1
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Benman W, Datta S, Gonzalez-Martinez D, Lee G, Hooper J, Qian G, Leavitt G, Salloum L, Ho G, Mhatre S, Magaraci MS, Patterson M, Mannickarottu SG, Malani S, Avalos JL, Chow BY, Bugaj LJ. High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates. Commun Biol 2023; 6:1192. [PMID: 38001175 PMCID: PMC10673842 DOI: 10.1038/s42003-023-05532-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.
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Affiliation(s)
- William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Saachi Datta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Gloria Lee
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Juliette Hooper
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Leavitt
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lana Salloum
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Ho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharvari Mhatre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael S Magaraci
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael Patterson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Saurabh Malani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jose L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
- The Andlinger Center for Energy and the Environment, Princeton, NJ, 08544, USA
- High Meadows Environmental Institute, Princeton, NJ, 08544, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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Hiefinger C, Mandl S, Wieland M, Kneuttinger A. Rational design, production and in vitro analysis of photoxenoproteins. Methods Enzymol 2023; 682:247-288. [PMID: 36948704 DOI: 10.1016/bs.mie.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In synthetic biology, the artificial control of proteins by light is of growing interest since it enables the spatio-temporal regulation of downstream molecular processes. This precise photocontrol can be established by the site-directed incorporation of photo-sensitive non-canonical amino acids (ncAAs) into proteins, which generates so-called photoxenoproteins. Photoxenoproteins can be engineered using ncAAs that facilitate the irreversible activation or reversible regulation of their activity upon irradiation. In this chapter, we provide a general outline of the engineering process based on the current methodological state-of-the-art to obtain artificial photocontrol in proteins using the ncAAs o-nitrobenzyl-O-tyrosine as example for photocaged ncAAs (irreversible), and phenylalanine-4'-azobenzene as example for photoswitchable ncAAs (reversible). We thereby focus on the initial design as well as the production and characterization of photoxenoproteins in vitro. Finally, we outline the analysis of photocontrol under steady-state and non-steady-state conditions using the allosteric enzyme complexes imidazole glycerol phosphate synthase and tryptophan synthase as examples.
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Affiliation(s)
- Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sabrina Mandl
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Wieland
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Kneuttinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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3
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Kumar S, Khammash M. Platforms for Optogenetic Stimulation and Feedback Control. Front Bioeng Biotechnol 2022; 10:918917. [PMID: 35757811 PMCID: PMC9213687 DOI: 10.3389/fbioe.2022.918917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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4
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Wagdi A, Malan D, Sathyanarayanan U, Beauchamp JS, Vogt M, Zipf D, Beiert T, Mansuroglu B, Dusend V, Meininghaus M, Schneider L, Kalthof B, Wiegert JS, König GM, Kostenis E, Patejdl R, Sasse P, Bruegmann T. Selective optogenetic control of G q signaling using human Neuropsin. Nat Commun 2022; 13:1765. [PMID: 35365606 PMCID: PMC8975936 DOI: 10.1038/s41467-022-29265-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/03/2022] [Indexed: 01/07/2023] Open
Abstract
Gq proteins are universally important for signal transduction in mammalian cells. The underlying kinetics and transformation from extracellular stimuli into intracellular signaling, however could not be investigated in detail so far. Here we present the human Neuropsin (hOPN5) for specific and repetitive manipulation of Gq signaling in vitro and in vivo with high spatio-temporal resolution. Properties and G protein specificity of hOPN5 are characterized by UV light induced IP3 generation, Ca2+ transients and inhibition of GIRK channel activity in HEK cells. In adult hearts from a transgenic animal model, light increases the spontaneous beating rate. In addition, we demonstrate light induced contractions in the small intestine, which are not detectable after pharmacological Gq protein block. All-optical high-throughput screening for TRPC6 inhibitors is more specific and sensitive than conventional pharmacological screening. Thus, we demonstrate specific Gq signaling of hOPN5 and unveil its potential for optogenetic applications.
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Affiliation(s)
- Ahmed Wagdi
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany ,grid.452396.f0000 0004 5937 5237German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Present Address: Department of Cardiology and Pulmonology, University Medical Center Göttingen, Georg August University of Göttingen, Göttingen, Germany
| | - Daniela Malan
- grid.10388.320000 0001 2240 3300Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany
| | - Udhayabhaskar Sathyanarayanan
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Janosch S. Beauchamp
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Vogt
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - David Zipf
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Beiert
- grid.15090.3d0000 0000 8786 803XDepartment of Internal Medicine II, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Berivan Mansuroglu
- grid.10388.320000 0001 2240 3300Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany ,grid.10388.320000 0001 2240 3300Research Training Group 1873, University of Bonn, Bonn, Germany
| | - Vanessa Dusend
- grid.10388.320000 0001 2240 3300Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany ,grid.10388.320000 0001 2240 3300Research Training Group 1873, University of Bonn, Bonn, Germany
| | - Mark Meininghaus
- grid.420044.60000 0004 0374 4101Bayer AG, Research & Development, Pharmaceuticals, 42096 Wuppertal, Germany
| | - Linn Schneider
- grid.420044.60000 0004 0374 4101Bayer AG, Research & Development, Pharmaceuticals, 42096 Wuppertal, Germany
| | - Bernd Kalthof
- grid.420044.60000 0004 0374 4101Bayer AG, Research & Development, Pharmaceuticals, 42096 Wuppertal, Germany
| | - J. Simon Wiegert
- grid.13648.380000 0001 2180 3484Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele M. König
- grid.10388.320000 0001 2240 3300Molecular, Cellular and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Evi Kostenis
- grid.10388.320000 0001 2240 3300Molecular, Cellular and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Robert Patejdl
- grid.413108.f0000 0000 9737 0454Oscar-Langendorff Institute of Physiology, Rostock University Medical Center, Rostock, Germany
| | - Philipp Sasse
- grid.10388.320000 0001 2240 3300Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany
| | - Tobias Bruegmann
- grid.411984.10000 0001 0482 5331Institute for Cardiovascular Physiology, University Medical Center Göttingen, Göttingen, Germany ,grid.452396.f0000 0004 5937 5237German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany ,grid.10388.320000 0001 2240 3300Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany ,grid.10388.320000 0001 2240 3300Research Training Group 1873, University of Bonn, Bonn, Germany ,grid.7450.60000 0001 2364 4210Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
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5
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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6
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Repina NA, McClave T, Johnson HJ, Bao X, Kane RS, Schaffer DV. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics. Cell Rep 2021; 31:107737. [PMID: 32521262 PMCID: PMC9357365 DOI: 10.1016/j.celrep.2020.107737] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 10/31/2022] Open
Abstract
Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics affect cell behavior. Here, we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). By patterning human embryonic stem cell (hESC) cultures with varying light intensities, LAVA devices enabled dose-responsive control of optoWnt activation and Brachyury expression. Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models the embryonic presentation of Wnt signals in vitro. LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.
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Affiliation(s)
- Nicole A Repina
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas McClave
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hunter J Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoping Bao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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7
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Bounds AD, Bailey RD, Adams CT, Callaghan DC, Girkin JM. LightBox: A multiwell plate illumination system for photoactive molecule characterization. JOURNAL OF BIOPHOTONICS 2021; 14:e202000481. [PMID: 33576569 DOI: 10.1002/jbio.202000481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Multiwell plates (MWPs) are the workhorses of the life sciences. However, biophotonics research with MWPs is limited, in part due to the lack of equipment suitable for photo-irradiation of photoactive molecules in a MWP-suitable, high-throughput manner, either commercially or through open-source MWP systems. Here we present "LightBox", a calibrated controllable MWP illumination system with broad applications including screening of photoactive molecules and characterization of photocatalytic chemicals. LightBox is a high intensity, accurately controllable, uniform illumination system designed for MWPs with electronics and a control unit that provides a simple and intuitive interface. LightBox can reach intensities of 0.23 mW/mm2 at wavelengths of 405 nm with variance between well sites of <5%. The usefulness of LightBox is demonstrated by assessing the IC50 of a photosensitizing compound using a live/dead assay following simultaneous irradiation of the sample at a range of concentrations, eliminating uncontrolled variables between concentrations and drastically increasing assessment speed.
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Affiliation(s)
- A D Bounds
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - R D Bailey
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - C T Adams
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - D C Callaghan
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - J M Girkin
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
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8
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Gutzeit VA, Acosta-Ruiz A, Munguba H, Häfner S, Landra-Willm A, Mathes B, Mony J, Yarotski D, Börjesson K, Liston C, Sandoz G, Levitz J, Broichhagen J. A fine-tuned azobenzene for enhanced photopharmacology in vivo. Cell Chem Biol 2021; 28:1648-1663.e16. [PMID: 33735619 DOI: 10.1016/j.chembiol.2021.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/23/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Despite the power of photopharmacology for interrogating signaling proteins, many photopharmacological systems are limited by their efficiency, speed, or spectral properties. Here, we screen a library of azobenzene photoswitches and identify a urea-substituted "azobenzene-400" core that offers bistable switching between cis and trans with improved kinetics, light sensitivity, and a red-shift. We then focus on the metabotropic glutamate receptors (mGluRs), neuromodulatory receptors that are major pharmacological targets. Synthesis of "BGAG12,400," a photoswitchable orthogonal, remotely tethered ligand (PORTL), enables highly efficient, rapid optical agonism following conjugation to SNAP-tagged mGluR2 and permits robust optical control of mGluR1 and mGluR5 signaling. We then produce fluorophore-conjugated branched PORTLs to enable dual imaging and manipulation of mGluRs and highlight their power in ex vivo slice and in vivo behavioral experiments in the mouse prefrontal cortex. Finally, we demonstrate the generalizability of our strategy by developing an improved soluble, photoswitchable pore blocker for potassium channels.
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Affiliation(s)
- Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amanda Acosta-Ruiz
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Stephanie Häfner
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Arnaud Landra-Willm
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Bettina Mathes
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Jürgen Mony
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Dzianis Yarotski
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Karl Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Conor Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Guillaume Sandoz
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Joshua Levitz
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany; Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.
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9
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Holland I, Davies JA. Automation in the Life Science Research Laboratory. Front Bioeng Biotechnol 2020; 8:571777. [PMID: 33282848 PMCID: PMC7691657 DOI: 10.3389/fbioe.2020.571777] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/26/2020] [Indexed: 12/22/2022] Open
Abstract
Protocols in the academic life science laboratory are heavily reliant on the manual manipulation of tools, reagents and instruments by a host of research staff and students. In contrast to industrial and clinical laboratory environments, the usage of automation to augment or replace manual tasks is limited. Causes of this 'automation gap' are unique to academic research, with rigid short-term funding structures, high levels of protocol variability and a benevolent culture of investment in people over equipment. Automation, however, can bestow multiple benefits through improvements in reproducibility, researcher efficiency, clinical translation, and safety. Less immediately obvious are the accompanying limitations, including obsolescence and an inhibitory effect on the freedom to innovate. Growing the range of automation options suitable for research laboratories will require more flexible, modular and cheaper designs. Academic and commercial developers of automation will increasingly need to design with an environmental awareness and an understanding that large high-tech robotic solutions may not be appropriate for laboratories with constrained financial and spatial resources. To fully exploit the potential of laboratory automation, future generations of scientists will require both engineering and biology skills. Automation in the research laboratory is likely to be an increasingly critical component of future research programs and will continue the trend of combining engineering and science expertise together to answer novel research questions.
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Affiliation(s)
- Ian Holland
- Deanery of Biomedical Science and Synthsys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
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10
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Bugaj LJ, Lim WA. High-throughput multicolor optogenetics in microwell plates. Nat Protoc 2019; 14:2205-2228. [PMID: 31235951 DOI: 10.1038/s41596-019-0178-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/09/2019] [Indexed: 12/27/2022]
Abstract
Optogenetic probes can be powerful tools for dissecting complexity in cell biology, but there is a lack of instrumentation to exploit their potential for automated, high-information-content experiments. This protocol describes the construction and use of the optoPlate-96, a platform for high-throughput three-color optogenetics experiments that allows simultaneous manipulation of common red- and blue-light-sensitive optogenetic probes. The optoPlate-96 enables illumination of individual wells in 96-well microwell plates or in groups of wells in 384-well plates. Its design ensures that there will be no cross-illumination between microwells in 96-well plates, and an active cooling system minimizes sample heating during light-intensive experiments. This protocol details the steps to assemble, test, and use the optoPlate-96. The device can be fully assembled without specialized equipment beyond a 3D printer and a laser cutter, starting from open-source design files and commercially available components. We then describe how to perform a typical optogenetics experiment using the optoPlate-96 to stimulate adherent mammalian cells. Although optoPlate-96 experiments are compatible with any plate-based readout, we describe analysis using quantitative single-cell immunofluorescence. This workflow thus allows complex optogenetics experiments (independent control of stimulation colors, intensity, dynamics, and time points) with high-dimensional outputs at single-cell resolution. Starting from 3D-printed and laser-cut components, assembly and testing of the optoPlate-96 can be accomplished in 3-4 h, at a cost of ~$600. A full optoPlate-96 experiment with immunofluorescence analysis can be performed within ~24 h, but this estimate is variable depending on the cell type and experimental parameters.
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Affiliation(s)
- Lukasz J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA, USA
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11
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Dietler J, Stabel R, Möglich A. Pulsatile illumination for photobiology and optogenetics. Methods Enzymol 2019; 624:227-248. [PMID: 31370931 DOI: 10.1016/bs.mie.2019.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Living organisms exhibit a wide range of intrinsic adaptive responses to incident light. Likewise, in optogenetics, biological systems are tailored to initiate predetermined cellular processes upon light exposure. As genetically encoded, light-gated actuators, sensory photoreceptors are at the heart of these responses in both the natural and engineered scenarios. Upon light absorption, photoreceptors enter a series of generally rapid photochemical reactions leading to population of the light-adapted signaling state of the receptor. Notably, this state persists for a while before thermally reverting to the original dark-adapted resting state. As a corollary, the inactivation of photosensitive biological circuits upon light withdrawal can exhibit substantial inertia. Intermittent illumination of suitable pulse frequency can hence maintain the photoreceptor in its light-adapted state while greatly reducing overall light dose, thereby mitigating adverse side effects. Moreover, several photoreceptor systems may be actuated sequentially with a single light color if they sufficiently differ in their inactivation kinetics. Here, we detail the construction of programmable illumination devices for the rapid and parallelized testing of biological responses to diverse lighting regimes. As the technology is based on open electronics and readily available, inexpensive components, it can be adopted by most laboratories at moderate expenditure. As we exemplify for two use cases, the programmable devices enable the facile interrogation of diverse illumination paradigms and their application in optogenetics and photobiology.
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Affiliation(s)
- Julia Dietler
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Robert Stabel
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany; Research Center for Bio-Macromolecules, Universität Bayreuth, Bayreuth, Germany; Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany; North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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12
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Stüven B, Stabel R, Ohlendorf R, Beck J, Schubert R, Möglich A. Characterization and engineering of photoactivated adenylyl cyclases. Biol Chem 2019; 400:429-441. [DOI: 10.1515/hsz-2018-0375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/07/2018] [Indexed: 12/28/2022]
Abstract
Abstract
Cyclic nucleoside monophosphates (cNMP) serve as universal second messengers in signal transduction across prokaryotes and eukaryotes. As signaling often relies on transiently formed microdomains of elevated second messenger concentration, means to precisely perturb the spatiotemporal dynamics of cNMPs are uniquely poised for the interrogation of the underlying physiological processes. Optogenetics appears particularly suited as it affords light-dependent, accurate control in time and space of diverse cellular processes. Several sensory photoreceptors function as photoactivated adenylyl cyclases (PAC) and hence serve as light-regulated actuators for the control of intracellular levels of 3′, 5′-cyclic adenosine monophosphate. To characterize PACs and to refine their properties, we devised a test bed for the facile analysis of these photoreceptors. Cyclase activity is monitored in bacterial cells via expression of a fluorescent reporter, and programmable illumination allows the rapid exploration of multiple lighting regimes. We thus probed two PACs responding to blue and red light, respectively, and observed significant dark activity for both. We next engineered derivatives of the red-light-sensitive PAC with altered responses to light, with one variant, denoted DdPAC, showing enhanced response to light. These PAC variants stand to enrich the optogenetic toolkit and thus facilitate the detailed analysis of cNMP metabolism and signaling.
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Affiliation(s)
- Birthe Stüven
- Lehrstuhl für Biochemie , Universität Bayreuth , D-95447 Bayreuth , Germany
| | - Robert Stabel
- Lehrstuhl für Biochemie , Universität Bayreuth , D-95447 Bayreuth , Germany
| | - Robert Ohlendorf
- Institut für Biologie , Humboldt-Universität zu Berlin , D-10115 Berlin , Germany
| | - Julian Beck
- Lehrstuhl für Biochemie , Universität Bayreuth , D-95447 Bayreuth , Germany
| | - Roman Schubert
- Institut für Biologie , Humboldt-Universität zu Berlin , D-10115 Berlin , Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , D-95447 Bayreuth , Germany
- Institut für Biologie , Humboldt-Universität zu Berlin , D-10115 Berlin , Germany
- Research Center for Bio-Macromolecules , Universität Bayreuth , D-95447 Bayreuth , Germany
- Bayreuth Center for Biochemistry and Molecular Biology , Universität Bayreuth , D-95447 Bayreuth , Germany
- North-Bavarian NMR Center , Universität Bayreuth , D-95447 Bayreuth , Germany
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13
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Szymula KP, Magaraci MS, Patterson M, Clark A, Mannickarottu SG, Chow BY. An Open-Source Plate Reader. Biochemistry 2018; 58:468-473. [PMID: 30511843 DOI: 10.1021/acs.biochem.8b00952] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microplate readers are foundational instruments in experimental biology and bioengineering that enable multiplexed spectrophotometric measurements. To enhance their accessibility, we here report the design, construction, validation, and benchmarking of an open-source microplate reader. The system features full-spectrum absorbance and fluorescence emission detection, in situ optogenetic stimulation, and stand-alone touch screen programming of automated assay protocols. The total system costs less than $3500, a fraction of the cost of commercial plate readers, and can detect the fluorescence of common dyes at concentrations as low as ∼10 nM. Functional capabilities were demonstrated in the context of synthetic biology, optogenetics, and photosensory biology: by steady-state measurements of ligand-induced reporter gene expression in a model of bacterial quorum sensing and by flavin photocycling kinetic measurements of a LOV (light-oxygen-voltage) domain photoreceptor used for optogenetic transcriptional activation. Fully detailed guides for assembling the device and automating it using the custom Python-based API (Application Program Interface) are provided. This work contributes a key technology to the growing community-wide infrastructure of open-source biology-focused hardware, whose creation is facilitated by rapid prototyping capabilities and low-cost electronics, optoelectronics, and microcomputers.
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Affiliation(s)
- Karol P Szymula
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael S Magaraci
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael Patterson
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Andrew Clark
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Sevile G Mannickarottu
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Brian Y Chow
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
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14
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Pilizota T, Yang YT. "Do It Yourself" Microbial Cultivation Techniques for Synthetic and Systems Biology: Cheap, Fun, and Flexible. Front Microbiol 2018; 9:1666. [PMID: 30105008 PMCID: PMC6077191 DOI: 10.3389/fmicb.2018.01666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
With the emergence of inexpensive 3D printing technology, open-source platforms for electronic prototyping and single-board computers, "Do it Yourself" (DIY) approaches to the cultivation of microbial cultures are becoming more feasible, user-friendly, and thus wider spread. In this perspective, we survey some of these approaches, as well as add-on solutions to commercial instruments for synthetic and system biology applications. We discuss different cultivation designs, including capabilities and limitations. Our intention is to encourage the reader to consider the DIY solutions. Overall, custom cultivation devices offer controlled growth environments with in-line monitoring of, for example, optical density, fluorescence, pH, and dissolved oxygen, all at affordable prices. Moreover, they offer a great degree of flexibility for different applications and requirements and are fun to design and construct. We include several illustrative examples, such as gaining optogenetic control and adaptive laboratory evolution experiments.
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Affiliation(s)
- Teuta Pilizota
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ya-Tang Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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15
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Hennemann J, Iwasaki RS, Grund TN, Diensthuber RP, Richter F, Möglich A. Optogenetic Control by Pulsed Illumination. Chembiochem 2018; 19:1296-1304. [PMID: 29442428 DOI: 10.1002/cbic.201800030] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Indexed: 12/18/2022]
Abstract
Sensory photoreceptors evoke numerous adaptive responses in nature and serve as light-gated actuators in optogenetics to enable the spatiotemporally precise, reversible, and noninvasive control of cellular events. The output of optogenetic circuits can often be dialed in by varying illumination quality, quantity, and duration. A programmable matrix of light-emitting diodes has been devised to efficiently probe the response of optogenetic systems to intermittently applied light of varying intensity and pulse frequency. Circuits for light-regulated gene expression markedly differed in their responses to pulsed illumination of a single color which sufficed for their sequential triggering. In addition to quantity and quality, the pulse frequency of intermittent light hence provides a further input variable for output control in optogenetics and photobiology. Pulsed illumination schemes allow the reduction of overall light dose and facilitate the multiplexing of several lightdependent actuators and reporters.
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Affiliation(s)
- Julia Hennemann
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447, Bayreuth, Germany
| | - Roman S Iwasaki
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Tamara N Grund
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447, Bayreuth, Germany
| | - Ralph P Diensthuber
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447, Bayreuth, Germany.,Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
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16
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Du W, Burbano PC, Hellingwerf KJ, Branco Dos Santos F. Challenges in the Application of Synthetic Biology Toward Synthesis of Commodity Products by Cyanobacteria via "Direct Conversion". ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:3-26. [PMID: 30091089 DOI: 10.1007/978-981-13-0854-3_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyanobacterial direct conversion of CO2 to several commodity chemicals has been recognized as a potential contributor to support the much-needed sustainable development of human societies. However, the feasibility of this "green conversion" hinders on our ability to overcome the hurdles presented by the natural evolvability of microbes. The latter may result in the genetic instability of engineered cyanobacterial strains leading to impaired productivity. This challenge is general to any "cell factory" approach in which the cells grow for multiple generations, and based on several studies carried out in different microbial hosts, we could identify that three distinct strategies have been proposed to tackle it. These are (1) to reduce microbial evolvability by decreasing the native mutation rate, (2) to align product formation with cell growth/fitness, and, paradoxically, (3) to efficiently reallocate cellular resources to product formation by uncoupling it from growth. The implementation of either of these strategies requires an advanced synthetic biology toolkit. Here, we review the existing methods available for cyanobacteria and identify areas of focus in which specific developments are still needed. Furthermore, we discuss how potentially stabilizing strategies may be used in combination leading to further increases of productivity while ensuring the stability of the cyanobacterial-based direct conversion process.
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Affiliation(s)
- Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Patricia Caicedo Burbano
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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17
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Wang H, Yang YT. Mini Photobioreactors for in Vivo Real-Time Characterization and Evolutionary Tuning of Bacterial Optogenetic Circuit. ACS Synth Biol 2017; 6:1793-1796. [PMID: 28532145 DOI: 10.1021/acssynbio.7b00091] [Citation(s) in RCA: 9] [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
The current standard protocols for characterizing the optogenetic circuit of bacterial cells using flow cytometry in light tubes and light exposure of culture plates are tedious, labor-intensive, and cumbersome. In this work, we engineer a bioreactor with working volume of ∼10 mL for in vivo real-time optogenetic characterization of E. coli with a CcaS-CcaR light-sensing system. In the bioreactor, optical density measurements, reporter protein fluorescence detection, and light input stimuli are provided by four light-emitting diode sources and two photodetectors. Once calibrated, the device can cultivate microbial cells and record their growth and gene expression without human intervention. We measure gene expression during cell growth with different organic substrates (glucose, succinate, acetate, pyruvate) as carbon sources in minimal medium and demonstrate evolutionary tuning of the optogenetic circuit by serial dilution passages.
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Affiliation(s)
- Hsinkai Wang
- Department of Electrical
Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, R.O.C
| | - Ya-Tang Yang
- Department of Electrical
Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, R.O.C
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18
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Agus V, Janovjak H. Optogenetic methods in drug screening: technologies and applications. Curr Opin Biotechnol 2017; 48:8-14. [PMID: 28273648 DOI: 10.1016/j.copbio.2017.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 12/19/2022]
Abstract
The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function.
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Affiliation(s)
- Viviana Agus
- AXXAM SpA, via Meucci 3, 20091 Bresso, Milan, Italy
| | - Harald Janovjak
- Institute of Science and Technology (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
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19
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Schumacher CH, Körschen HG, Nicol C, Gasser C, Seifert R, Schwärzel M, Möglich A. A Fluorometric Activity Assay for Light-Regulated Cyclic-Nucleotide-Monophosphate Actuators. Methods Mol Biol 2016; 1408:93-105. [PMID: 26965118 DOI: 10.1007/978-1-4939-3512-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
As a transformative approach in neuroscience and cell biology, optogenetics grants control over manifold cellular events with unprecedented spatiotemporal definition, reversibility, and noninvasiveness. Sensory photoreceptors serve as genetically encoded, light-regulated actuators and hence embody the cornerstone of optogenetics. To expand the scope of optogenetics, ever more naturally occurring photoreceptors are being characterized, and synthetic photoreceptors with customized, light-regulated function are being engineered. Perturbational control over intracellular cyclic-nucleotide-monophosphate (cNMP) levels is achieved via sensory photoreceptors that catalyze the making and breaking of these second messengers in response to light. To facilitate discovery, engineering and quantitative characterization of such light-regulated cNMP actuators, we have developed an efficient fluorometric assay. Both the formation and the hydrolysis of cNMPs are accompanied by proton release which can be quantified with the fluorescent pH indicator 2',7'-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF). This assay equally applies to nucleotide cyclases, e.g., blue-light-activated bPAC, and to cNMP phosphodiesterases, e.g., red-light-activated LAPD. Key benefits include potential for parallelization and automation, as well as suitability for both purified enzymes and crude cell lysates. The BCECF assay hence stands to accelerate discovery and characterization of light-regulated actuators of cNMP metabolism.
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Affiliation(s)
| | - Heinz G Körschen
- Department of Molecular Sensory Systems, Research Center Caesar, Bonn, Germany
| | - Christopher Nicol
- Institut für Biologie, Neurobiologie, Freie Universität Berlin, Berlin, Germany
| | - Carlos Gasser
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Reinhard Seifert
- Department of Molecular Sensory Systems, Research Center Caesar, Bonn, Germany
| | - Martin Schwärzel
- Institut für Biologie, Neurobiologie, Freie Universität Berlin, Berlin, Germany
| | - Andreas Möglich
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany. .,Faculty of Biology, Chemistry and Earth Sciences, Lehrstuhl für Biochemie, Universität Bayreuth, Building NW III, Universitätsstraße 30, Bayreuth, 95440, Germany.
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20
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An open-hardware platform for optogenetics and photobiology. Sci Rep 2016; 6:35363. [PMID: 27805047 PMCID: PMC5096413 DOI: 10.1038/srep35363] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/28/2016] [Indexed: 12/27/2022] Open
Abstract
In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.
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21
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Abstract
Environmental insult, disease or trauma can affect the physical integrity of neuronal circuits, and the inability of many neurons to regenerate injured axons invariably leads to irreversible neural dysfunction. The conserved second messenger cyclic adenosine monophosphate (cAMP) can promote axonal re-growth. Widely used pharmacological or genetic approaches to increase intracellular levels of cAMP are often inadequate for precise neural-circuit reconstruction because their activity cannot be easily timed to specific target cells. These shortcomings have prevented the controlled repair of pre-defined neurons at selected time points in whole specimens. Thus, technologies to guide neuronal repair in time and space would enable studies of neural-circuit recovery with unprecedented resolution. Towards this aim, we have implemented a proof-of-principle optogenetic method to promote the selective regeneration of refractory axons in a living vertebrate.
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Affiliation(s)
- Yan Xiao
- Helmholtz Zentrum München, Munich, Germany
| | - Weili Tian
- Helmholtz Zentrum München, Munich, Germany
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22
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Mehlhorn J, Lindtner T, Richter F, Glass K, Steinocher H, Beck S, Hegemann P, Kennis JTM, Mathes T. Light-Induced Rearrangement of the β5 Strand in the BLUF Photoreceptor SyPixD (Slr1694). J Phys Chem Lett 2015; 6:4749-4753. [PMID: 26631358 DOI: 10.1021/acs.jpclett.5b02245] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The structural changes that facilitate signal transduction in blue light sensors using FAD (BLUF) photoreceptors and confer the stability of the rearranged hydrogen bond network between flavin and protein in the signaling state are still poorly understood. Here, we investigate a semiconserved Trp residue in SyPixD (Slr1694) by isotope-edited vibrational spectroscopy and site-directed mutagenesis. In the signaling state, a β-sheet structure involving the backbone of W91 is formed without apparent change of environment of the W91 indole side chain. Mutation of W91, however, significantly influences the stability of the light-adapted state, suggesting that backbone rigidity rather than discrete side-chain conformations govern the stability of the light-adapted state. On the basis of computational and crystallographic models, we interpret these changes as a +1 register shift of the β2/β5 interaction with an unaffected indole side-chain conformation, rather than a +2 register shift accompanied by an indole side-chain flip that was previously proposed on the basis of X-ray structures.
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Affiliation(s)
- Jennifer Mehlhorn
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - Tom Lindtner
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - Florian Richter
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - Kathrin Glass
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - Helena Steinocher
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universität zu Berlin , Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Peter Hegemann
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Biophysics Section, Faculty of Sciences, Vrije Universiteit , De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Tilo Mathes
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
- Department of Physics and Astronomy, Biophysics Section, Faculty of Sciences, Vrije Universiteit , De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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23
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Light-assisted small-molecule screening against protein kinases. Nat Chem Biol 2015; 11:952-4. [PMID: 26457372 PMCID: PMC4652335 DOI: 10.1038/nchembio.1933] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that obviates the addition of chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small molecule screen against human protein kinases including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.
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24
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Paramonov VM, Mamaeva V, Sahlgren C, Rivero-Müller A. Genetically-encoded tools for cAMP probing and modulation in living systems. Front Pharmacol 2015; 6:196. [PMID: 26441653 PMCID: PMC4569861 DOI: 10.3389/fphar.2015.00196] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/28/2015] [Indexed: 11/19/2022] Open
Abstract
Intracellular 3′-5′-cyclic adenosine monophosphate (cAMP) is one of the principal second messengers downstream of a manifold of signal transduction pathways, including the ones triggered by G protein-coupled receptors. Not surprisingly, biochemical assays for cAMP have been instrumental for basic research and drug discovery for decades, providing insights into cellular physiology and guiding pharmaceutical industry. However, despite impressive track record, the majority of conventional biochemical tools for cAMP probing share the same fundamental shortcoming—all the measurements require sample disruption for cAMP liberation. This common bottleneck, together with inherently low spatial resolution of measurements (as cAMP is typically analyzed in lysates of thousands of cells), underpin the ensuing limitations of the conventional cAMP assays: (1) genuine kinetic measurements of cAMP levels over time in a single given sample are unfeasible; (2) inability to obtain precise information on cAMP spatial distribution and transfer at subcellular levels, let alone the attempts to pinpoint dynamic interactions of cAMP and its effectors. At the same time, tremendous progress in synthetic biology over the recent years culminated in drastic refinement of our toolbox, allowing us not only to bypass the limitations of conventional assays, but to put intracellular cAMP life-span under tight control—something, that seemed scarcely attainable before. In this review article we discuss the main classes of modern genetically-encoded tools tailored for cAMP probing and modulation in living systems. We examine the capabilities and weaknesses of these different tools in the context of their operational characteristics and applicability to various experimental set-ups involving living cells, providing the guidance for rational selection of the best tools for particular needs.
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Affiliation(s)
- Valeriy M Paramonov
- Department of Physiology, Institute of Biomedicine, University of Turku , Turku, Finland ; Turku Center for Biotechnology, University of Turku and Åbo Akademi University , Turku, Finland
| | - Veronika Mamaeva
- Department of Clinical Science, University of Bergen , Bergen, Norway
| | - Cecilia Sahlgren
- Turku Center for Biotechnology, University of Turku and Åbo Akademi University , Turku, Finland ; Department of Biomedical Engineering, Eindhoven University of Technology , Eindhoven, Netherlands
| | - Adolfo Rivero-Müller
- Department of Physiology, Institute of Biomedicine, University of Turku , Turku, Finland ; Faculty of Natural Sciences and Technology, Åbo Akademi University , Turku, Finland ; Department of Biochemistry and Molecular Biology, Medical University of Lublin , Lublin, Poland
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25
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High-Throughput All-Optical Analysis of Synaptic Transmission and Synaptic Vesicle Recycling in Caenorhabditis elegans. PLoS One 2015; 10:e0135584. [PMID: 26312752 PMCID: PMC4552474 DOI: 10.1371/journal.pone.0135584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 07/24/2015] [Indexed: 12/13/2022] Open
Abstract
Synaptic vesicles (SVs) undergo a cycle of biogenesis and membrane fusion to release transmitter, followed by recycling. How exocytosis and endocytosis are coupled is intensively investigated. We describe an all-optical method for identification of neurotransmission genes that can directly distinguish SV recycling factors in C. elegans, by motoneuron photostimulation and muscular RCaMP Ca2+ imaging. We verified our approach on mutants affecting synaptic transmission. Mutation of genes affecting SV recycling (unc-26 synaptojanin, unc-41 stonin, unc-57 endophilin, itsn-1 intersectin, snt-1 synaptotagmin) showed a distinct ‘signature’ of muscle Ca2+ dynamics, induced by cholinergic motoneuron photostimulation, i.e. faster rise, and earlier decrease of the signal, reflecting increased synaptic fatigue during ongoing photostimulation. To facilitate high throughput, we measured (3–5 times) ~1000 nematodes for each gene. We explored if this method enables RNAi screening for SV recycling genes. Previous screens for synaptic function genes, based on behavioral or pharmacological assays, allowed no distinction of the stage of the SV cycle in which a protein might act. We generated a strain enabling RNAi specifically only in cholinergic neurons, thus resulting in healthier animals and avoiding lethal phenotypes resulting from knockdown elsewhere. RNAi of control genes resulted in Ca2+ measurements that were consistent with results obtained in the respective genomic mutants, albeit to a weaker extent in most cases, and could further be confirmed by opto-electrophysiological measurements for mutants of some of the genes, including synaptojanin. We screened 95 genes that were previously implicated in cholinergic transmission, and several controls. We identified genes that clustered together with known SV recycling genes, exhibiting a similar signature of their Ca2+ dynamics. Five of these genes (C27B7.7, erp-1, inx-8, inx-10, spp-10) were further assessed in respective genomic mutants; however, while all showed electrophysiological phenotypes indicative of reduced cholinergic transmission, no obvious SV recycling phenotypes could be uncovered for these genes.
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Abstract
Sensory photoreceptors not only control diverse adaptive responses in Nature, but as light-regulated actuators they also provide the foundation for optogenetics, the non-invasive and spatiotemporally precise manipulation of cellular events by light. Novel photoreceptors have been engineered that establish control by light over manifold biological processes previously inaccessible to optogenetic intervention. Recently, photoreceptor engineering has witnessed a rapid development, and light-regulated actuators for the perturbation of a plethora of cellular events are now available. Here, we review fundamental principles of photoreceptors and light-regulated allostery. Photoreceptors dichotomize into associating receptors that alter their oligomeric state as part of light-regulated allostery and non-associating receptors that do not. A survey of engineered photoreceptors pinpoints light-regulated association reactions and order-disorder transitions as particularly powerful and versatile design principles. Photochromic photoreceptors that are bidirectionally toggled by two light colors augur enhanced spatiotemporal resolution and use as photoactivatable fluorophores. By identifying desirable traits in engineered photoreceptors, we provide pointers for the design of future, light-regulated actuators.
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Affiliation(s)
- Thea Ziegler
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany ; Lehrstuhl für Biochemie, Universität Bayreuth Bayreuth, Germany
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany ; Lehrstuhl für Biochemie, Universität Bayreuth Bayreuth, Germany
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Castillo-Hair SM, Igoshin OA, Tabor JJ. How to train your microbe: methods for dynamically characterizing gene networks. Curr Opin Microbiol 2015; 24:113-23. [PMID: 25677419 DOI: 10.1016/j.mib.2015.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/06/2015] [Accepted: 01/10/2015] [Indexed: 12/31/2022]
Abstract
Gene networks regulate biological processes dynamically. However, researchers have largely relied upon static perturbations, such as growth media variations and gene knockouts, to elucidate gene network structure and function. Thus, much of the regulation on the path from DNA to phenotype remains poorly understood. Recent studies have utilized improved genetic tools, hardware, and computational control strategies to generate precise temporal perturbations outside and inside of live cells. These experiments have, in turn, provided new insights into the organizing principles of biology. Here, we introduce the major classes of dynamical perturbations that can be used to study gene networks, and discuss technologies available for creating them in a wide range of microbial pathways.
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Affiliation(s)
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, United States; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, United States; Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, TX 77005, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, United States; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, United States.
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