51
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Caged oligonucleotides for studying biological systems. J Inorg Biochem 2015; 150:182-8. [PMID: 25865001 DOI: 10.1016/j.jinorgbio.2015.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/08/2023]
Abstract
Light-activated ("caged") compounds have been widely employed for studying biological processes with high spatial and temporal control. In the past decade, several new approaches for caging the structure and function of DNA and RNA oligonucleotides have been developed. This review focuses on caged oligonucleotides that incorporate site-specifically one or two photocleavable linkers, whose photolysis yields oligonucleotides with dramatic structural and functional changes. This technique has been employed by our laboratory and others to photoregulate gene expression in cells and living organisms, typically using near UV-activated organic chromophores. To improve capabilities for in vivo studies, we harnessed the rich inorganic photochemistry of ruthenium bipyridyl complexes to synthesize Ru-caged morpholino antisense oligonucleotides that remain inactive in zebrafish embryos until uncaged with visible light. Expanding into new caged oligonucleotide applications, our lab has developed Transcriptome In Vivo Analysis (TIVA) technology, which provides the first noninvasive, unbiased method for isolating mRNA from single neurons in brain tissues. TIVA-isolated mRNA can be amplified and then analyzed using next-generation sequencing (RNA-seq).
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52
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Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins. Nat Commun 2015; 6:6256. [PMID: 25708714 DOI: 10.1038/ncomms7256] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/09/2015] [Indexed: 12/24/2022] Open
Abstract
Optogenetic methods take advantage of photoswitches to control the activity of cellular proteins. Here, we completed a multi-directional engineering of the fungal photoreceptor Vivid to develop pairs of distinct photoswitches named Magnets. These new photoswitches were engineered to recognize each other based on the electrostatic interactions, thus preventing homodimerization and enhancing light-induced heterodimerization. Furthermore, we tuned the switch-off kinetics by four orders of magnitude and developed several variants, including those with substantially faster kinetics than any of the other conventional dimerization-based blue spectrum photoswitches. We demonstrate the utility of Magnets as powerful tools that can optogenetically manipulate molecular processes in biological systems.
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53
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UVB-based optogenetic tools. Trends Biotechnol 2015; 33:59-61. [DOI: 10.1016/j.tibtech.2014.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/20/2022]
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54
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Müller K, Naumann S, Weber W, Zurbriggen MD. Optogenetics for gene expression in mammalian cells. Biol Chem 2015; 396:145-52. [DOI: 10.1515/hsz-2014-0199] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/29/2014] [Indexed: 12/14/2022]
Abstract
Abstract
Molecular switches that are controlled by chemicals have evolved as central research instruments in mammalian cell biology. However, these tools are limited in terms of their spatiotemporal resolution due to freely diffusing inducers. These limitations have recently been addressed by the development of optogenetic, genetically encoded, and light-responsive tools that can be controlled with the unprecedented spatiotemporal precision of light. In this article, we first provide a brief overview of currently available optogenetic tools that have been designed to control diverse cellular processes. Then, we focus on recent developments in light-controlled gene expression technologies and provide the reader with a guideline for choosing the most suitable gene expression system.
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55
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Rockwell NC, Martin SS, Lagarias JC. Identification of DXCF cyanobacteriochrome lineages with predictable photocycles. Photochem Photobiol Sci 2015; 14:929-41. [DOI: 10.1039/c4pp00486h] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two specialized subgroups of cyanobacteriochromes with predictable green/blue and blue/orange photocycles are defined by these studies.
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Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
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56
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Abstract
The coupling of light-inducible protein-protein interactions with gene regulation systems has enabled the control of gene expression with light. In particular, heterodimer protein pairs from plants can be used to engineer a gene regulation system in mammalian cells that is reversible, repeatable, tunable, controllable in a spatiotemporal manner, and targetable to any DNA sequence. This system, Light-Inducible Transcription using Engineered Zinc finger proteins (LITEZ), is based on the blue light-induced interaction of GIGANTEA and the LOV domain of FKF1 that drives the localization of a transcriptional activator to the DNA-binding site of a highly customizable engineered zinc finger protein. This chapter provides methods for modifying LITEZ to target new DNA sequences, engineering a programmable LED array to illuminate cell cultures, and using the modified LITEZ system to achieve spatiotemporal control of transgene expression in mammalian cells.
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Affiliation(s)
- Lauren R Polstein
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, 90281, Durham, NC, 27708-0281, USA
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57
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Ryu MH, Gomelsky M. Near-infrared light responsive synthetic c-di-GMP module for optogenetic applications. ACS Synth Biol 2014; 3:802-10. [PMID: 24926804 PMCID: PMC4277780 DOI: 10.1021/sb400182x] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Enormous
potential of cell-based therapeutics is hindered by the
lack of effective means to control genetically engineered cells in
mammalian tissues. Here, we describe a synthetic module for remote
photocontrol of engineered cells that can be adapted for such applications.
The module involves photoactivated synthesis of cyclic dimeric GMP
(c-di-GMP), a stable small molecule that is not produced by higher
eukaryotes and therefore is suitable for orthogonal regulation. The
key component of the photocontrol module is an engineered bacteriophytochrome
diguanylate cyclase, which synthesizes c-di-GMP from GTP in a light-dependent
manner. Bacteriophytochromes are particularly attractive photoreceptors
because they respond to light in the near-infrared window of the spectrum,
where absorption by mammalian tissues is minimal, and also because
their chromophore, biliverdin IXα, is naturally available in
mammalian cells. The second component of the photocontrol module,
a c-di-GMP phosphodiesterase, maintains near-zero background levels
of c-di-GMP in the absence of light, which enhances the photodynamic
range of c-di-GMP concentrations. In the E. coli model
used in this study, the intracellular c-di-GMP levels could be upregulated
by light by >50-fold. Various c-di-GMP-responsive proteins and
riboswitches
identified in bacteria can be linked downstream of the c-di-GMP-mediated
photocontrol module for orthogonal regulation of biological activities
in mammals as well as in other organisms lacking c-di-GMP signaling.
Here, we linked the photocontrol module to a gene expression output
via a c-di-GMP-responsive transcription factor and achieved a 40-fold
photoactivation of gene expression.
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Affiliation(s)
- Min-Hyung Ryu
- Department of Molecular Biology, University of Wyoming, 1000 East
University Avenue, Dept. 3944, Laramie, Wyoming 82071, United States
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, 1000 East
University Avenue, Dept. 3944, Laramie, Wyoming 82071, United States
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58
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Müller K, Engesser R, Timmer J, Zurbriggen MD, Weber W. Orthogonal optogenetic triple-gene control in Mammalian cells. ACS Synth Biol 2014; 3:796-801. [PMID: 25343333 DOI: 10.1021/sb500305v] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Optogenetic gene switches allow gene expression control at an unprecedented spatiotemporal resolution. Recently, light-responsive transgene expression systems that are activated by UV-B, blue, or red light have been developed. These systems perform well on their own, but their integration into genetic networks has been hampered by the overlapping absorbance spectra of the photoreceptors. We identified a lack of orthogonality between UV-B and blue light-controlled gene expression as the bottleneck and employed a model-based approach that identified the need for a blue light-responsive gene switch that is insensitive to low-intensity light. Based on this prediction, we developed a blue light-responsive and rapidly reversible expression system. Finally, we employed this expression system to demonstrate orthogonality between UV-B, blue, and red/far-red light-responsive gene switches in a single mammalian cell culture. We expect this approach to enable the spatiotemporal control of gene networks and to expand the applications of optogenetics in synthetic biology.
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Affiliation(s)
- Konrad Müller
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Raphael Engesser
- Institute
of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
- BIOSS
Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Jens Timmer
- Institute
of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
- BIOSS
Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Freiburg
Centre for Biosystems Analysis (ZBSA), 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
| | - 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
- Freiburg
Centre for Biosystems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse
49, 79104 Freiburg, Germany
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59
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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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60
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Grusch M, Schelch K, Riedler R, Reichhart E, Differ C, Berger W, Inglés-Prieto Á, Janovjak H. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO J 2014; 33:1713-26. [PMID: 24986882 DOI: 10.15252/embj.201387695] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour.
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Affiliation(s)
- Michael Grusch
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Karin Schelch
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Robert Riedler
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Eva Reichhart
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Christopher Differ
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Álvaro Inglés-Prieto
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Harald Janovjak
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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61
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Müller K, Siegel D, Rodriguez Jahnke F, Gerrer K, Wend S, Decker EL, Reski R, Weber W, Zurbriggen MD. A red light-controlled synthetic gene expression switch for plant systems. MOLECULAR BIOSYSTEMS 2014; 10:1679-88. [PMID: 24469598 DOI: 10.1039/c3mb70579j] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens.
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Affiliation(s)
- Konrad Müller
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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62
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Abstract
Bacteriophytochromes sense light in the near-infrared window, the spectral region where absorption by mammalian tissues is minimal, and their chromophore, biliverdin IXα, is naturally present in animal cells. These properties make bacteriophytochromes particularly attractive for optogenetic applications. However, the lack of understanding of how light-induced conformational changes control output activities has hindered engineering of bacteriophytochrome-based optogenetic tools. Many bacteriophytochromes function as homodimeric enzymes, in which light-induced conformational changes are transferred via α-helical linkers to the rigid output domains. We hypothesized that heterologous output domains requiring homodimerization can be fused to the photosensory modules of bacteriophytochromes to generate light-activated fusions. Here, we tested this hypothesis by engineering adenylate cyclases regulated by light in the near-infrared spectral window using the photosensory module of the Rhodobacter sphaeroides bacteriophytochrome BphG1 and the adenylate cyclase domain from Nostoc sp. CyaB1. We engineered several light-activated fusion proteins that differed from each other by approximately one or two α-helical turns, suggesting that positioning of the output domains in the same phase of the helix is important for light-dependent activity. Extensive mutagenesis of one of these fusions resulted in an adenylate cyclase with a sixfold photodynamic range. Additional mutagenesis produced an enzyme with a more stable photoactivated state. When expressed in cholinergic neurons in Caenorhabditis elegans, the engineered adenylate cyclase affected worm behavior in a light-dependent manner. The insights derived from this study can be applied to the engineering of other homodimeric bacteriophytochromes, which will further expand the optogenetic toolset.
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63
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Wend S, Wagner HJ, Müller K, Zurbriggen MD, Weber W, Radziwill G. Optogenetic control of protein kinase activity in mammalian cells. ACS Synth Biol 2014; 3:280-5. [PMID: 24090449 DOI: 10.1021/sb400090s] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light-dependent dimerization is the basis for recently developed noninvasive optogenetic tools. Here we present a novel tool combining optogenetics with the control of protein kinase activity to investigate signal transduction pathways. Mediated by Arabidopsis thaliana photoreceptor cryptochrome 2, we activated the protein kinase C-RAF by blue light-dependent dimerization, allowing for decoupling from upstream signaling events induced by surface receptors. The activation by light is fast, reversible, and not only time but also dose dependent as monitored by phosphorylation of ERK1/2. Additionally, light-activated C-RAF controls serum response factor-mediated gene expression. Light-induced heterodimerization of C-RAF with a kinase-dead mutant of B-RAF demonstrates the enhancing role of B-RAF as a scaffold for C-RAF activity, which leads to the paradoxical activation of C-RAF found in human cancers. This optogenetic tool enables reversible control of protein kinase activity in signal duration and strength. These properties can help to shed light onto downstream signaling processes of protein kinases in living cells.
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Affiliation(s)
- Sabrina Wend
- Faculty
of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann
Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Hanna J. Wagner
- Faculty
of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Konrad Müller
- Faculty
of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Wilfried Weber
- Faculty
of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann
Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- BIOSS
Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty
of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS
Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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64
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Rockwell NC, Martin SS, Gulevich AG, Lagarias JC. Conserved Phenylalanine Residues Are Required for Blue-Shifting of Cyanobacteriochrome Photoproducts. Biochemistry 2014; 53:3118-30. [DOI: 10.1021/bi500037a] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Alexander G. Gulevich
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
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65
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Optobiology: optical control of biological processes via protein engineering. Biochem Soc Trans 2014; 41:1183-8. [PMID: 24059506 DOI: 10.1042/bst20130150] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enabling optical control over biological processes is a defining goal of the new field of optogenetics. Control of membrane voltage by natural rhodopsin family ion channels has found widespread acceptance in neuroscience, due to the fact that these natural proteins control membrane voltage without further engineering. In contrast, optical control of intracellular biological processes has been a fragmented effort, with various laboratories engineering light-responsive properties into proteins in different manners. In the present article, we review the various systems that have been developed for controlling protein functions with light based on vertebrate rhodopsins, plant photoregulatory proteins and, most recently, the photoswitchable fluorescent protein Dronpa. By allowing biology to be controlled with spatiotemporal specificity and tunable dynamics, light-controllable proteins will find applications in the understanding of cellular and organismal biology and in synthetic biology.
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66
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Müller K, Engesser R, Timmer J, Nagy F, Zurbriggen MD, Weber W. Synthesis of phycocyanobilin in mammalian cells. Chem Commun (Camb) 2014; 49:8970-2. [PMID: 23963496 DOI: 10.1039/c3cc45065a] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromophore 3-Z phycocyanobilin (PCB, (2R,3Z)-8,12-bis(2-carboxyethyl)-18-ethyl-3-ethylidene-2,7,13,17-tetramethyl-2,3-dihydrobilin-1,19(21H,24H)-dione) mediates red and far-red light perception in natural and synthetic biological systems. Here we describe a PCB synthesis strategy in mammalian cells. We optimize the production by co-localizing the biocatalysts to the substrate source, by coordinating the availability of the biocatalysts and by reducing the degradation of the reaction product. We show that the resulting PCB levels of 2 μM are sufficient to sustain the functionality of red light-responsive optogenetic tools suitable for the light-inducible control of gene expression in mammalian cells.
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Affiliation(s)
- Konrad Müller
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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67
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Nihongaki Y, Suzuki H, Kawano F, Sato M. Genetically engineered photoinducible homodimerization system with improved dimer-forming efficiency. ACS Chem Biol 2014; 9:617-21. [PMID: 24428544 DOI: 10.1021/cb400836k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Vivid (VVD) is a photoreceptor derived from Neurospora Crassa that rapidly forms a homodimer in response to blue light. Although VVD has several advantages over other photoreceptors as photoinducible homodimerization system, VVD has a critical limitation in its low dimer-forming efficiency. To overcome this limitation of wild-type VVD, here we conduct site-directed saturation mutagenesis in the homodimer interface of VVD. We have found that the Ile52Cys mutation of VVD (VVD-52C) substantially improves its homodimer-forming efficiency up to 180%. We have demonstrated the utility of VVD-52C for making a light-inducible gene expression system more robust. In addition, using VVD-52C, we have developed photoactivatable caspase-9, which enables optical control of apoptosis of mammalian cells. The present genetically engineered photoinducible homodimerization system can provide a powerful tool to optically control a broad range of molecular processes in the cell.
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Affiliation(s)
- Yuta Nihongaki
- Graduate
School of Arts and
Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hideyuki Suzuki
- Graduate
School of Arts and
Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Fuun Kawano
- Graduate
School of Arts and
Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Moritoshi Sato
- Graduate
School of Arts and
Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
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68
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Müller K, Zurbriggen MD, Weber W. Control of gene expression using a red- and far-red light–responsive bi-stable toggle switch. Nat Protoc 2014; 9:622-32. [DOI: 10.1038/nprot.2014.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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69
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Kawano F, Aono Y, Suzuki H, Sato M. Fluorescence imaging-based high-throughput screening of fast- and slow-cycling LOV proteins. PLoS One 2013; 8:e82693. [PMID: 24367542 PMCID: PMC3867380 DOI: 10.1371/journal.pone.0082693] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 11/04/2013] [Indexed: 12/05/2022] Open
Abstract
Light-oxygen-voltage (LOV) domains function as blue light-inducible molecular switches. The photosensory LOV domains derived from plants and fungi have provided an indispensable tool for optogenetics. Here we develop a high-throughput screening system to efficiently improve switch-off kinetics of LOV domains. The present system is based on fluorescence imaging of thermal reversion of a flavin cofactor bound to LOV domains. We conducted multi site-directed random mutagenesis of seven amino acid residues surrounding the flavin cofactor of the second LOV domain derived from Avena sativa phototropin 1 (AsLOV2). The gene library was introduced into Escherichia coli cells. Then thermal reversion of AsLOV2 variants, respectively expressed in different bacterial colonies on agar plate, was imaged with a stereoscopic fluorescence microscope. Based on the mutagenesis and imaging-based screening, we isolated 12 different variants showing substantially faster thermal reversion kinetics than wild-type AsLOV2. Among them, AsLOV2-V416T exhibited thermal reversion with a time constant of 2.6 s, 21-fold faster than wild-type AsLOV2. With a slight modification of the present approach, we also have efficiently isolated 8 different decelerated variants, represented by AsLOV2-V416L that exhibited thermal reversion with a time constant of 4.3×103 s (78-fold slower than wild-type AsLOV2). The present approach based on fluorescence imaging of the thermal reversion of the flavin cofactor is generally applicable to a variety of blue light-inducible molecular switches and may provide a new opportunity for the development of molecular tools for emerging optogenetics.
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Affiliation(s)
- Fuun Kawano
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Yuki Aono
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Hideyuki Suzuki
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
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70
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71
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Tilbrook K, Arongaus AB, Binkert M, Heijde M, Yin R, Ulm R. The UVR8 UV-B Photoreceptor: Perception, Signaling and Response. THE ARABIDOPSIS BOOK 2013; 11:e0164. [PMID: 23864838 PMCID: PMC3711356 DOI: 10.1199/tab.0164] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ultraviolet-B radiation (UV-B) is an intrinsic part of sunlight that is accompanied by significant biological effects. Plants are able to perceive UV-B using the UV-B photoreceptor UVR8 which is linked to a specific molecular signaling pathway and leads to UV-B acclimation. Herein we review the biological process in plants from initial UV-B perception and signal transduction through to the known UV-B responses that promote survival in sunlight. The UVR8 UV-B photoreceptor exists as a homodimer that instantly monomerises upon UV-B absorption via specific intrinsic tryptophans which act as UV-B chromophores. The UVR8 monomer interacts with COP1, an E3 ubiquitin ligase, initiating a molecular signaling pathway that leads to gene expression changes. This signaling output leads to UVR8-dependent responses including UV-B-induced photomorphogenesis and the accumulation of UV-B-absorbing flavonols. Negative feedback regulation of the pathway is provided by the WD40-repeat proteins RUP1 and RUP2, which facilitate UVR8 redimerization, disrupting the UVR8-COP1 interaction. Despite rapid advancements in the field of recent years, further components of UVR8 UV-B signaling are constantly emerging, and the precise interplay of these and the established players UVR8, COP1, RUP1, RUP2 and HY5 needs to be defined. UVR8 UV-B signaling represents our further understanding of how plants are able to sense their light environment and adjust their growth accordingly.
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Affiliation(s)
- Kimberley Tilbrook
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Adriana B. Arongaus
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Melanie Binkert
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Marc Heijde
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Ruohe Yin
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
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Müller K, Engesser R, Schulz S, Steinberg T, Tomakidi P, Weber CC, Ulm R, Timmer J, Zurbriggen MD, Weber W. Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Res 2013; 41:e124. [PMID: 23625964 PMCID: PMC3695509 DOI: 10.1093/nar/gkt340] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The emergence and future of mammalian synthetic biology depends on technologies for orchestrating and custom tailoring complementary gene expression and signaling processes in a predictable manner. Here, we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths. To this end, we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1. The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells. Based on a quantitative model, we determined critical system parameters. By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes. This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
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Affiliation(s)
- Konrad Müller
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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