1
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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2
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Li X, Hou W, Lei J, Chen H, Wang Q. The Unique Light-Harvesting System of the Algal Phycobilisome: Structure, Assembly Components, and Functions. Int J Mol Sci 2023; 24:ijms24119733. [PMID: 37298688 DOI: 10.3390/ijms24119733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
The phycobilisome (PBS) is the major light-harvesting apparatus in cyanobacteria and red algae. It is a large multi-subunit protein complex of several megadaltons that is found on the stromal side of thylakoid membranes in orderly arrays. Chromophore lyases catalyse the thioether bond between apoproteins and phycobilins of PBSs. Depending on the species, composition, spatial assembly, and, especially, the functional tuning of different phycobiliproteins mediated by linker proteins, PBSs can absorb light between 450 and 650 nm, making them efficient and versatile light-harvesting systems. However, basic research and technological innovations are needed, not only to understand their role in photosynthesis but also to realise the potential applications of PBSs. Crucial components including phycobiliproteins, phycobilins, and lyases together make the PBS an efficient light-harvesting system, and these provide a scheme to explore the heterologous synthesis of PBS. Focusing on these topics, this review describes the essential components needed for PBS assembly, the functional basis of PBS photosynthesis, and the applications of phycobiliproteins. Moreover, key technical challenges for heterologous biosynthesis of phycobiliproteins in chassis cells are discussed.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wenwen Hou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jiaxi Lei
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475001, China
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3
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Oda S, Sato-Ebine E, Nakamura A, Kimura KD, Aoki K. Optical Control of Cell Signaling with Red/Far-Red Light-Responsive Optogenetic Tools in Caenorhabditis elegans. ACS Synth Biol 2023; 12:700-708. [PMID: 36802521 DOI: 10.1021/acssynbio.2c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Optogenetic techniques have been intensively applied to the nematode Caenorhabditis elegans to investigate its neural functions. However, as most of these optogenetics are responsive to blue light and the animal exhibits avoidance behavior to blue light, the application of optogenetic tools responsive to longer wavelength light has been eagerly anticipated. In this study, we report the implementation in C. elegans of a phytochrome-based optogenetic tool that responds to red/near-infrared light and manipulates cell signaling. We first introduced the SynPCB system, which enabled us to synthesize phycocyanobilin (PCB), a chromophore for phytochrome, and confirmed the biosynthesis of PCB in neurons, muscles, and intestinal cells. We further confirmed that the amount of PCBs synthesized by the SynPCB system was sufficient for photoswitching of phytochrome B (PhyB)-phytochrome interacting factor 3 (PIF3). In addition, optogenetic elevation of intracellular Ca2+ levels in intestinal cells induced a defecation motor program. These SynPCB system and phytochrome-based optogenetic techniques would be of great value in elucidating the molecular mechanisms underlying C. elegans behaviors.
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Affiliation(s)
- Shigekazu Oda
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Emi Sato-Ebine
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Akinobu Nakamura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Koutarou D Kimura
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan.,Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki 444-8787, Japan
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4
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Controlling cellular activities with light. Nat Methods 2023; 20:357-358. [PMID: 36823334 DOI: 10.1038/s41592-022-01745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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5
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Jang J, Tang K, Youn J, McDonald S, Beyer HM, Zurbriggen MD, Uppalapati M, Woolley GA. Engineering of bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL)s. Nat Methods 2023; 20:432-441. [PMID: 36823330 DOI: 10.1038/s41592-023-01764-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 12/21/2022] [Indexed: 02/25/2023]
Abstract
Optogenetic tools for controlling protein-protein interactions (PPIs) have been developed from a small number of photosensory modules that respond to a limited selection of wavelengths. Cyanobacteriochrome (CBCR) GAF domain variants respond to an unmatched array of colors; however, their natural molecular mechanisms of action cannot easily be exploited for optogenetic control of PPIs. Here we developed bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL)s by engineering synthetic light-dependent interactors for a red/green GAF domain. The systematic approach enables the future engineering of the broad chromatic palette of CBCRs for optogenetics use. BICYCLs are among the smallest optogenetic tools for controlling PPIs and enable either green-ON/red-OFF (BICYCL-Red) or red-ON/green-OFF (BICYCL-Green) control with up to 800-fold state selectivity. The access to green wavelengths creates new opportunities for multiplexing with existing tools. We demonstrate the utility of BICYCLs for controlling protein subcellular localization and transcriptional processes in mammalian cells and for multiplexing with existing blue-light tools.
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Affiliation(s)
- Jaewan Jang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kun Tang
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jeffrey Youn
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-Universität, Düsseldorf, Germany. .,CEPLAS - Cluster of Excellence on Plant Science, Düsseldorf, Germany.
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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6
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Wu XJ, Qu JY, Wang CT, Zhang YP, Li PP. Biliverdin incorporation into the cyanobacteriochrome SPI1085g3 from Spirulina. Front Microbiol 2022; 13:952678. [PMID: 35983329 PMCID: PMC9378818 DOI: 10.3389/fmicb.2022.952678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/11/2022] [Indexed: 11/14/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) bind linear tetrapyrrole chromophores, mostly phycocyanobilin (PCB), and exhibit considerable spectral diversity with a high potential for biotechnological applications. Particular attention has been given to the conversion into intrinsic biliverdin (BV) incorporation due to the absence of PCB in mammalian cells. Our recent study discovered that a red/green CBCR of Spirulina subsalsa, SPI1085g3, was covalently attached to PCB and exhibited strong red fluorescence with a unique red/dark switch. In this study, we found that SPI1085g3 could be modestly chromophorylated with BV and absorb somewhat shifted (10 nm) red light, while the single C448S mutant could efficiently bind BV and exhibit unidirectional photoconversion and moderate dark reversion. The fluorescence in its dark-adapted state was switched off by red light, followed by a moderate recovery in the dark, and these were properties similar to those of PCB-binding SPI1085g3. Furthermore, by introducing the CY motif into the conserved CH motif for chromophore attachment, we developed another variant, C448S_CY, which showed increased BV-binding efficiency. As expected, C448S_CY had a significant enhancement in fluorescence quantum yield, reaching that of PCB-binding SPI1085g3 (0.14). These BV-binding CBCRs offer an improved platform for the development of unique photoswitchable fluorescent proteins compared with PCB-binding CBCRs.
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Affiliation(s)
- Xian-Jun Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China
- National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, China
- *Correspondence: Xian-Jun Wu,
| | - Jia-Ying Qu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chang-Tian Wang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ya-Ping Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ping-Ping Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China
- National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, China
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7
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Osteikoetxea X, Silva A, Lázaro-Ibáñez E, Salmond N, Shatnyeva O, Stein J, Schick J, Wren S, Lindgren J, Firth M, Madsen A, Mayr LM, Overman R, Davies R, Dekker N. Engineered Cas9 extracellular vesicles as a novel gene editing tool. J Extracell Vesicles 2022; 11:e12225. [PMID: 35585651 PMCID: PMC9117459 DOI: 10.1002/jev2.12225] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022] Open
Abstract
Extracellular vesicles (EVs) have shown promise as biological delivery vehicles, but therapeutic applications require efficient cargo loading. Here, we developed new methods for CRISPR/Cas9 loading into EVs through reversible heterodimerization of Cas9‐fusions with EV sorting partners. Cas9‐loaded EVs were collected from engineered Expi293F cells using standard methodology, characterized using nanoparticle tracking analysis, western blotting, and transmission electron microscopy and analysed for CRISPR/Cas9‐mediated functional gene editing in a Cre‐reporter cellular assay. Light‐induced dimerization using Cryptochrome 2 combined with CD9 or a Myristoylation‐Palmitoylation‐Palmitoylation lipid modification resulted in efficient loading with approximately 25 Cas9 molecules per EV and high functional delivery with 51% gene editing of the Cre reporter cassette in HEK293 and 25% in HepG2 cells, respectively. This approach was also effective for targeting knock‐down of the therapeutically relevant PCSK9 gene with 6% indel efficiency in HEK293. Cas9 transfer was detergent‐sensitive and associated with the EV fractions after size exclusion chromatography, indicative of EV‐mediated transfer. Considering the advantages of EVs over other delivery vectors we envision that this study will prove useful for a range of therapeutic applications, including CRISPR/Cas9 mediated genome editing.
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Affiliation(s)
- Xabier Osteikoetxea
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK.,HCEMM-SU Extracellular Vesicles Research Group, Budapest, Hungary.,Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Andreia Silva
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elisa Lázaro-Ibáñez
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Nikki Salmond
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Olga Shatnyeva
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Josia Stein
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Jan Schick
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Stephen Wren
- Global Product Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield, UK
| | - Julia Lindgren
- Translational Genomics, Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Alexandra Madsen
- Genome Engineering, Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lorenz M Mayr
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ross Overman
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Rick Davies
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Niek Dekker
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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8
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Baumschlager A. Engineering Light-Control in Biology. Front Bioeng Biotechnol 2022; 10:901300. [PMID: 35573251 PMCID: PMC9096073 DOI: 10.3389/fbioe.2022.901300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Unraveling the transformative power of optogenetics in biology requires sophisticated engineering for the creation and optimization of light-regulatable proteins. In addition, diverse strategies have been used for the tuning of these light-sensitive regulators. This review highlights different protein engineering and synthetic biology approaches, which might aid in the development and optimization of novel optogenetic proteins (Opto-proteins). Focusing on non-neuronal optogenetics, chromophore availability, general strategies for creating light-controllable functions, modification of the photosensitive domains and their fusion to effector domains, as well as tuning concepts for Opto-proteins are discussed. Thus, this review shall not serve as an encyclopedic summary of light-sensitive regulators but aims at discussing important aspects for the engineering of light-controllable proteins through selected examples.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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9
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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10
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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11
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Sakai K, Kondo Y, Fujioka H, Kamiya M, Aoki K, Goto Y. Near-infrared imaging in fission yeast using a genetically encoded phycocyanobilin biosynthesis system. J Cell Sci 2021; 134:273759. [PMID: 34806750 DOI: 10.1242/jcs.259315] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Near-infrared fluorescent protein (iRFP) is a bright and stable fluorescent protein with near-infrared excitation and emission maxima. Unlike the other conventional fluorescent proteins, iRFP requires biliverdin (BV) as a chromophore. Here, we report that phycocyanobilin (PCB) functions as a brighter chromophore for iRFP than BV, and that biosynthesis of PCB allows live-cell imaging with iRFP in the fission yeast Schizosaccharomyces pombe. We initially found that fission yeast cells did not produce BV and therefore did not show any iRFP fluorescence. The brightness of iRFP-PCB was higher than that of iRFP-BV both in vitro and in fission yeast. We introduced SynPCB2.1, a PCB biosynthesis system, into fission yeast, resulting in the brightest iRFP fluorescence. To make iRFP readily available in fission yeast, we developed an endogenous gene tagging system with iRFP and all-in-one integration plasmids carrying the iRFP-fused marker proteins together with SynPCB2.1. These tools not only enable the easy use of multiplexed live-cell imaging in fission yeast with a broader color palette, but also open the door to new opportunities for near-infrared fluorescence imaging in a wider range of living organisms. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hiroyoshi Fujioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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12
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Kramer MM, Lataster L, Weber W, Radziwill G. Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways. Int J Mol Sci 2021; 22:5300. [PMID: 34069904 PMCID: PMC8157557 DOI: 10.3390/ijms22105300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events.
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Affiliation(s)
- Markus M. Kramer
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Levin Lataster
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
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13
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Figueroa D, Rojas V, Romero A, Larrondo LF, Salinas F. The rise and shine of yeast optogenetics. Yeast 2020; 38:131-146. [PMID: 33119964 DOI: 10.1002/yea.3529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.
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Affiliation(s)
- David Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Vicente Rojas
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andres Romero
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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14
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Uda Y, Miura H, Goto Y, Yamamoto K, Mii Y, Kondo Y, Takada S, Aoki K. Improvement of Phycocyanobilin Synthesis for Genetically Encoded Phytochrome-Based Optogenetics. ACS Chem Biol 2020; 15:2896-2906. [PMID: 33164485 DOI: 10.1021/acschembio.0c00477] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Optogenetics is a powerful technique using photoresponsive proteins, and the light-inducible dimerization (LID) system, an optogenetic tool, allows to manipulate intracellular signaling pathways. One of the red/far-red responsive LID systems, phytochrome B (PhyB)-phytochrome interacting factor (PIF), has a unique property of controlling both association and dissociation by light on the second time scale, but PhyB requires a linear tetrapyrrole chromophore such as phycocyanobilin (PCB), and such chromophores are present only in higher plants and cyanobacteria. Here, we report that we further improved our previously developed PCB synthesis system (SynPCB) and successfully established a stable cell line containing a genetically encoded PhyB-PIF LID system. First, four genes responsible for PCB synthesis, namely, PcyA, HO1, Fd, and Fnr, were replaced with their counterparts derived from thermophilic cyanobacteria. Second, Fnr was truncated, followed by fusion with Fd to generate a chimeric protein, tFnr-Fd. Third, these genes were concatenated with P2A peptide cDNAs for polycistronic expression, resulting in an approximately 4-fold increase in PCB synthesis compared with the previous version. Finally, we incorporated the PhyB, PIF, and SynPCB system into drug inducible lentiviral and transposon vectors, which enabled us to induce PCB synthesis and the PhyB-PIF LID system by doxycycline treatment. These tools provide a new opportunity to advance our understanding of the causal relationship between intracellular signaling and cellular functions.
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Affiliation(s)
- Youichi Uda
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Haruko Miura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kei Yamamoto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yusuke Mii
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinji Takada
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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15
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Kahle N, Sheerin DJ, Fischbach P, Koch LA, Schwenk P, Lambert D, Rodriguez R, Kerner K, Hoecker U, Zurbriggen MD, Hiltbrunner A. COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1038-1053. [PMID: 32890447 DOI: 10.1111/tpj.14979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development. Phytochromes can sense the light environment and contribute to measuring day length; thereby, they allow plants to respond and adapt to changes in the ambient environment. Two well-characterized signalling pathways act downstream of phytochromes and link light perception to the regulation of gene expression. The CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA-105 (COP1/SPA) E3 ubiquitin ligase complex and the PHYTOCHROME INTERACTING FACTORs (PIFs) are key components of these pathways and repress light responses in the dark. In light-grown seedlings, phytochromes inhibit COP1/SPA and PIF activity and thereby promote light signalling. In a yeast-two-hybrid screen for proteins binding to light-activated phytochromes, we identified COLD-REGULATED GENE 27 (COR27). COR27 and its homologue COR28 bind to phyA and phyB, the two primary phytochromes in seed plants. COR27 and COR28 have been described previously with regard to a function in the regulation of freezing tolerance, flowering and the circadian clock. Here, we show that COR27 and COR28 repress early seedling development in blue, far-red and in particular red light. COR27 and COR28 contain a conserved Val-Pro (VP)-peptide motif, which mediates binding to the COP1/SPA complex. COR27 and COR28 are targeted for degradation by COP1/SPA and mutant versions with a VP to AA amino acid substitution in the VP-peptide motif are stabilized. Overall, our data suggest that COR27 and COR28 accumulate in light but act as negative regulators of light signalling during early seedling development, thereby preventing an exaggerated response to light.
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Affiliation(s)
- Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Patrick Fischbach
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Philipp Schwenk
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, 79104, Germany
| | - Dorothee Lambert
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Ryan Rodriguez
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Konstantin Kerner
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Ute Hoecker
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
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16
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Lu X, Shen Y, Campbell RE. Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators. Int J Mol Sci 2020; 21:E6522. [PMID: 32906617 PMCID: PMC7555876 DOI: 10.3390/ijms21186522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022] Open
Abstract
Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).
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Affiliation(s)
- Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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17
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Yen ST, Trimmer KA, Aboul-Fettouh N, Mullen RD, Culver JC, Dickinson ME, Behringer RR, Eisenhoffer GT. CreLite: An optogenetically controlled Cre/loxP system using red light. Dev Dyn 2020; 249:1394-1403. [PMID: 32745301 DOI: 10.1002/dvdy.232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Precise manipulation of gene expression with temporal and spatial control is essential for functional analysis and determining cell lineage relationships in complex biological systems. The cyclic recombinase (Cre)-loxP system is commonly used for gene manipulation at desired times and places. However, specificity is dependent on the availability of tissue- or cell-specific regulatory elements used in combination with Cre. Here, we present CreLite, an optogenetically controlled Cre system using red light in developing zebrafish embryos. RESULTS Cre activity is disabled by splitting Cre and fusing with the Arabidopsis thaliana red light-inducible binding partners, PhyB and PIF6. Upon red light illumination, the PhyB-CreC and PIF6-CreN fusion proteins come together in the presence of the cofactor phycocyanobilin (PCB) to restore Cre activity. Red light exposure of zebrafish embryos harboring a Cre-dependent multicolor fluorescent protein reporter injected with CreLite mRNAs and PCB resulted in Cre activity as measured by the generation of multispectral cell labeling in several different tissues. CONCLUSIONS Our data show that CreLite can be used for gene manipulations in whole embryos or small groups of cells at different developmental stages, and suggests CreLite may also be useful for temporal and spatial control of gene expression in cell culture, ex vivo organ culture, and other animal models.
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Affiliation(s)
- Shuo-Ting Yen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kenneth A Trimmer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Nader Aboul-Fettouh
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rachel D Mullen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - James C Culver
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard R Behringer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - George T Eisenhoffer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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18
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de Mena L, Rincon-Limas DE. PhotoGal4: A Versatile Light-Dependent Switch for Spatiotemporal Control of Gene Expression in Drosophila Explants. iScience 2020; 23:101308. [PMID: 32652492 PMCID: PMC7347995 DOI: 10.1016/j.isci.2020.101308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/15/2020] [Accepted: 06/19/2020] [Indexed: 12/04/2022] Open
Abstract
We present here PhotoGal4, a phytochrome B-based optogenetic switch for fine-tuned spatiotemporal control of gene expression in Drosophila explants. This switch integrates the light-dependent interaction between phytochrome B and PIF6 from plants with regulatory elements from the yeast Gal4/UAS system. We found that PhotoGal4 efficiently activates and deactivates gene expression upon red- or far-red-light irradiation, respectively. In addition, this optogenetic tool reacts to different illumination conditions, allowing for fine modulation of the light-dependent response. Importantly, by simply focusing a laser beam, PhotoGal4 induces intricate patterns of expression in a customized manner. For instance, we successfully sketched personalized patterns of GFP fluorescence such as emoji-like shapes or letterform logos in Drosophila explants, which illustrates the exquisite precision and versatility of this tool. Hence, we anticipate that PhotoGal4 will expand the powerful Drosophila toolbox and will provide a new avenue to investigate intricate and complex problems in biomedical research.
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Affiliation(s)
- Lorena de Mena
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA.
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA; Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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19
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Stücheli P, Sieber S, Fuchs DW, Scheller L, Strittmatter T, Saxena P, Gademann K, Fussenegger M. Genetically encoded betaxanthin-based small-molecular fluorescent reporter for mammalian cells. Nucleic Acids Res 2020; 48:e67. [PMID: 32421771 PMCID: PMC7337513 DOI: 10.1093/nar/gkaa342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/25/2020] [Accepted: 05/14/2020] [Indexed: 01/04/2023] Open
Abstract
We designed and engineered a dye production cassette encoding a heterologous pathway, including human tyrosine hydroxylase and Amanita muscaria 4,5-DOPA dioxygenase, for the biosynthesis of the betaxanthin family of plant and fungal pigments in mammalian cells. The system does not impair cell viability, and can be used as a non-protein reporter system to directly visualize the dynamics of gene expression by profiling absorbance or fluorescence in the supernatant of cell cultures, as well as for fluorescence labeling of individual cells. Pigment profiling can also be multiplexed with reporter proteins such as mCherry or the human model glycoprotein SEAP (secreted alkaline phosphatase). Furthermore, absorbance measurement with a smartphone camera using standard application software enables inexpensive, low-tech reporter quantification.
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Affiliation(s)
- Pascal Stücheli
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - David W Fuchs
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Leo Scheller
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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20
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Huang Z, Wu Y, Allen ME, Pan Y, Kyriakakis P, Lu S, Chang YJ, Wang X, Chien S, Wang Y. Engineering light-controllable CAR T cells for cancer immunotherapy. SCIENCE ADVANCES 2020; 6:eaay9209. [PMID: 32128416 PMCID: PMC7030928 DOI: 10.1126/sciadv.aay9209] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/03/2019] [Indexed: 05/16/2023]
Abstract
T cells engineered to express chimeric antigen receptors (CARs) can recognize and engage with target cancer cells with redirected specificity for cancer immunotherapy. However, there is a lack of ideal CARs for solid tumor antigens, which may lead to severe adverse effects. Here, we developed a light-inducible nuclear translocation and dimerization (LINTAD) system for gene regulation to control CAR T activation. We first demonstrated light-controllable gene expression and functional modulation in human embryonic kidney 293T and Jurkat T cell lines. We then improved the LINTAD system to achieve optimal efficiency in primary human T cells. The results showed that pulsed light stimulations can activate LINTAD CAR T cells with strong cytotoxicity against target cancer cells, both in vitro and in vivo. Therefore, our LINTAD system can serve as an efficient tool to noninvasively control gene activation and activate inducible CAR T cells for precision cancer immunotherapy.
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Affiliation(s)
- Ziliang Huang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Yiqian Wu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Molly E. Allen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Yijia Pan
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Phillip Kyriakakis
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shaoying Lu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ya-Ju Chang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Xin Wang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shu Chien
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yingxiao Wang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Corresponding author.
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21
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Wiltbank LB, Kehoe DM. Diverse light responses of cyanobacteria mediated by phytochrome superfamily photoreceptors. Nat Rev Microbiol 2020; 17:37-50. [PMID: 30410070 DOI: 10.1038/s41579-018-0110-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyanobacteria are an evolutionarily and ecologically important group of prokaryotes. They exist in diverse habitats, ranging from hot springs and deserts to glaciers and the open ocean. The range of environments that they inhabit can be attributed in part to their ability to sense and respond to changing environmental conditions. As photosynthetic organisms, one of the most crucial parameters for cyanobacteria to monitor is light. Cyanobacteria can sense various wavelengths of light and many possess a range of bilin-binding photoreceptors belonging to the phytochrome superfamily. Vital cellular processes including growth, phototaxis, cell aggregation and photosynthesis are tuned to environmental light conditions by these photoreceptors. In this Review, we examine the physiological responses that are controlled by members of this diverse family of photoreceptors and discuss the signal transduction pathways through which these photoreceptors operate. We highlight specific examples where the activities of multiple photoreceptors function together to fine-tune light responses. We also discuss the potential application of these photosensing systems in optogenetics and synthetic biology.
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Affiliation(s)
- Lisa B Wiltbank
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, USA.
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22
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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23
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Mansouri M, Strittmatter T, Fussenegger M. Light-Controlled Mammalian Cells and Their Therapeutic Applications in Synthetic Biology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800952. [PMID: 30643713 PMCID: PMC6325585 DOI: 10.1002/advs.201800952] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Indexed: 05/12/2023]
Abstract
The ability to remote control the expression of therapeutic genes in mammalian cells in order to treat disease is a central goal of synthetic biology-inspired therapeutic strategies. Furthermore, optogenetics, a combination of light and genetic sciences, provides an unprecedented ability to use light for precise control of various cellular activities with high spatiotemporal resolution. Recent work to combine optogenetics and therapeutic synthetic biology has led to the engineering of light-controllable designer cells, whose behavior can be regulated precisely and noninvasively. This Review focuses mainly on non-neural optogenetic systems, which are often used in synthetic biology, and their applications in genetic programing of mammalian cells. Here, a brief overview of the optogenetic tool kit that is available to build light-sensitive mammalian cells is provided. Then, recently developed strategies for the control of designer cells with specific biological functions are summarized. Recent translational applications of optogenetically engineered cells are also highlighted, ranging from in vitro basic research to in vivo light-controlled gene therapy. Finally, current bottlenecks, possible solutions, and future prospects for optogenetics in synthetic biology are discussed.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
- Faculty of ScienceUniversity of BaselMattenstrasse 26CH‐4058BaselSwitzerland
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24
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Perspectives of RAS and RHEB GTPase Signaling Pathways in Regenerating Brain Neurons. Int J Mol Sci 2018; 19:ijms19124052. [PMID: 30558189 PMCID: PMC6321366 DOI: 10.3390/ijms19124052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Cellular activation of RAS GTPases into the GTP-binding “ON” state is a key switch for regulating brain functions. Molecular protein structural elements of rat sarcoma (RAS) and RAS homolog protein enriched in brain (RHEB) GTPases involved in this switch are discussed including their subcellular membrane localization for triggering specific signaling pathways resulting in regulation of synaptic connectivity, axonal growth, differentiation, migration, cytoskeletal dynamics, neural protection, and apoptosis. A beneficial role of neuronal H-RAS activity is suggested from cellular and animal models of neurodegenerative diseases. Recent experiments on optogenetic regulation offer insights into the spatiotemporal aspects controlling RAS/mitogen activated protein kinase (MAPK) or phosphoinositide-3 kinase (PI3K) pathways. As optogenetic manipulation of cellular signaling in deep brain regions critically requires penetration of light through large distances of absorbing tissue, we discuss magnetic guidance of re-growing axons as a complementary approach. In Parkinson’s disease, dopaminergic neuronal cell bodies degenerate in the substantia nigra. Current human trials of stem cell-derived dopaminergic neurons must take into account the inability of neuronal axons navigating over a large distance from the grafted site into striatal target regions. Grafting dopaminergic precursor neurons directly into the degenerating substantia nigra is discussed as a novel concept aiming to guide axonal growth by activating GTPase signaling through protein-functionalized intracellular magnetic nanoparticles responding to external magnets.
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25
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de Mena L, Rizk P, Rincon-Limas DE. Bringing Light to Transcription: The Optogenetics Repertoire. Front Genet 2018; 9:518. [PMID: 30450113 PMCID: PMC6224442 DOI: 10.3389/fgene.2018.00518] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/15/2018] [Indexed: 11/13/2022] Open
Abstract
The ability to manipulate expression of exogenous genes in particular regions of living organisms has profoundly transformed the way we study biomolecular processes involved in both normal development and disease. Unfortunately, most of the classical inducible systems lack fine spatial and temporal accuracy, thereby limiting the study of molecular events that strongly depend on time, duration of activation, or cellular localization. By exploiting genetically engineered photo sensing proteins that respond to specific wavelengths, we can now provide acute control of numerous molecular activities with unprecedented precision. In this review, we present a comprehensive breakdown of all of the current optogenetic systems adapted to regulate gene expression in both unicellular and multicellular organisms. We focus on the advantages and disadvantages of these different tools and discuss current and future challenges in the successful translation to more complex organisms.
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Affiliation(s)
- Lorena de Mena
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Patrick Rizk
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States.,Department of Neuroscience, Genetics Institute, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, United States
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26
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Regulation of the heme biosynthetic pathway for combinational biosynthesis of phycocyanobilin in Escherichia coli. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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27
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Iijima E, Gleeson MP, Unno M, Mori S. QM/MM Investigation for Protonation States in a Bilin Reductase PcyA-Biliverdin IXα Complex. Chemphyschem 2018; 19:1809-1813. [PMID: 29732737 DOI: 10.1002/cphc.201800031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 02/28/2024]
Abstract
Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXα (BV), which has the C-pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two-electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H3 O+ ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.
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Affiliation(s)
- Eri Iijima
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
| | - M Paul Gleeson
- Department of Biomedical Engineering, Faculty of Engineering, King Mongkut's institute of Technology Ladkrabang, Thailand
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10903, Thailand
| | - Masaki Unno
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, 319-1106, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, 319-1106, Japan
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28
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Near-infrared light-controlled systems for gene transcription regulation, protein targeting and spectral multiplexing. Nat Protoc 2018; 13:1121-1136. [PMID: 29700485 DOI: 10.1038/nprot.2018.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Near-infrared (NIR, 740-780 nm) optogenetic systems are well-suited to spectral multiplexing with blue-light-controlled tools. Here, we present two protocols, one for regulation of gene transcription and another for control of protein localization, that use a NIR-responsive bacterial phytochrome BphP1-QPAS1 optogenetic pair. In the first protocol, cells are transfected with the optogenetic constructs for independently controlling gene transcription by NIR (BphP1-QPAS1) and blue (LightOn) light. The NIR and blue-light-controlled gene transcription systems show minimal spectral crosstalk and induce a 35- to 40-fold increase in reporter gene expression. In the second protocol, the BphP1-QPAS1 pair is combined with a light-oxygen-voltage-sensing (LOV) domain-based construct into a single optogenetic tool, termed iRIS. This dual-light-controllable protein localization tool allows tridirectional protein translocation among the cytoplasm, nucleus and plasma membrane. Both procedures can be performed within 3-5 d. Use of NIR light-controlled optogenetic systems should advance basic and biomedical research.
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29
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Benedetti L, Barentine AES, Messa M, Wheeler H, Bewersdorf J, De Camilli P. Light-activated protein interaction with high spatial subcellular confinement. Proc Natl Acad Sci U S A 2018; 115:E2238-E2245. [PMID: 29463750 PMCID: PMC5877946 DOI: 10.1073/pnas.1713845115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other component (the prey) is fused to the protein of interest. Upon illumination, binding of the prey to the bait results in its subcellular redistribution. Here, we compared and quantified the extent of light-dependent dimer occurrence in small, subcellular volumes controlled by three such tools: Cry2/CIB1, iLID, and Magnets. We show that both the location of the photoreceptor protein(s) in the dimer pair and its (their) switch-off kinetics determine the subcellular volume where dimer formation occurs and the amount of protein recruited in the illuminated volume. Efficient spatial confinement of dimer to the area of illumination is achieved when the photosensitive component of the dimerization pair is tethered to the membrane of intracellular compartments and when on and off kinetics are extremely fast, as achieved with iLID or Magnets. Magnets and the iLID variants with the fastest switch-off kinetics induce and maintain protein dimerization in the smallest volume, although this comes at the expense of the total amount of dimer. These findings highlight the distinct features of different optical dimerization systems and will be useful guides in the choice of tools for specific applications.
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Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
| | - Mirko Messa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Heather Wheeler
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510;
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
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30
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Kyriakakis P, Catanho M, Hoffner N, Thavarajah W, Hu VJ, Chao SS, Hsu A, Pham V, Naghavian L, Dozier LE, Patrick GN, Coleman TP. Biosynthesis of Orthogonal Molecules Using Ferredoxin and Ferredoxin-NADP + Reductase Systems Enables Genetically Encoded PhyB Optogenetics. ACS Synth Biol 2018; 7:706-717. [PMID: 29301067 PMCID: PMC5820651 DOI: 10.1021/acssynbio.7b00413] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transplanting metabolic reactions from one species into another has many uses as a research tool with applications ranging from optogenetics to crop production. Ferredoxin (Fd), the enzyme that most often supplies electrons to these reactions, is often overlooked when transplanting enzymes from one species to another because most cells already contain endogenous Fd. However, we have shown that the production of chromophores used in Phytochrome B (PhyB) optogenetics is greatly enhanced in mammalian cells by expressing bacterial and plant Fds with ferredoxin-NADP+ reductases (FNR). We delineated the rate limiting factors and found that the main metabolic precursor, heme, was not the primary limiting factor for producing either the cyanobacterial or plant chromophores, phycocyanobilin or phytochromobilin, respectively. In fact, Fd is limiting, followed by Fd+FNR and finally heme. Using these findings, we optimized the PCB production system and combined it with a tissue penetrating red/far-red sensing PhyB optogenetic gene switch in animal cells. We further characterized this system in several mammalian cell lines using red and far-red light. Importantly, we found that the light-switchable gene system remains active for several hours upon illumination, even with a short light pulse, and requires very small amounts of light for maximal activation. Boosting chromophore production by matching metabolic pathways with specific ferredoxin systems will enable the unparalleled use of the many PhyB optogenetic tools and has broader implications for optimizing synthetic metabolic pathways.
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Affiliation(s)
- Phillip Kyriakakis
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Marianne Catanho
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Nicole Hoffner
- Neurosciences
Graduate Program, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Walter Thavarajah
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Vincent J. Hu
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Syh-Shiuan Chao
- Frank
H. Better School of Medicine, Quinnipiac University, 370 Bassett Road, North Haven, Connecticut 06473, United States
| | - Athena Hsu
- School
of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Vivian Pham
- Roy J. and
Lucille A. Carver College of Medicine, University of Iowa, 451 Newton Road, Iowa City, Iowa 52242, United States
| | - Ladan Naghavian
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Lara E. Dozier
- Section
of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0347, United States
| | - Gentry N. Patrick
- Section
of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0347, United States
| | - Todd P. Coleman
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
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31
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Repurposing a photosynthetic antenna protein as a super-resolution microscopy label. Sci Rep 2017; 7:16807. [PMID: 29196704 PMCID: PMC5711914 DOI: 10.1038/s41598-017-16834-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/16/2017] [Indexed: 11/08/2022] Open
Abstract
Techniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd 1 ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy.
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32
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Optogenetic Tools for Subcellular Applications in Neuroscience. Neuron 2017; 96:572-603. [PMID: 29096074 DOI: 10.1016/j.neuron.2017.09.047] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/30/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications.
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33
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Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling. Proc Natl Acad Sci U S A 2017; 114:11962-11967. [PMID: 29078307 DOI: 10.1073/pnas.1707190114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Optogenetics is a powerful tool to precisely manipulate cell signaling in space and time. For example, protein activity can be regulated by several light-induced dimerization (LID) systems. Among them, the phytochrome B (PhyB)-phytochrome-interacting factor (PIF) system is the only available LID system controlled by red and far-red lights. However, the PhyB-PIF system requires phycocyanobilin (PCB) or phytochromobilin as a chromophore, which must be artificially added to mammalian cells. Here, we report an expression vector that coexpresses HO1 and PcyA with Ferredoxin and Ferredoxin-NADP+ reductase for the efficient synthesis of PCB in the mitochondria of mammalian cells. An even higher intracellular PCB concentration was achieved by the depletion of biliverdin reductase A, which degrades PCB. The PCB synthesis and PhyB-PIF systems allowed us to optogenetically regulate intracellular signaling without any external supply of chromophores. Thus, we have provided a practical method for developing a fully genetically encoded PhyB-PIF system, which paves the way for its application to a living animal.
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34
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Hochrein L, Machens F, Messerschmidt K, Mueller-Roeber B. PhiReX: a programmable and red light-regulated protein expression switch for yeast. Nucleic Acids Res 2017; 45:9193-9205. [PMID: 28911120 PMCID: PMC5587811 DOI: 10.1093/nar/gkx610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiReX is based on the combination of a customizable synTALE DNA-binding domain, the VP64 activation domain and the light-sensitive dimerization of the photoreceptor PhyB and its interacting partner PIF3 from Arabidopsis thaliana. Robust gene expression and high protein levels are achieved by combining genome integrated red light-sensing components with an episomal high-copy reporter construct. The gene of interest as well as the synTALE DNA-binding domain can be easily exchanged, allowing the flexible regulation of any desired gene by targeting endogenous or heterologous promoter regions. To allow low-cost induction of gene expression for industrial fermentation processes, we engineered yeast to endogenously produce the chromophore required for the effective dimerization of PhyB and PIF3. Time course experiments demonstrate high-level induction over a period of at least 48 h.
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Affiliation(s)
- Lena Hochrein
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Katrin Messerschmidt
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Department of Molecular Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.,Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
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35
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Adrian M, Nijenhuis W, Hoogstraaten RI, Willems J, Kapitein LC. A Phytochrome-Derived Photoswitch for Intracellular Transport. ACS Synth Biol 2017; 6:1248-1256. [PMID: 28340532 PMCID: PMC5525101 DOI: 10.1021/acssynbio.6b00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells depend on the proper positioning of their organelles, suggesting that active manipulation of organelle positions can be used to explore spatial cell biology and to restore cellular defects caused by organelle misplacement. Recently, blue-light dependent recruitment of specific motors to selected organelles has been shown to alter organelle motility and positioning, but these approaches lack rapid and active reversibility. The light-dependent interaction of phytochrome B with its interacting factors has been shown to function as a photoswitch, dimerizing under red light and dissociating under far-red light. Here we engineer phytochrome domains into photoswitches for intracellular transport that enable the reversible interaction between organelles and motor proteins. Using patterned illumination and live-cell imaging, we demonstrate that this system provides unprecedented spatiotemporal control. We also demonstrate that it can be used in combination with a blue-light dependent system to independently control the positioning of two different organelles. Precise optogenetic control of organelle motility and positioning will provide a better understanding of and control over the spatial biology of cells.
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Affiliation(s)
- Max Adrian
- Cell Biology, Department
of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Wilco Nijenhuis
- Cell Biology, Department
of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Rein I. Hoogstraaten
- Cell Biology, Department
of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jelmer Willems
- Cell Biology, Department
of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Department
of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
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36
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Ge B, Lin X, Chen Y, Wang X, Chen H, Jiang P, Huang F. Combinational biosynthesis of dual-functional streptavidin-phycobiliproteins for high-throughput-compatible immunoassay. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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38
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Chernov KG, Redchuk TA, Omelina ES, Verkhusha VV. Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes. Chem Rev 2017; 117:6423-6446. [DOI: 10.1021/acs.chemrev.6b00700] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Konstantin G. Chernov
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Taras A. Redchuk
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Evgeniya S. Omelina
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Vladislav V. Verkhusha
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
- Department
of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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39
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Jansen V, Jikeli JF, Wachten D. How to control cyclic nucleotide signaling by light. Curr Opin Biotechnol 2017; 48:15-20. [PMID: 28288335 DOI: 10.1016/j.copbio.2017.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/15/2017] [Indexed: 12/28/2022]
Abstract
Optogenetics allows to non-invasively manipulate cellular functions with spatio-temporal precision by combining genetic engineering with the control of protein function by light. Since the discovery of channelrhodopsin has pioneered the field, the optogenetic toolkit has been ever expanding and allows now not only to control neuronal activity by light, but rather a multitude of other cellular functions. One important application that has been established in recent years is the light-dependent control of second messenger signaling. The optogenetic toolkit now allows to control cyclic nucleotide-dependent signaling by light in vitro and in vivo.
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Affiliation(s)
- Vera Jansen
- Center of Advanced European Studies and Research (caesar), Minerva Max Planck Research Group, Molecular Physiology, Bonn, Germany
| | - Jan F Jikeli
- Center of Advanced European Studies and Research (caesar), Minerva Max Planck Research Group, Molecular Physiology, Bonn, Germany
| | - Dagmar Wachten
- Center of Advanced European Studies and Research (caesar), Minerva Max Planck Research Group, Molecular Physiology, Bonn, Germany; Institute of Innate Immunity, University Hospital, University of Bonn, Bonn, Germany.
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40
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Salinas F, Rojas V, Delgado V, Agosin E, Larrondo LF. Optogenetic switches for light-controlled gene expression in yeast. Appl Microbiol Biotechnol 2017; 101:2629-2640. [DOI: 10.1007/s00253-017-8178-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 02/06/2023]
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41
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Mühlhäuser WW, Fischer A, Weber W, Radziwill G. Optogenetics - Bringing light into the darkness of mammalian signal transduction. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:280-292. [DOI: 10.1016/j.bbamcr.2016.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 01/01/2023]
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Di Ventura B, Kuhlman B. Go in! Go out! Inducible control of nuclear localization. Curr Opin Chem Biol 2016; 34:62-71. [PMID: 27372352 DOI: 10.1016/j.cbpa.2016.06.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/19/2022]
Abstract
Cells have evolved a variety of mechanisms to regulate the enormous complexity of processes taking place inside them. One mechanism consists in tightly controlling the localization of macromolecules, keeping them away from their place of action until needed. Since a large fraction of the cellular response to external stimuli is mediated by gene expression, it is not surprising that transcriptional regulators are often subject to stimulus-induced nuclear import or export. Here we review recent methods in chemical biology and optogenetics for controlling the nuclear localization of proteins of interest inside living cells. These methods allow researchers to regulate protein activity with exquisite spatiotemporal control, and open up new possibilities for studying the roles of proteins in a broad array of cellular processes and biological functions.
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Affiliation(s)
- Barbara Di Ventura
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg, Germany.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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43
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Buckley CE, Moore RE, Reade A, Goldberg AR, Weiner OD, Clarke JDW. Reversible Optogenetic Control of Subcellular Protein Localization in a Live Vertebrate Embryo. Dev Cell 2016; 36:117-126. [PMID: 26766447 PMCID: PMC4712025 DOI: 10.1016/j.devcel.2015.12.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 11/09/2015] [Accepted: 12/08/2015] [Indexed: 12/13/2022]
Abstract
We demonstrate the utility of the phytochrome system to rapidly and reversibly recruit proteins to specific subcellular regions within specific cells in a living vertebrate embryo. Light-induced heterodimerization using the phytochrome system has previously been used as a powerful tool to dissect signaling pathways for single cells in culture but has not previously been used to reversibly manipulate the precise subcellular location of proteins in multicellular organisms. Here we report the experimental conditions necessary to use this system to manipulate proteins in vivo. As proof of principle, we demonstrate that we can manipulate the localization of the apical polarity protein Pard3 with high temporal and spatial precision in both the neural tube and the embryo’s enveloping layer epithelium. Our optimizations of optogenetic component expression and chromophore purification and delivery should significantly lower the barrier for establishing this powerful optogenetic system in other multicellular organisms. The phytochrome system has been optimized for use within multicellular organisms Protein recruitment can be tightly controlled to a specific subcellular region Protein recruitment occurs with high binding and reversal kinetics The subcellular localization of the apical polarity protein Pard3 is manipulated
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Affiliation(s)
- Clare E Buckley
- MRC Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Rachel E Moore
- MRC Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Reade
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158-9001, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Anna R Goldberg
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158-9001, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158-9001, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158-2517, USA.
| | - Jonathan D W Clarke
- MRC Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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44
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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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45
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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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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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47
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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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48
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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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49
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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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50
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Abstract
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Optical dimerizers are a powerful
new class of optogenetic tools
that allow light-inducible control of protein–protein interactions.
Such tools have been useful for regulating cellular pathways and processes
with high spatiotemporal resolution in live cells, and a growing number
of dimerizer systems are available. As these systems have been characterized
by different groups using different methods, it has been difficult
for users to compare their properties. Here, we set about to systematically
benchmark the properties of four optical dimerizer systems, CRY2/CIB1,
TULIPs, phyB/PIF3, and phyB/PIF6. Using a yeast transcriptional assay,
we find significant differences in light sensitivity and fold-activation
levels between the red light regulated systems but similar responses
between the CRY2/CIB and TULIP systems. Further comparison of the
ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK
signaling pathway also showed similar responses, with slightly less
background activity in the dark observed with CRY2/CIB. In the process
of developing this work, we also generated an improved blue-light-regulated
transcriptional system using CRY2/CIB in yeast. In addition, we demonstrate
successful application of the CRY2/CIB dimerizers using a membrane-tethered
CRY2, which may allow for better local control of protein interactions.
Taken together, this work allows for a better understanding of the
capacities of these different dimerization systems and demonstrates
new uses of these dimerizers to control signaling and transcription
in yeast.
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Affiliation(s)
- Gopal P. Pathak
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Devin Strickland
- Department
of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Justin D. Vrana
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Chandra L. Tucker
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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