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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Signaling proteins comprise interaction and effector modules connected by linkers. Throughout evolution, these recurring modules have multiply been recombined to produce the present-day plethora of signaling proteins. Likewise, modular recombination lends itself to the engineering of hybrid signal receptors, whose functionality hinges on linker topology, sequence, and length. Often, numerous linkers must be assessed to obtain functional receptors. To expedite linker optimization, we devised the PATCHY strategy (primer-aided truncation for the creation of hybrid proteins) for the facile construction of hybrid gene libraries with defined linker distributions. Empowered by PATCHY, we engineered photoreceptors whose signal response was governed by linker length: whereas blue-light-repressed variants possessed linkers of 7n or 7n+5 residues, variants with 7n+1 residues were blue-light-activated. Related natural receptors predominantly displayed linker lengths of 7n and 7n+5 residues but rarely of 7n+1 residues. PATCHY efficiently explores linker sequence space to yield functional hybrid proteins including variants transcending the natural repertoire of signaling proteins.
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Affiliation(s)
- Robert Ohlendorf
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, Invalidenstraße 42, 10115 Berlin, Germany
| | - Charlotte Helene Schumacher
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, Invalidenstraße 42, 10115 Berlin, Germany
| | - Florian Richter
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, Invalidenstraße 42, 10115 Berlin, Germany
| | - Andreas Möglich
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, Invalidenstraße 42, 10115 Berlin, Germany
- Universität Bayreuth, Lehrstuhl für Biochemie, Universitätsstraße 30,
Geb. NW III, 95447 Bayreuth, Germany
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Richter F, Fonfara I, Bouazza B, Schumacher CH, Bratovič M, Charpentier E, Möglich A. Engineering of temperature- and light-switchable Cas9 variants. Nucleic Acids Res 2016; 44:10003-10014. [PMID: 27744350 PMCID: PMC5175372 DOI: 10.1093/nar/gkw930] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 01/18/2023] Open
Abstract
Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain (RsLOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of RsLOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, RsLOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.
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Affiliation(s)
- Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Ines Fonfara
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Boris Bouazza
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | | | - Majda Bratovič
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany
| | - Emmanuelle Charpentier
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany .,Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany
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Abstract
Sensory photoreceptors underpin optogenetics by mediating the noninvasive and reversible perturbation of living cells by light with unprecedented temporal and spatial resolution. Spurred by seminal optogenetic applications of natural photoreceptors, the engineering of photoreceptors has recently garnered wide interest and has led to the construction of a broad palette of novel light-regulated actuators. Photoreceptors are modularly built of photosensors that receive light signals, and of effectors that carry out specific cellular functions. These modules have to be precisely connected to allow efficient communication, such that light stimuli are relayed from photosensor to effector. The engineering of photoreceptors benefits from a thorough understanding of the underlying signaling mechanisms. This chapter gives a brief overview of key characteristics and signal-transduction mechanisms of sensory photoreceptors. Adaptation of these concepts in photoreceptor engineering has enabled the generation of novel optogenetic tools that greatly transcend the repertoire of natural photoreceptors.
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Affiliation(s)
- Thea Ziegler
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätstraße 30, Bldg. NW III, 95440, Bayreuth, 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, Universitätstraße 30, Bldg. NW III, 95440, Bayreuth, Germany.
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