016/j.jmb.2021.167107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Sensory photoreceptors enable organisms to adjust their physiology, behavior, and development in response to light, generally with spatiotemporal acuity and reversibility. These traits underlie the use of photoreceptors as genetically encoded actuators to alter by light the state and properties of heterologous organisms. Subsumed as optogenetics, pertinent approaches enable regulating diverse cellular processes, not least gene expression. Here, we controlled the widely used Tet repressor by coupling to light-oxygen-voltage (LOV) modules that either homodimerize or dissociate under blue light. Repression could thus be elevated or relieved, and consequently protein expression was modulated by light. Strikingly, the homodimeric RsLOV module from Rhodobacter sphaeroides not only dissociated under light but intrinsically reacted to temperature. The limited light responses of wild-type RsLOV at 37 °C were enhanced in two variants that exhibited closely similar photochemistry and structure. One variant improved the weak homodimerization affinity of 40 µM by two-fold and thus also bestowed light sensitivity on a receptor tyrosine kinase. Certain photoreceptors, exemplified by RsLOV, can evidently moonlight as temperature sensors which immediately bears on their application in optogenetics and biotechnology. Properly accounted for, the temperature sensitivity can be leveraged for the construction of signal-responsive cellular circuits.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Roman Schubert
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Tobias G A Krafft
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Simone Meiler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Stephanie Kainrath
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Florian Richter
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany; Bayreuth Center for Biochemistry & Molecular Biology, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany.
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20
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Seong J, Lin MZ. Optobiochemistry: Genetically Encoded Control of Protein Activity by Light. Annu Rev Biochem 2021; 90:475-501. [PMID: 33781076 DOI: 10.1146/annurev-biochem-072420-112431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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21
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Dansen TB, De Henau S. Modulating organelle distribution using light-inducible heterodimerization in C. elegans. STAR Protoc 2021; 2:100273. [PMID: 33490987 PMCID: PMC7811173 DOI: 10.1016/j.xpro.2020.100273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The relative positioning of organelles underlies fundamental cellular processes, including signaling, polarization, and cellular growth. Here, we describe the usage of a light-dependent heterodimerization system, LOVpep-ePDZ, to alter organelle positioning locally and reversibly in order to study the functional consequences of organelle positioning. The protocol gives details on how to accomplish expression of fusion proteins encoding this system, describes the imaging parameters to achieve subcellular activation in C. elegans, and may be adapted for use in other model systems. For complete details on the use and execution of this protocol, please refer to De Henau et al. (2020).
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Affiliation(s)
- Tobias B. Dansen
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Sasha De Henau
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
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22
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Abstract
Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY's photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.
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23
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Paez Segala MG, Looger LL. Optogenetics. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00092-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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24
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Renzl C, Kakoti A, Mayer G. Aptamer‐Mediated Reversible Transactivation of Gene Expression by Light. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Renzl
- LIMES University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Ankana Kakoti
- LIMES University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Günter Mayer
- LIMES University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
- Center of Aptamer Research & Development University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
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25
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Renzl C, Kakoti A, Mayer G. Aptamer-Mediated Reversible Transactivation of Gene Expression by Light. Angew Chem Int Ed Engl 2020; 59:22414-22418. [PMID: 32865316 PMCID: PMC7756287 DOI: 10.1002/anie.202009240] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/27/2020] [Indexed: 12/11/2022]
Abstract
The investigation and manipulation of cellular processes with subcellular resolution requires non-invasive tools with spatiotemporal precision and reversibility. Building on the interaction of the photoreceptor PAL with an RNA aptamer, we describe a variation of the CRISPR/dCAS9 system for light-controlled activation of gene expression. This platform significantly reduces the coding space required for genetic manipulation and provides a strong on-switch with almost no residual activity in the dark. It adds to the current set of modular building blocks for synthetic biological circuit design and is broadly applicable.
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Affiliation(s)
- Christian Renzl
- LIMESUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Ankana Kakoti
- LIMESUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Günter Mayer
- LIMESUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
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26
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Figueroa D, Rojas V, Romero A, Larrondo LF, Salinas F. The rise and shine of yeast optogenetics. Yeast 2020; 38:131-146. [PMID: 33119964 DOI: 10.1002/yea.3529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.
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Affiliation(s)
- David Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Vicente Rojas
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andres Romero
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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27
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Ma L, Guan Z, Wang Q, Yan X, Wang J, Wang Z, Cao J, Zhang D, Gong X, Yin P. Structural insights into the photoactivation of Arabidopsis CRY2. NATURE PLANTS 2020; 6:1432-1438. [PMID: 33199893 DOI: 10.1038/s41477-020-00800-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. Here, we report the cryogenic electron microscopy structure of a blue-light-activated CRY2 tetramer at a resolution of 3.1 Å, which shows how the CRY2 tetramer assembles. Our study provides insights into blue-light-mediated activation of CRY2 and a theoretical basis for developing regulators of CRYs for optogenetic manipulation.
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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
- Kobilka Institute of Innovative Drug Discovery, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xuhui Yan
- 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
| | - Zhizheng Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P. R. China
| | - Jianbo Cao
- Public Laboratory of Electron Microscopy, 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
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 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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28
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Corrigendum to "Syntaxin Clustering and Optogenetic Control for Synaptic Membrane Fusion" [J. Mol. Biol. 432 (2020) 4773-4782]. J Mol Biol 2020; 432:6228-6229. [PMID: 33153726 DOI: 10.1016/j.jmb.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Benedetti L, Marvin JS, Falahati H, Guillén-Samander A, Looger LL, De Camilli P. Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells. eLife 2020; 9:e63230. [PMID: 33174843 PMCID: PMC7735757 DOI: 10.7554/elife.63230] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/10/2020] [Indexed: 12/28/2022] Open
Abstract
Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from the Neurospora crassa photoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28°C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these 'enhanced' Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.
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Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Jonathan S Marvin
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Hanieh Falahati
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Andres Guillén-Samander
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Pietro De Camilli
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
- Kavli Institute for Neuroscience, Yale University School of MedicineNew HavenUnited States
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of MedicineNew HavenUnited States
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30
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Yamada M, Nagasaki SC, Suzuki Y, Hirano Y, Imayoshi I. Optimization of Light-Inducible Gal4/UAS Gene Expression System in Mammalian Cells. iScience 2020; 23:101506. [PMID: 32919371 PMCID: PMC7491154 DOI: 10.1016/j.isci.2020.101506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/06/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Light-inducible gene expression systems represent powerful methods for studying the functional roles of dynamic gene expression. Here, we developed an optimized light-inducible Gal4/UAS gene expression system for mammalian cells. We designed photoactivatable (PA)-Gal4 transcriptional activators based on the concept of split transcription factors, in which light-dependent interactions between Cry2-CIB1 PA-protein interaction modules can reconstitute a split Gal4 DNA-binding domain and p65 transcription activation domain. We developed a set of PA-Gal4 transcriptional activators (PA-Gal4cc), which differ in terms of induced gene expression levels following pulsed or prolonged light exposure, and which have different activation/deactivation kinetics. These systems offer optogenetic tools for the precise manipulation of gene expression at fine spatiotemporal resolution in mammalian cells.
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Affiliation(s)
- Mayumi Yamada
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- World Premier International Research Initiative–Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shinji C. Nagasaki
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Yusuke Suzuki
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yukinori Hirano
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
| | - Itaru Imayoshi
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- World Premier International Research Initiative–Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama 332-0012, Japan
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31
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Li M, Oh TJ, Fan H, Diao J, Zhang K. Syntaxin Clustering and Optogenetic Control for Synaptic Membrane Fusion. J Mol Biol 2020; 432:4773-4782. [PMID: 32682743 DOI: 10.1016/j.jmb.2020.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/05/2020] [Accepted: 07/12/2020] [Indexed: 01/01/2023]
Abstract
Membrane fusion during synaptic transmission mediates the trafficking of chemical signals and neuronal communication. The fast kinetics of membrane fusion on the order of millisecond is precisely regulated by the assembly of SNAREs and accessory proteins. It is believed that the formation of the SNARE complex is a key step during membrane fusion. Little is known, however, about the molecular machinery that mediates the formation of a large pre-fusion complex, including multiple SNAREs and accessory proteins. Syntaxin, a transmembrane protein on the plasma membrane, has been observed to undergo oligomerization to form clusters. Whether this clustering plays a critical role in membrane fusion is poorly understood in live cells. Optogenetics is an emerging biotechnology armed with the capacity to precisely modulate protein-protein interaction in time and space. Here, we propose an experimental scheme that combines optogenetics with single-vesicle membrane fusion, aiming to gain a better understanding of the molecular mechanism by which the syntaxin cluster regulates membrane fusion. We envision that newly developed optogenetic tools could facilitate the mechanistic understanding of synaptic transmission in live cells and animals.
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Affiliation(s)
- Miaoling Li
- Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Teak-Jung Oh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huaxun Fan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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32
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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: 39] [Impact Index Per Article: 9.8] [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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33
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Woloschuk RM, Reed PMM, McDonald S, Uppalapati M, Woolley GA. Yeast Two-Hybrid Screening of Photoswitchable Protein-Protein Interaction Libraries. J Mol Biol 2020; 432:3113-3126. [PMID: 32198111 DOI: 10.1016/j.jmb.2020.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023]
Abstract
Although widely used in the detection and characterization of protein-protein interactions, Y2H screening has been under-used for the engineering of new optogenetic tools or the improvement of existing tools. Here we explore the feasibility of using Y2H selection and screening to evaluate libraries of photoswitchable protein-protein interactions. We targeted the interaction between circularly permuted photoactive yellow protein (cPYP) and its binding partner binder of PYP dark-state (BoPD) by mutating a set of four surface residues of cPYP that contribute to the binding interface. A library of ~10,000 variants was expressed in yeast together with BoPD in a Y2H format. An initial selection for the cPYP/BoPD interaction was performed using a range of concentrations of the cPYP chromophore. As expected, the majority (>90% of cPYP variants) no longer bound to BoPD. Replica plating was then used to evaluate the photoswitchability of the surviving clones. Photoswitchable cPYP variants with BoPD affinities equal to, or higher than, native cPYP were recovered in addition to variants with altered photocycles and binders that interacted with BoPD as apo-proteins. Y2H results reflected protein-protein interaction affinity, expression, photoswitchability, and chromophore uptake, and correlated well with results obtained both in vitro and in mammalian cells. Thus, by systematic variation of selection parameters, Y2H screens can be effectively used to generate new optogenetic tools for controlling protein-protein interactions for use in diverse settings.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - P Maximilian M Reed
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6.
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34
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Light-mediated control of Gene expression in mammalian cells. Neurosci Res 2020; 152:66-77. [DOI: 10.1016/j.neures.2019.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
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35
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Berlew EE, Kuznetsov IA, Yamada K, Bugaj LJ, Chow BY. Optogenetic Rac1 engineered from membrane lipid-binding RGS-LOV for inducible lamellipodia formation. Photochem Photobiol Sci 2020; 19:353-361. [PMID: 32048687 PMCID: PMC7141788 DOI: 10.1039/c9pp00434c] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/03/2020] [Indexed: 01/01/2023]
Abstract
We report the construction of a single-component optogenetic Rac1 (opto-Rac1) to control actin polymerization by dynamic membrane recruitment. Opto-Rac1 is a fusion of wildtype human Rac1 small GTPase to the C-terminal region of BcLOV4, a LOV (light-oxygen-voltage) photoreceptor that rapidly binds the plasma membrane upon blue-light activation via a direct electrostatic interaction with anionic membrane phospholipids. Translocation of the fused wildtype Rac1 effector permits its activation by GEFs (guanine nucleotide exchange factors) and consequent actin polymerization and lamellipodia formation, unlike in existing single-chain systems that operate by allosteric photo-switching of constitutively active Rac1 or the heterodimerization-based (i.e. two-component) membrane recruitment of a Rac1-activating GEF. Opto-Rac1 induction of lamellipodia formation was spatially restricted to the patterned illumination field and was efficient, requiring sparse stimulation duty ratios of ∼1-2% (at the sensitivity threshold for flavin photocycling) to cause significant changes in cell morphology. This work exemplifies how the discovery of LOV proteins of distinct signal transmission modes can beget new classes of optogenetic tools for controlling cellular function.
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Affiliation(s)
- Erin E Berlew
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, 19104, Philadelphia, PA, USA
| | - Ivan A Kuznetsov
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, 19104, Philadelphia, PA, USA
| | - Keisuke Yamada
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, 19104, Philadelphia, PA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, 19104, Philadelphia, PA, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, 19104, Philadelphia, PA, USA.
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36
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Parag-Sharma K, O’Banion CP, Henry EC, Musicant AM, Cleveland JL, Lawrence DS, Amelio AL. Engineered BRET-Based Biologic Light Sources Enable Spatiotemporal Control over Diverse Optogenetic Systems. ACS Synth Biol 2020; 9:1-9. [PMID: 31834783 PMCID: PMC7875091 DOI: 10.1021/acssynbio.9b00277] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-inducible optogenetic systems offer precise spatiotemporal control over a myriad of biologic processes. Unfortunately, current systems are inherently limited by their dependence on external light sources for their activation. Further, the utility of laser/LED-based illumination strategies are often constrained by the need for invasive surgical procedures to deliver such devices and local heat production, photobleaching and phototoxicity that compromises cell and tissue viability. To overcome these limitations, we developed a novel BRET-activated optogenetics (BEACON) system that employs biologic light to control optogenetic tools. BEACON is driven by self-illuminating bioluminescent-fluorescent proteins that generate "spectrally tuned" biologic light via bioluminescence resonance energy transfer (BRET). Notably, BEACON robustly activates a variety of commonly used optogenetic systems in a spatially restricted fashion, and at physiologically relevant time scales, to levels that are achieved by conventional laser/LED light sources.
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Affiliation(s)
- Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology and Physiology, Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Colin P. O’Banion
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, United States
| | - Erin C. Henry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Adele M. Musicant
- Graduate Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John L. Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - David S. Lawrence
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Molecular Therapeutics Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Antonio L. Amelio
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Cancer Cell Biology Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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37
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Light Control of the Tet Gene Expression System in Mammalian Cells. Cell Rep 2019; 25:487-500.e6. [PMID: 30304687 DOI: 10.1016/j.celrep.2018.09.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 07/27/2018] [Accepted: 09/07/2018] [Indexed: 11/22/2022] Open
Abstract
Gene expression and its network structure are dynamically altered in multicellular systems during morphological, functional, and pathological changes. To precisely analyze the functional roles of dynamic gene expression changes, tools that manipulate gene expression at fine spatiotemporal resolution are needed. The tetracycline (Tet)-controlled gene expression system is a reliable drug-inducible method, and it is used widely in many mammalian cultured cells and model organisms. Here, we develop a photoactivatable (PA)-Tet-OFF/ON system for precise temporal control of gene expression at single-cell resolution. By integrating the cryptochrome 2-cryptochrome-interacting basic helix-loop-helix 1 (Cry2-CIB1) light-inducible binding switch, expression of the gene of interest is tightly regulated under the control of light illumination and drug application in our PA-Tet-OFF/ON system. This system has a large dynamic range of downstream gene expression and rapid activation/deactivation kinetics. We also demonstrate the optogenetic regulation of exogenous gene expression in vivo, such as in developing and adult mouse brains.
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38
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Kinjo T, Terai K, Horita S, Nomura N, Sumiyama K, Togashi K, Iwata S, Matsuda M. FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics. Nat Methods 2019; 16:1029-1036. [DOI: 10.1038/s41592-019-0541-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022]
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39
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D'Acunzo P, Strappazzon F, Caruana I, Meneghetti G, Di Rita A, Simula L, Weber G, Del Bufalo F, Dalla Valle L, Campello S, Locatelli F, Cecconi F. Reversible induction of mitophagy by an optogenetic bimodular system. Nat Commun 2019; 10:1533. [PMID: 30948710 PMCID: PMC6449392 DOI: 10.1038/s41467-019-09487-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
Autophagy-mediated degradation of mitochondria (mitophagy) is a key process in cellular quality control. Although mitophagy impairment is involved in several patho-physiological conditions, valuable methods to induce mitophagy with low toxicity in vivo are still lacking. Herein, we describe a new optogenetic tool to stimulate mitophagy, based on light-dependent recruitment of pro-autophagy protein AMBRA1 to mitochondrial surface. Upon illumination, AMBRA1-RFP-sspB is efficiently relocated from the cytosol to mitochondria, where it reversibly mediates mito-aggresome formation and reduction of mitochondrial mass. Finally, as a proof of concept of the biomedical relevance of this method, we induced mitophagy in an in vitro model of neurotoxicity, fully preventing cell death, as well as in human T lymphocytes and in zebrafish in vivo. Given the unique features of this tool, we think it may turn out to be very useful for a wide range of both therapeutic and research applications. Autophagic degradation of mitochondria (mitophagy) is a key quality control mechanism in cellular homeostasis, and its misregulation is involved in neurodegenerative diseases. Here the authors develop an optogenetic system for reversible induction of mitophagy and validate its use in cell culture and zebrafish embryos.
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Affiliation(s)
- Pasquale D'Acunzo
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Flavie Strappazzon
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143, Rome, Italy.,Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Ignazio Caruana
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Giacomo Meneghetti
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131, Padova, Italy
| | - Anthea Di Rita
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143, Rome, Italy.,Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Luca Simula
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy.,Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Gerrit Weber
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Francesca Del Bufalo
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Luisa Dalla Valle
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131, Padova, Italy
| | - Silvia Campello
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143, Rome, Italy.,Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy.,Department of Gynecology/Obstetrics and Pediatrics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Cecconi
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy. .,Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy. .,Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
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40
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Perspectives of RAS and RHEB GTPase Signaling Pathways in Regenerating Brain Neurons. Int J Mol Sci 2018; 19:ijms19124052. [PMID: 30558189 PMCID: PMC6321366 DOI: 10.3390/ijms19124052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Cellular activation of RAS GTPases into the GTP-binding “ON” state is a key switch for regulating brain functions. Molecular protein structural elements of rat sarcoma (RAS) and RAS homolog protein enriched in brain (RHEB) GTPases involved in this switch are discussed including their subcellular membrane localization for triggering specific signaling pathways resulting in regulation of synaptic connectivity, axonal growth, differentiation, migration, cytoskeletal dynamics, neural protection, and apoptosis. A beneficial role of neuronal H-RAS activity is suggested from cellular and animal models of neurodegenerative diseases. Recent experiments on optogenetic regulation offer insights into the spatiotemporal aspects controlling RAS/mitogen activated protein kinase (MAPK) or phosphoinositide-3 kinase (PI3K) pathways. As optogenetic manipulation of cellular signaling in deep brain regions critically requires penetration of light through large distances of absorbing tissue, we discuss magnetic guidance of re-growing axons as a complementary approach. In Parkinson’s disease, dopaminergic neuronal cell bodies degenerate in the substantia nigra. Current human trials of stem cell-derived dopaminergic neurons must take into account the inability of neuronal axons navigating over a large distance from the grafted site into striatal target regions. Grafting dopaminergic precursor neurons directly into the degenerating substantia nigra is discussed as a novel concept aiming to guide axonal growth by activating GTPase signaling through protein-functionalized intracellular magnetic nanoparticles responding to external magnets.
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41
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de Mena L, Rizk P, Rincon-Limas DE. Bringing Light to Transcription: The Optogenetics Repertoire. Front Genet 2018; 9:518. [PMID: 30450113 PMCID: PMC6224442 DOI: 10.3389/fgene.2018.00518] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/15/2018] [Indexed: 11/13/2022] Open
Abstract
The ability to manipulate expression of exogenous genes in particular regions of living organisms has profoundly transformed the way we study biomolecular processes involved in both normal development and disease. Unfortunately, most of the classical inducible systems lack fine spatial and temporal accuracy, thereby limiting the study of molecular events that strongly depend on time, duration of activation, or cellular localization. By exploiting genetically engineered photo sensing proteins that respond to specific wavelengths, we can now provide acute control of numerous molecular activities with unprecedented precision. In this review, we present a comprehensive breakdown of all of the current optogenetic systems adapted to regulate gene expression in both unicellular and multicellular organisms. We focus on the advantages and disadvantages of these different tools and discuss current and future challenges in the successful translation to more complex organisms.
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Affiliation(s)
- Lorena de Mena
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Patrick Rizk
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States.,Department of Neuroscience, Genetics Institute, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, United States
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42
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Reis JM, Xu X, McDonald S, Woloschuk RM, Jaikaran ASI, Vizeacoumar FS, Woolley GA, Uppalapati M. Discovering Selective Binders for Photoswitchable Proteins Using Phage Display. ACS Synth Biol 2018; 7:2355-2364. [PMID: 30203962 DOI: 10.1021/acssynbio.8b00123] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nature provides an array of proteins that change conformation in response to light. The discovery of a complementary array of proteins that bind only the light-state or dark-state conformation of their photoactive partner proteins would allow each light-switchable protein to be used as an optogenetic tool to control protein-protein interactions. However, as many photoactive proteins have no known binding partner, the advantages of optogenetic control-precise spatial and temporal resolution-are currently restricted to a few well-defined natural systems. In addition, the affinities and kinetics of native interactions are often suboptimal and are difficult to engineer in the absence of any structural information. We report a phage display strategy using a small scaffold protein that can be used to discover new binding partners for both light and dark states of a given light-switchable protein. We used our approach to generate binding partners that interact specifically with the light state or the dark state conformation of two light-switchable proteins: PYP, a test case for a protein with no known partners, and AsLOV2, a well-characterized protein. We show that these novel light-switchable protein-protein interactions can function in living cells to control subcellular localization processes.
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Affiliation(s)
- Jakeb M. Reis
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Xiuling Xu
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - Ryan M. Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Anna S. I. Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
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Fielmich LE, Schmidt R, Dickinson DJ, Goldstein B, Akhmanova A, van den Heuvel S. Optogenetic dissection of mitotic spindle positioning in vivo. eLife 2018; 7:38198. [PMID: 30109984 PMCID: PMC6214656 DOI: 10.7554/elife.38198] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/14/2018] [Indexed: 12/25/2022] Open
Abstract
The position of the mitotic spindle determines the plane of cell cleavage, and thereby daughter cell location, size, and content. Spindle positioning is driven by dynein-mediated pulling forces exerted on astral microtubules, which requires an evolutionarily conserved complex of Gα∙GDP, GPR-1/2Pins/LGN, and LIN-5Mud/NuMA proteins. To examine individual functions of the complex components, we developed a genetic strategy for light-controlled localization of endogenous proteins in C. elegans embryos. By replacing Gα and GPR-1/2 with a light-inducible membrane anchor, we demonstrate that Gα∙GDP, Gα∙GTP, and GPR-1/2 are not required for pulling-force generation. In the absence of Gα and GPR-1/2, cortical recruitment of LIN-5, but not dynein itself, induced high pulling forces. The light-controlled localization of LIN-5 overruled normal cell-cycle and polarity regulation and provided experimental control over the spindle and cell-cleavage plane. Our results define Gα∙GDP–GPR-1/2Pins/LGN as a regulatable membrane anchor, and LIN-5Mud/NuMA as a potent activator of dynein-dependent spindle-positioning forces. A cell about to divide must decide where exactly to cut itself in two. Split right down the middle, and the two daughter cells will be identical; offset the cleavage plane to one side, and the resulting siblings will have different sizes, places and fates. In animals, the splitting of cells is dictated by the location of the spindle, a structure that forms when cable-like microtubules stretch from the cell membrane to attach to the chromosomes. At the membrane, a group of proteins tugs on the microtubules to bring the spindle into the correct position. One of these proteins, dynein, is a motor that uses microtubules as its track to pull the spindle into place. What the other parts of the complex do is still unclear, but a general assumption is that they may be serving as an anchor for dynein. To test this model, Fielmich, Schmidt et al. removed one or more proteins from the complex in the developing embryos of the nematode worm Caenorhabditis elegans. A light-activated system then linked the remaining proteins to the membrane by tying them to an artificial anchor. Two of the proteins in the complex could be replaced with the artificial anchor, but pulling forces were absent when dynein was artificially tied to the membrane. This indicates that the motor being anchored at the edge of the cell is not enough for it to pull on microtubules. Instead, the experiments showed that dynein needs to be activated by another component of the complex, a protein called LIN-5. This suggests that individual proteins in the complex have specialized roles that go beyond simply tethering dynein. In fact, steering where LIN-5 was attached on the membrane helped to control the location of the spindle, and therefore of the cleavage plane. As mammals have a protein similar to LIN-5, dissecting the roles of the components involved in positioning the spindle in C. elegans could help to understand normal and abnormal human development. In addition, these results demonstrate that creating artificial interactions between proteins using light is a powerful technique to study biological processes.
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Affiliation(s)
- Lars-Eric Fielmich
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Ruben Schmidt
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands.,Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Daniel J Dickinson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bob Goldstein
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
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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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Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids. Proc Natl Acad Sci U S A 2018; 115:E7720-E7727. [PMID: 30065115 PMCID: PMC6099885 DOI: 10.1073/pnas.1802832115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Light–oxygen–voltage (LOV) domain photoreceptors are found ubiquitously in nature and possess highly diverse signaling roles and mechanisms. Here, we show that a class of fungal LOV proteins dynamically associates with anionic plasma membrane phospholipids by a blue light-switched electrostatic interaction. This reversible association is rapidly triggered by blue light and ceases within seconds when illumination ceases. Within the native host, we predict that these proteins regulate G-protein signaling by the controlled recruitment of fused regulator of G-protein signaling (RGS) domains; in applied contexts, we anticipate that engineered chimeric versions of such proteins will be useful for rapid optogenetic membrane localization of fused proteins through direct interaction with the membrane itself, without requiring additional components to direct subcellular localization. We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helix in the linker region between the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction is nonselective among anionic phospholipids, exhibiting binding strengths dependent on the total anionic content of the membrane without preference for a specific headgroup. The in vitro and cellular responses were also observed with a BcLOV4 homolog and thus are likely to be general across the dikarya LOV class, whose members are associated with regulator of G-protein signaling (RGS) domains. Natural photoreceptors are not previously known to directly associate with membrane phospholipids in a light-dependent manner, and thus this work establishes both a photosensory signal transmission mode and a single-component optogenetic tool with rapid membrane localization kinetics that approaches the diffusion limit.
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Hughes RM. A compendium of chemical and genetic approaches to light-regulated gene transcription. Crit Rev Biochem Mol Biol 2018; 53:453-474. [PMID: 30040498 DOI: 10.1080/10409238.2018.1487382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
On-cue regulation of gene transcription is an invaluable tool for the study of biological processes and the development and integration of next-generation therapeutics. Ideal reagents for the precise regulation of gene transcription should be nontoxic to the host system, highly tunable, and provide a high level of spatial and temporal control. Light, when coupled with protein or small molecule-linked photoresponsive elements, presents an attractive means of meeting the demands of an ideal system for regulating gene transcription. In this review, we cover recent developments in the burgeoning field of light-regulated gene transcription, covering both genetically encoded and small-molecule based strategies for optical regulation of transcription during the period 2012 till present.
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Affiliation(s)
- Robert M Hughes
- a Department of Chemistry , East Carolina University , Greenville , NC , USA
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Ma G, Zhang Q, He L, Nguyen NT, Liu S, Gong Z, Huang Y, Zhou Y. Genetically encoded tags for real time dissection of protein assembly in living cells. Chem Sci 2018; 9:5551-5555. [PMID: 30061986 PMCID: PMC6048692 DOI: 10.1039/c8sc00839f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
Simple methods with straightforward readouts that enable real-time interrogation of protein quaternary structure are much needed to facilitate the physicochemical characterization of proteins at the single-cell level. After screening over a series of microtubule (MT) binders, we report herein the development of two genetically encoded tags (designated as "MoTags" for the monomer/oligomer detection tag) that can be conveniently fused to a given protein to probe its oligomeric state in cellulo when combined with routine fluorescence microscopy. In their monomeric form, MoTags are evenly distributed in the cytosol; whereas oligomerization enables MoTags to label MT or track MT tips in an oligomeric state-dependent manner. We demonstrate here the broad utility of engineered MoTags to aid the determination of protein oligomeric states, dissection of protein structure and function, and monitoring of protein-target interactions under physiological conditions in living cells.
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Affiliation(s)
- Guolin Ma
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Qian Zhang
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
- Department of Infectious Diseases , Renmin Hospital of Wuhan University , Wuhan 430060 , China
| | - Lian He
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Nhung T Nguyen
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Shuzhong Liu
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Zuojiong Gong
- Department of Infectious Diseases , Renmin Hospital of Wuhan University , Wuhan 430060 , China
| | - Yun Huang
- Center for Epigenetics and Disease Prevention , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA .
- Department of Molecular and Cellular Medicine , College of Medicine , Texas A&M University , College Station , TX 77843 , USA
| | - Yubin Zhou
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
- Department of Medical Physiology , College of Medicine , Texas A&M University , Temple , TX 76504 , USA
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O'Banion CP, Lawrence DS. Optogenetics: A Primer for Chemists. Chembiochem 2018; 19:1201-1216. [DOI: 10.1002/cbic.201800013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Colin P. O'Banion
- Department of Chemistry; Division of Chemical Biology and Medicinal Chemistry and; Department of Pharmacology; University of North Carolina; Chapel Hill NC 27599 USA
| | - David S. Lawrence
- Department of Chemistry; Division of Chemical Biology and Medicinal Chemistry and; Department of Pharmacology; University of North Carolina; Chapel Hill NC 27599 USA
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Gainza-Cirauqui P, Correia BE. Computational protein design-the next generation tool to expand synthetic biology applications. Curr Opin Biotechnol 2018; 52:145-152. [PMID: 29729544 DOI: 10.1016/j.copbio.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022]
Abstract
One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells.
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Affiliation(s)
- Pablo Gainza-Cirauqui
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Bruno Emanuel Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland.
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Vesicle Docking Is a Key Target of Local PI(4,5)P 2 Metabolism in the Secretory Pathway of INS-1 Cells. Cell Rep 2018; 20:1409-1421. [PMID: 28793264 PMCID: PMC5613661 DOI: 10.1016/j.celrep.2017.07.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/31/2017] [Accepted: 07/14/2017] [Indexed: 12/29/2022] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) signaling is transient and spatially confined in live cells. How this pattern of signaling regulates transmitter release and hormone secretion has not been addressed. We devised an optogenetic approach to control PI(4,5)P2 levels in time and space in insulin-secreting cells. Combining this approach with total internal reflection fluorescence microscopy, we examined individual vesicle-trafficking steps. Unlike long-term PI(4,5)P2 perturbations, rapid and cell-wide PI(4,5)P2 reduction in the plasma membrane (PM) strongly inhibits secretion and intracellular Ca2+ concentration ([Ca2+]i) responses, but not sytaxin1a clustering. Interestingly, local PI(4,5)P2 reduction selectively at vesicle docking sites causes remarkable vesicle undocking from the PM without affecting [Ca2+]i. These results highlight a key role of local PI(4,5)P2 in vesicle tethering and docking, coordinated with its role in priming and fusion. Thus, different spatiotemporal PI(4,5)P2 signaling regulates distinct steps of vesicle trafficking, and vesicle docking may be a key target of local PI(4,5)P2 signaling in vivo.
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