101
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Vennin C, Herrmann D, Lucas MC, Timpson P. Intravital imaging reveals new ancillary mechanisms co-opted by cancer cells to drive tumor progression. F1000Res 2016; 5. [PMID: 27239290 PMCID: PMC4870995 DOI: 10.12688/f1000research.8090.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 12/15/2022] Open
Abstract
Intravital imaging is providing new insights into the dynamics of tumor progression in native tissues and has started to reveal the layers of complexity found in cancer. Recent advances in intravital imaging have allowed us to look deeper into cancer behavior and to dissect the interactions between tumor cells and the ancillary host niche that promote cancer development. In this review, we provide an insight into the latest advances in cancer biology achieved by intravital imaging, focusing on recently discovered mechanisms by which tumor cells manipulate normal tissue to facilitate disease progression.
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Affiliation(s)
- Claire Vennin
- The Kinghorn Cancer Centre, Cancer Division, The Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - David Herrmann
- The Kinghorn Cancer Centre, Cancer Division, The Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Morghan C Lucas
- The Kinghorn Cancer Centre, Cancer Division, The Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Paul Timpson
- The Kinghorn Cancer Centre, Cancer Division, The Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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102
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A bacterial phytochrome-based optogenetic system controllable with near-infrared light. Nat Methods 2016; 13:591-7. [PMID: 27159085 PMCID: PMC4927390 DOI: 10.1038/nmeth.3864] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 04/10/2016] [Indexed: 12/23/2022]
Abstract
Light-mediated control of protein-protein interactions to regulate metabolic pathways is an important approach of optogenetics. Here, we report the first optogenetic system based on a reversible light-induced binding between a bacterial phytochrome BphP1 and its natural partner PpsR2 from Rhodopseudomonas palustris bacteria. We extensively characterized the BphP1–PpsR2 interaction both in vitro and in mammalian cells, and then used it to translocate target proteins to specific cellular compartments, such as plasma membrane and nucleus. Applying this approach we achieved a light-control of cell morphology resulting in the substantial increase of cell area. We next demonstrated the light-induced gene expression with the 40-fold contrast in cultured cells, 32-fold subcutaneously and 5.7-fold in deep tissues in mice. The unique characteristics of the BphP1–PpsR2 optogenetic system are its sensitivity to 740–780 nm near-infrared light, ability to utilize an endogenous biliverdin chromophore in eukaryotes including mammals, and spectral compatibility with blue-light optogenetic systems.
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103
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Reichhart E, Ingles-Prieto A, Tichy AM, McKenzie C, Janovjak H. A Phytochrome Sensory Domain Permits Receptor Activation by Red Light. Angew Chem Int Ed Engl 2016; 55:6339-42. [PMID: 27101018 DOI: 10.1002/anie.201601736] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 12/31/2022]
Abstract
Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases-the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light.
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Affiliation(s)
- Eva Reichhart
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Alvaro Ingles-Prieto
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Alexandra-Madelaine Tichy
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Catherine McKenzie
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Harald Janovjak
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria.
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104
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Reichhart E, Ingles-Prieto A, Tichy AM, McKenzie C, Janovjak H. Eine Phytochrom-Sensordomäne ermöglicht eine Rezeptoraktivierung durch rotes Licht. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Eva Reichhart
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Alvaro Ingles-Prieto
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Alexandra-Madelaine Tichy
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Catherine McKenzie
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Harald Janovjak
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
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105
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Lee J, Papatzimas JW, Bromby AD, Gorobets E, Derksen DJ. Thiaporphyrin-mediated photocatalysis using red light. RSC Adv 2016. [DOI: 10.1039/c6ra11374e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Thiophene-containing porphyrin compounds are capable of catalytic, photo-reductive dehalogenation on an array of α-halo ketone model substrates with low catalyst loadings (0.1 mol%), in the presence of low energy, red light (>645 nm).
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Affiliation(s)
- JinGyu Lee
- Department of Chemistry
- University of Calgary
- 2500 University Drive NW
- Calgary
- Canada
| | - James W. Papatzimas
- Department of Chemistry
- University of Calgary
- 2500 University Drive NW
- Calgary
- Canada
| | - Ashley D. Bromby
- Department of Chemistry
- University of Calgary
- 2500 University Drive NW
- Calgary
- Canada
| | - Evgueni Gorobets
- Department of Chemistry
- University of Calgary
- 2500 University Drive NW
- Calgary
- Canada
| | - Darren J. Derksen
- Department of Chemistry
- University of Calgary
- 2500 University Drive NW
- Calgary
- Canada
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106
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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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107
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Ihalainen JA, Takala H, Lehtivuori H. Fast Photochemistry of Prototypical Phytochromes-A Species vs. Subunit Specific Comparison. Front Mol Biosci 2015; 2:75. [PMID: 26779488 PMCID: PMC4689126 DOI: 10.3389/fmolb.2015.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/07/2015] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are multi-domain red light photosensor proteins, which convert red light photons to biological activity utilizing the multitude of structural and chemical reactions. The steady increase in structural information obtained from various bacteriophytochromes has increased understanding about the functional mechanism of the photochemical processes of the phytochromes. Furthermore, a number of spectroscopic studies have revealed kinetic information about the light-induced reactions. The spectroscopic changes are, however, challenging to connect with the structural changes of the chromophore and the protein environment, as the excited state properties of the chromophores are very sensitive to the small structural and chemical changes of their environment. In this article, we concentrate on the results of ultra-fast spectroscopic experiments which reveal information about the important initial steps of the photoreactions of the phytochromes. We survey the excited state properties obtained during the last few decades. The differences in kinetics between different research laboratories are traditionally related to the differences of the studied species. However, we notice that the variation in the excited state properties depends on the subunit composition of the protein as well. This observation illustrates a feedback mechanism from the other domains to the chromophore. We propose that two feedback routes exist in phytochromes between the chromophore and the remotely located effector domain. The well-known connection between the subunits is the so-called tongue region, which changes its secondary structure while changing the light-activated state of the system. The other feedback route which we suggest is less obvious, it is made up of several water molecules ranging from the dimer interface to the vicinity of the chromophore, allowing even proton transfer reactions nearby the chromophore.
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Affiliation(s)
- Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Sciences, Nanoscience Center, University of JyväskyläJyväskylä, Finland; Department of Anatomy, Institute of Biomedicine, University of HelsinkiHelsinki, Finland
| | - Heli Lehtivuori
- Department of Biological and Environmental Sciences, Nanoscience Center, University of JyväskyläJyväskylä, Finland; Department of Physics, Nanoscience Center, University of JyväskyläJyväskylä, Finland
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108
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Richter F, Scheib US, Mehlhorn J, Schubert R, Wietek J, Gernetzki O, Hegemann P, Mathes T, Möglich A. Upgrading a microplate reader for photobiology and all-optical experiments. Photochem Photobiol Sci 2015; 14:270-9. [PMID: 25373866 DOI: 10.1039/c4pp00361f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Automation can vastly reduce the cost of experimental labor and thus facilitate high experimental throughput, but little off-the-shelf hardware for the automation of illumination experiments is commercially available. Here, we use inexpensive open-source electronics to add programmable illumination capabilities to a multimode microplate reader. We deploy this setup to characterize light-triggered phenomena in three different sensory photoreceptors. First, we study the photoactivation of Arabidopsis thaliana phytochrome B by light of different wavelengths. Second, we investigate the dark-state recovery kinetics of the Synechocystis sp. blue-light sensor Slr1694 at multiple temperatures and imidazole concentrations; while the kinetics of the W91F mutant of Slr1694 are strongly accelerated by imidazole, the wild-type protein is hardly affected. Third, we determine the light response of the Beggiatoa sp. photoactivatable adenylate cyclase bPAC in Chinese hamster ovary cells. bPAC is activated by blue light in dose-dependent manner with a half-maximal intensity of 0.58 mW cm(-2); intracellular cAMP spikes generated upon bPAC activation decay with a half time of about 5 minutes after light switch-off. Taken together, we present a setup which is easily assembled and which thus offers a facile approach to conducting illumination experiments at high throughput, reproducibility and fidelity.
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Affiliation(s)
- Florian Richter
- Humboldt-Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Berlin, Germany.
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109
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Boularan C, Gales C. Cardiac cAMP: production, hydrolysis, modulation and detection. Front Pharmacol 2015; 6:203. [PMID: 26483685 PMCID: PMC4589651 DOI: 10.3389/fphar.2015.00203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/03/2015] [Indexed: 01/04/2023] Open
Abstract
Cyclic adenosine 3′,5′-monophosphate (cAMP) modulates a broad range of biological processes including the regulation of cardiac myocyte contractile function where it constitutes the main second messenger for β-adrenergic receptors' signaling to fulfill positive chronotropic, inotropic and lusitropic effects. A growing number of studies pinpoint the role of spatial organization of the cAMP signaling as an essential mechanism to regulate cAMP outcomes in cardiac physiology. Here, we will briefly discuss the complexity of cAMP synthesis and degradation in the cardiac context, describe the way to detect it and review the main pharmacological arsenal to modulate its availability.
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Affiliation(s)
- Cédric Boularan
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale, U1048, Université Toulouse III Paul Sabatier Toulouse, France
| | - Céline Gales
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale, U1048, Université Toulouse III Paul Sabatier Toulouse, France
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110
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Beyer HM, Juillot S, Herbst K, Samodelov SL, Müller K, Schamel WW, Römer W, Schäfer E, Nagy F, Strähle U, Weber W, Zurbriggen MD. Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish. ACS Synth Biol 2015; 4:951-8. [PMID: 25803699 DOI: 10.1021/acssynbio.5b00004] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein trafficking in and out of the nucleus represents a key step in controlling cell fate and function. Here we report the development of a red light-inducible and far-red light-reversible synthetic system for controlling nuclear localization of proteins in mammalian cells and zebrafish. First, we synthetically reconstructed and validated the red light-dependent Arabidopsis phytochrome B nuclear import mediated by phytochrome-interacting factor 3 in a nonplant environment and support current hypotheses on the import mechanism in planta. On the basis of this principle we next regulated nuclear import and activity of target proteins by the spatiotemporal projection of light patterns. A synthetic transcription factor was translocated into the nucleus of mammalian cells and zebrafish to drive transgene expression. These data demonstrate the first in vivo application of a plant phytochrome-based optogenetic tool in vertebrates and expand the repertoire of available light-regulated molecular devices.
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Affiliation(s)
- Hannes M. Beyer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Samuel Juillot
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Kathrin Herbst
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology and University of Heidelberg, D-76344 Eggenstein-Leopoldshafen, Germany
- BIF-IGS − BioInterfaces International Graduate School, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sophia L. Samodelov
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Konrad Müller
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Wolfgang W. Schamel
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
- CCI, Centre
for Chronic Immunodeficiency, University Clinincs Freiburg, Breisacher
Strasse 117, 79106 Freiburg, Germany
| | - Winfried Römer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Eberhard Schäfer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Ferenc Nagy
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- Biological
Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Uwe Strähle
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology and University of Heidelberg, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Wilfried Weber
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
- ZBSA
− Centre for Biosystems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Matias D. Zurbriggen
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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111
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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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112
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Gao S, Nagpal J, Schneider MW, Kozjak-Pavlovic V, Nagel G, Gottschalk A. Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp. Nat Commun 2015; 6:8046. [PMID: 26345128 PMCID: PMC4569695 DOI: 10.1038/ncomms9046] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/11/2015] [Indexed: 12/28/2022] Open
Abstract
Cyclic GMP (cGMP) signalling regulates multiple biological functions through activation of protein kinase G and cyclic nucleotide-gated (CNG) channels. In sensory neurons, cGMP permits signal modulation, amplification and encoding, before depolarization. Here we implement a guanylyl cyclase rhodopsin from Blastocladiella emersonii as a new optogenetic tool (BeCyclOp), enabling rapid light-triggered cGMP increase in heterologous cells (Xenopus oocytes, HEK293T cells) and in Caenorhabditis elegans. Among five different fungal CyclOps, exhibiting unusual eight transmembrane topologies and cytosolic N-termini, BeCyclOp is the superior optogenetic tool (light/dark activity ratio: 5,000; no cAMP production; turnover (20 °C) ∼17 cGMP s−1). Via co-expressed CNG channels (OLF in oocytes, TAX-2/4 in C. elegans muscle), BeCyclOp photoactivation induces a rapid conductance increase and depolarization at very low light intensities. In O2/CO2 sensory neurons of C. elegans, BeCyclOp activation evokes behavioural responses consistent with their normal sensory function. BeCyclOp therefore enables precise and rapid optogenetic manipulation of cGMP levels in cells and animals. Cyclic guanosine monophosphate (cGMP) is a cellular second messenger involved in many processes including regulation of neuronal excitability and vascular tone. Gao, Nagpal et al., employ a fungal rhodopsin to optogenetically control cGMP levels in multiple systems including C. elegans sensory neurons.
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Affiliation(s)
- Shiqiang Gao
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Jatin Nagpal
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max von Laue Strasse 15, D-60438 Frankfurt, Germany.,Department for Biochemistry, Chemistry and Pharmacy, Institute of Biochemistry, Goethe University, Max von Laue Strasse 9, D-60438 Frankfurt, Germany
| | - Martin W Schneider
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max von Laue Strasse 15, D-60438 Frankfurt, Germany.,Department for Biochemistry, Chemistry and Pharmacy, Institute of Biochemistry, Goethe University, Max von Laue Strasse 9, D-60438 Frankfurt, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Biocenter, Julius-Maximilians-University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Georg Nagel
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max von Laue Strasse 15, D-60438 Frankfurt, Germany.,Department for Biochemistry, Chemistry and Pharmacy, Institute of Biochemistry, Goethe University, Max von Laue Strasse 9, D-60438 Frankfurt, Germany.,Cluster of Excellence Frankfurt-Macromolecular Complexes (CEF-MC), Goethe University, Max von Laue Strasse 15, D-60438 Frankfurt, Germany
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113
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Yang X, Montano S, Ren Z. How Does Photoreceptor UVR8 Perceive a UV-B Signal? Photochem Photobiol 2015; 91:993-1003. [PMID: 25996910 PMCID: PMC4560659 DOI: 10.1111/php.12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/06/2015] [Indexed: 11/30/2022]
Abstract
UVR8 is the only known plant photoreceptor that mediates light responses to UV-B (280-315 nm) of the solar spectrum. UVR8 perceives a UV-B signal via light-induced dimer dissociation, which triggers a wide range of cellular responses involved in photomorphogenesis and photoprotection. Two recent crystal structures of Arabidopsis thaliana UVR8 (AtUVR8) have revealed unusual clustering of UV-B-absorbing Trp pigments at the dimer interface and provided a structural framework for further mechanistic investigation. This review summarizes recent advances in spectroscopic, computational and crystallographic studies on UVR8 that are directed toward full understanding of UV-B perception at the molecular level.
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Affiliation(s)
- Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sherwin Montano
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
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114
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Anders K, Essen LO. The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Curr Opin Struct Biol 2015; 35:7-16. [PMID: 26241319 DOI: 10.1016/j.sbi.2015.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 11/17/2022]
Abstract
Bilin-dependent GAF domain photoreceptors cover the whole spectrum of light with their absorbance properties. They can be divided into three groups according to the domain architecture of their photosensory module. Group I and Group II harbor phytochromes with PAS-GAF-PHY and GAF-PHY domain architecture, respectively. Group III consists of stand-alone GAF domain photoreceptors, the cyanobacteriochromes. Crystal structures of all three groups are now available to shed light on possible downstream signaling pathways. Structures of Group I and III photoreceptors in both states display changes in the secondary structures during photoconversion. The knowledge about the photoconversion in phytochromes and CBCRs make them promising targets for applications in life science and synthetic biology.
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Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany.
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115
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Zhou XX, Pan M, Lin MZ. Investigating neuronal function with optically controllable proteins. Front Mol Neurosci 2015; 8:37. [PMID: 26257603 PMCID: PMC4508517 DOI: 10.3389/fnmol.2015.00037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/09/2015] [Indexed: 11/13/2022] Open
Abstract
In the nervous system, protein activities are highly regulated in space and time. This regulation allows for fine modulation of neuronal structure and function during development and adaptive responses. For example, neurite extension and synaptogenesis both involve localized and transient activation of cytoskeletal and signaling proteins, allowing changes in microarchitecture to occur rapidly and in a localized manner. To investigate the role of specific protein regulation events in these processes, methods to optically control the activity of specific proteins have been developed. In this review, we focus on how photosensory domains enable optical control over protein activity and have been used in neuroscience applications. These tools have demonstrated versatility in controlling various proteins and thereby cellular functions, and possess enormous potential for future applications in nervous systems. Just as optogenetic control of neuronal firing using opsins has changed how we investigate the function of cellular circuits in vivo, optical control may yet yield another revolution in how we study the circuitry of intracellular signaling in the brain.
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Affiliation(s)
- Xin X Zhou
- Department of Bioengineering, Stanford University Stanford, CA, USA
| | - Michael Pan
- Department of Pediatrics, Stanford University Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University Stanford, CA, USA ; Department of Pediatrics, Stanford University Stanford, CA, USA
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116
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O'Neill PR, Gautam N. Optimizing optogenetic constructs for control over signaling and cell behaviours. Photochem Photobiol Sci 2015; 14:1578-85. [PMID: 26135203 DOI: 10.1039/c5pp00171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Optogenetic tools have recently been developed that enable dynamic control over the activities of select signaling proteins. They provide the unique ability to rapidly turn signaling events on or off with subcellular control in living cells and organisms. This capability is leading to new insights into how the spatial and temporal coordination of signaling events governs dynamic cell behaviours such as migration and neurite outgrowth. These tools can also be used to dissect a protein's signaling functions at different organelles. Here we review the properties of photoreceptors from diverse organisms that have been leveraged to control signaling in mammalian cells. We emphasize recent engineering approaches that have been used to create optogenetic constructs with optimized spectral, kinetic, and signaling properties for controlling cell behaviours.
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Affiliation(s)
- P R O'Neill
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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117
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Lindner R, Heintz U, Winkler A. Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors. Front Mol Biosci 2015; 2:33. [PMID: 26157802 PMCID: PMC4477167 DOI: 10.3389/fmolb.2015.00033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors. This review focuses on the potential of hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools.
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Affiliation(s)
- Robert Lindner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology Graz, Austria
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118
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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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119
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Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation. Proc Natl Acad Sci U S A 2015; 112:8082-7. [PMID: 26080423 DOI: 10.1073/pnas.1504228112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that have diverse spectral properties and domain compositions. Although large numbers of CBCR genes exist in cyanobacterial genomes, no studies have assessed whether multiple CBCRs work together. We recently showed that the diguanylate cyclase (DGC) activity of the CBCR SesA from Thermosynechococcus elongatus is activated by blue-light irradiation and that, when irradiated, SesA, via its product cyclic dimeric GMP (c-di-GMP), induces aggregation of Thermosynechococcus vulcanus cells at a temperature that is suboptimum for single-cell viability. For this report, we first characterize the photobiochemical properties of two additional CBCRs, SesB and SesC. Blue/teal light-responsive SesB has only c-di-GMP phosphodiesterase (PDE) activity, which is up-regulated by teal light and GTP. Blue/green light-responsive SesC has DGC and PDE activities. Its DGC activity is enhanced by blue light, whereas its PDE activity is enhanced by green light. A ΔsesB mutant cannot suppress cell aggregation under teal-green light. A ΔsesC mutant shows a less sensitive cell-aggregation response to ambient light. ΔsesA/ΔsesB/ΔsesC shows partial cell aggregation, which is accompanied by the loss of color dependency, implying that a nonphotoresponsive DGC(s) producing c-di-GMP can also induce the aggregation. The results suggest that SesB enhances the light color dependency of cell aggregation by degrading c-di-GMP, is particularly effective under teal light, and, therefore, seems to counteract the induction of cell aggregation by SesA. In addition, SesC seems to improve signaling specificity as an auxiliary backup to SesA/SesB activities. The coordinated action of these three CBCRs highlights why so many different CBCRs exist.
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Narikawa R, Fushimi K, Ni-Ni-Win, Ikeuchi M. Red-shifted red/green-type cyanobacteriochrome AM1_1870g3 from the chlorophyll d-bearing cyanobacterium Acaryochloris marina. Biochem Biophys Res Commun 2015; 461:390-5. [DOI: 10.1016/j.bbrc.2015.04.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 12/23/2022]
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121
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Fan LZ, Lin MZ. Optical control of biological processes by light-switchable proteins. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:545-54. [PMID: 25858669 DOI: 10.1002/wdev.188] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/27/2015] [Accepted: 02/26/2015] [Indexed: 01/01/2023]
Abstract
Cellular processes such as proliferation, differentiation, or migration depend on precise spatiotemporal coordination of protein activities. Correspondingly, reaching a quantitative understanding of cellular behavior requires experimental approaches that enable spatial and temporal modulation of protein activity. Recently, a variety of light-sensitive protein domains have been engineered as optogenetic actuators to spatiotemporally control protein activity. In the present review, we discuss the principle of these optical control methods and examples of their applications in modulating signaling pathways. By controlling protein activity with spatiotemporal specificity, tunable dynamics, and quantitative control, light-controllable proteins promise to accelerate our understanding of cellular and organismal biology.
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Affiliation(s)
- Linlin Z Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Pediatrics, Stanford University, Stanford, CA, USA
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122
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Shcherbakova DM, Shemetov AA, Kaberniuk AA, Verkhusha VV. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu Rev Biochem 2015; 84:519-50. [PMID: 25706899 DOI: 10.1146/annurev-biochem-060614-034411] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. Natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. Here, we give a brief overview of natural photoreceptors and their mechanisms of action. We then discuss fluorescent proteins and biosensors developed from light-oxygen-voltage-sensing (LOV) domains and phytochromes, as well as their properties and applications. These fluorescent tools possess unique characteristics not achievable with green fluorescent protein-like probes, including near-infrared fluorescence, independence of oxygen, small size, and photosensitizer activity. We next provide an overview of available optogenetic tools of various origins, such as LOV and BLUF (blue-light-utilizing flavin adenine dinucleotide) domains, cryptochromes, and phytochromes, enabling control of versatile cellular processes. We analyze the principles of their function and practical requirements for use. We focus mainly on optical tools with demonstrated use beyond bacteria, with a specific emphasis on their applications in mammalian cells.
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Affiliation(s)
- Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;
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123
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Schmidt D, Cho YK. Natural photoreceptors and their application to synthetic biology. Trends Biotechnol 2015; 33:80-91. [DOI: 10.1016/j.tibtech.2014.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/19/2014] [Accepted: 10/20/2014] [Indexed: 01/22/2023]
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Jansen V, Alvarez L, Balbach M, Strünker T, Hegemann P, Kaupp UB, Wachten D. Controlling fertilization and cAMP signaling in sperm by optogenetics. eLife 2015; 4. [PMID: 25601414 PMCID: PMC4298566 DOI: 10.7554/elife.05161] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/22/2014] [Indexed: 12/18/2022] Open
Abstract
Optogenetics is a powerful technique to control cellular activity by light. The light-gated Channelrhodopsin has been widely used to study and manipulate neuronal activity in vivo, whereas optogenetic control of second messengers in vivo has not been examined in depth. In this study, we present a transgenic mouse model expressing a photoactivated adenylyl cyclase (bPAC) in sperm. In transgenic sperm, bPAC mimics the action of the endogenous soluble adenylyl cyclase (SACY) that is required for motility and fertilization: light-stimulation rapidly elevates cAMP, accelerates the flagellar beat, and, thereby, changes swimming behavior of sperm. Furthermore, bPAC replaces endogenous adenylyl cyclase activity. In mutant sperm lacking the bicarbonate-stimulated SACY activity, bPAC restored motility after light-stimulation and, thereby, enabled sperm to fertilize oocytes in vitro. We show that optogenetic control of cAMP in vivo allows to non-invasively study cAMP signaling, to control behaviors of single cells, and to restore a fundamental biological process such as fertilization. DOI:http://dx.doi.org/10.7554/eLife.05161.001 Tiny hair-like structures called cilia on the outside of cells play many important roles, including detecting physical and chemical signals from the environment. Special cilia—called flagella—help cells to move around and perhaps the most well-known of these are sperm flagella, which propel sperm in their quest to fertilize the egg. A chemical messenger called cAMP is essential for the movement of sperm flagella. When a sperm cell enters the female reproductive tract, an enzyme called SACY is activated. Within seconds, SACY produces cAMP and, thereby, causes the flagella to beat faster so that the sperm cell speeds toward the egg. cAMP also controls sperm maturation, which is needed to penetrate the egg. However, the precise details of the role of cAMP in sperm cells are not clear. Here, Jansen et al. have investigated this role using a cutting-edge technique—called optogenetics—that was originally developed to study brain cells in living organisms. Jansen et al. genetically engineered a mouse so that exposing sperm to blue light activates a light-sensitive enzyme called bPAC that increases cAMP levels in sperm. In these mice, the activation of bPAC by light accelerated the beating of the flagella so the sperm moved faster, in a way that was similar to the effects that are normally observed after the activation of the SACY enzyme. In mice lacking among other things the SACY enzyme—whose sperm cells are unable to move or fertilize an egg—activating the light-sensitive bPAC enzyme restored sperm motility and enabled the sperm to fertilize an egg. These results show that optogenetics may be a useful tool for studying how flagella and other types of cilia work. DOI:http://dx.doi.org/10.7554/eLife.05161.002
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Affiliation(s)
- Vera Jansen
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Luis Alvarez
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Melanie Balbach
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Timo Strünker
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, Berlin, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Dagmar Wachten
- Minerva Research Group Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
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125
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Mathes T, Ravensbergen J, Kloz M, Gleichmann T, Gallagher KD, Woitowich NC, St Peter R, Kovaleva SE, Stojković EA, Kennis JTM. Femto- to Microsecond Photodynamics of an Unusual Bacteriophytochrome. J Phys Chem Lett 2015; 6:239-43. [PMID: 26263456 DOI: 10.1021/jz502408n] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A bacteriophytochrome from Stigmatella aurantiaca is an unusual member of the bacteriophytochrome family that is devoid of hydrogen bonding to the carbonyl group of ring D of the biliverdin (BV) chromophore. The photodynamics of BV in SaBphP1 wild type and the single mutant T289H reintroducing hydrogen bonding to ring D show that the strength of this particular weak interaction determines excited-state lifetime, Lumi-R quantum yield, and spectral heterogeneity. In particular, excited-state decay is faster in the absence of hydrogen-bonding to ring D, with excited-state half-lives of 30 and 80 ps for wild type and the T289H mutant, respectively. Concomitantly, the Lumi-R quantum yield is two times higher in wild type as compared with the T289H mutant. Furthermore, the spectral heterogeneity in the wild type is significantly higher than that in the T289H mutant. By extending the observable time domain to 25 μs, we observe a new deactivation pathway from the Lumi-R intermediate in the 100 ns time domain that corresponds to a backflip of ring D to the original Pr 15Za isomeric state.
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Affiliation(s)
- Tilo Mathes
- †Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Janneke Ravensbergen
- †Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Miroslav Kloz
- †Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Tobias Gleichmann
- †Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Kevin D Gallagher
- ‡Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Nicole C Woitowich
- ‡Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Rachael St Peter
- ‡Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Svetlana E Kovaleva
- ‡Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Emina A Stojković
- ‡Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - John T M Kennis
- †Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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126
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Burgie ES, Vierstra RD. Phytochromes: an atomic perspective on photoactivation and signaling. THE PLANT CELL 2014; 26:4568-83. [PMID: 25480369 PMCID: PMC4311201 DOI: 10.1105/tpc.114.131623] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/10/2014] [Accepted: 11/14/2014] [Indexed: 05/19/2023]
Abstract
The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents.
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Affiliation(s)
- E Sethe Burgie
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
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127
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Karunarathne WKA, O'Neill PR, Gautam N. Subcellular optogenetics - controlling signaling and single-cell behavior. J Cell Sci 2014; 128:15-25. [PMID: 25433038 DOI: 10.1242/jcs.154435] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Variation in signaling activity across a cell plays a crucial role in processes such as cell migration. Signaling activity specific to organelles within a cell also likely plays a key role in regulating cellular functions. To understand how such spatially confined signaling within a cell regulates cell behavior, tools that exert experimental control over subcellular signaling activity are required. Here, we discuss the advantages of using optogenetic approaches to achieve this control. We focus on a set of optical triggers that allow subcellular control over signaling through the activation of G-protein-coupled receptors (GPCRs), receptor tyrosine kinases and downstream signaling proteins, as well as those that inhibit endogenous signaling proteins. We also discuss the specific insights with regard to signaling and cell behavior that these subcellular optogenetic approaches can provide.
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Affiliation(s)
- W K Ajith Karunarathne
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Patrick R O'Neill
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Narasimhan Gautam
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
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128
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Survival strategies in the aquatic and terrestrial world: the impact of second messengers on cyanobacterial processes. Life (Basel) 2014; 4:745-69. [PMID: 25411927 PMCID: PMC4284465 DOI: 10.3390/life4040745] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/31/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022] Open
Abstract
Second messengers are intracellular substances regulated by specific external stimuli globally known as first messengers. Cells rely on second messengers to generate rapid responses to environmental changes and the importance of their roles is becoming increasingly realized in cellular signaling research. Cyanobacteria are photooxygenic bacteria that inhabit most of Earth's environments. The ability of cyanobacteria to survive in ecologically diverse habitats is due to their capacity to adapt and respond to environmental changes. This article reviews known second messenger-controlled physiological processes in cyanobacteria. Second messengers used in these systems include the element calcium (Ca2+), nucleotide-based guanosine tetraphosphate or pentaphosphate (ppGpp or pppGpp, represented as (p)ppGpp), cyclic adenosine 3',5'-monophosphate (cAMP), cyclic dimeric GMP (c-di-GMP), cyclic guanosine 3',5'-monophosphate (cGMP), and cyclic dimeric AMP (c-di-AMP), and the gaseous nitric oxide (NO). The discussion focuses on processes central to cyanobacteria, such as nitrogen fixation, light perception, photosynthesis-related processes, and gliding motility. In addition, we address future research trajectories needed to better understand the signaling networks and cross talk in the signaling pathways of these molecules in cyanobacteria. Second messengers have significant potential to be adapted as technological tools and we highlight possible novel and practical applications based on our understanding of these molecules and the signaling networks that they control.
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129
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Folcher M, Oesterle S, Zwicky K, Thekkottil T, Heymoz J, Hohmann M, Christen M, Daoud El-Baba M, Buchmann P, Fussenegger M. Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant. Nat Commun 2014; 5:5392. [PMID: 25386727 PMCID: PMC4241983 DOI: 10.1038/ncomms6392] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/26/2014] [Indexed: 12/21/2022] Open
Abstract
Synthetic devices for traceless remote control of gene expression may provide new treatment opportunities in future gene- and cell-based therapies. Here we report the design of a synthetic mind-controlled gene switch that enables human brain activities and mental states to wirelessly programme the transgene expression in human cells. An electroencephalography (EEG)-based brain–computer interface (BCI) processing mental state-specific brain waves programs an inductively linked wireless-powered optogenetic implant containing designer cells engineered for near-infrared (NIR) light-adjustable expression of the human glycoprotein SEAP (secreted alkaline phosphatase). The synthetic optogenetic signalling pathway interfacing the BCI with target gene expression consists of an engineered NIR light-activated bacterial diguanylate cyclase (DGCL) producing the orthogonal second messenger cyclic diguanosine monophosphate (c-di-GMP), which triggers the stimulator of interferon genes (STING)-dependent induction of synthetic interferon-β promoters. Humans generating different mental states (biofeedback control, concentration, meditation) can differentially control SEAP production of the designer cells in culture and of subcutaneous wireless-powered optogenetic implants in mice. Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al. couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery.
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Affiliation(s)
- Marc Folcher
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Sabine Oesterle
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Katharina Zwicky
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Thushara Thekkottil
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Julie Heymoz
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Muriel Hohmann
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Matthias Christen
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marie Daoud El-Baba
- Département Génie Biologique, Institut Universitaire de Technologie (IUTA), 74 Boulevard Niels Bohr, F-69622 Villeurbanne, France
| | - Peter Buchmann
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- 1] Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland [2] Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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Weitzman M, Hahn KM. Optogenetic approaches to cell migration and beyond. Curr Opin Cell Biol 2014; 30:112-20. [PMID: 25216352 DOI: 10.1016/j.ceb.2014.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 07/29/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
Optogenetics, the use of genetically encoded tools to control protein function with light, can generate localized changes in signaling within living cells and animals. For years it has been focused on channel proteins for neurobiology, but has recently expanded to cover many different types of proteins, using a broad array of different protein engineering approaches. These methods have largely been directed at proteins involved in motility, cytoskeletal regulation and gene expression. This review provides a survey of non-channel proteins that have been engineered for optogenetics. Existing molecules are used to illustrate the advantages and disadvantages of the many imaginative new approaches that the reader can use to create light-controlled proteins.
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Affiliation(s)
- Matthew Weitzman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Beyer HM, Naumann S, Weber W, Radziwill G. Optogenetic control of signaling in mammalian cells. Biotechnol J 2014; 10:273-83. [DOI: 10.1002/biot.201400077] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/16/2014] [Accepted: 08/13/2014] [Indexed: 11/08/2022]
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