1
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S A, Parida N, Patnaik S. SOX4 induces cytoskeleton remodeling and promotes cell motility via N-wasp/ARP2/3 pathway in colorectal cancer cells. Exp Cell Res 2024; 439:114059. [PMID: 38705228 DOI: 10.1016/j.yexcr.2024.114059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Filopodia are thin, actin-rich projection from the plasma membrane that promote cancer cell invasion and migration. Sex-determining region Y-related high-mobility group-box 4 (SOX4) is a crucial transcription factor that plays a role in the development and metastasis of colorectal cancer (CRC). However, the involvement of SOX4 in cytoskeleton remodeling in CRC remains unknown. For the first time, we demonstrate that SOX4 is a potent regulator of filopodia formation in CRC cells. Overexpression of SOX4 protein enhances both migration and invasion ability of HCT116, and CACO2 cells, which is relevant to the metastasis. Furthermore, through phalloidin staining, cytoskeleton re-assembly was observed in SOX4-modified cell lines. Enhanced expression of SOX4 increased the number and length of filopodia on cell surface. In contrast, silencing SOX4 in SW620 cells with higher endogenous expression of SOX4, impeded the filopodia formation. Moreover, SOX4 was found to be positively regulating the expression of central regulators of actin cytoskeleton - N-Wiskott-Aldrich syndrome protein (N-WASP); WAVE2; Actin related proteins, ARP2 and ARP3. Inhibiting the N-WASP/ARP2/3 pathway diminishes the filopodia formation and the migration of CRC cells. These results indicate the crucial role of SOX4 in the regulation of filopodia formation mediated by N-WASP/ARP2/3 pathway in CRC cells.
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Affiliation(s)
- Anupriya S
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, 751024, India.
| | - Nandita Parida
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, 751024, India.
| | - Srinivas Patnaik
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, 751024, India.
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2
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Jaeger M, Anastasio A, Chamy L, Brustlein S, Vincentelli R, Durbesson F, Gigan J, Thépaut M, Char R, Boussand M, Lechelon M, Argüello RJ, Marguet D, He HT, Lasserre R. Light-inducible T cell engagers trigger, tune, and shape the activation of primary T cells. Proc Natl Acad Sci U S A 2023; 120:e2302500120. [PMID: 37722050 PMCID: PMC10523538 DOI: 10.1073/pnas.2302500120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
To mount appropriate responses, T cells integrate complex sequences of receptor stimuli perceived during transient interactions with antigen-presenting cells. Although it has been hypothesized that the dynamics of these interactions influence the outcome of T cell activation, methodological limitations have hindered its formal demonstration. Here, we have engineered the Light-inducible T cell engager (LiTE) system, a recombinant optogenetics-based molecular tool targeting the T cell receptor (TCR). The LiTE system constitutes a reversible molecular switch displaying exquisite reactivity. As proof of concept, we dissect how specific temporal patterns of TCR stimulation shape T cell activation. We established that CD4+ T cells respond to intermittent TCR stimulation more efficiently than their CD8+ T cells counterparts and provide evidence that distinct sequences of TCR stimulation encode different cytokine programs. Finally, we show that the LiTE system could be exploited to create light-activated bispecific T cell engagers and manipulate tumor cell killing. Overall, the LiTE system provides opportunities to understand how T cells integrate TCR stimulations and to trigger T cell cytotoxicity with high spatiotemporal control.
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Affiliation(s)
- Morgane Jaeger
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Amandine Anastasio
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Léa Chamy
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Sophie Brustlein
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de neurobiologie de la Méditerranée, Turing Center for Living Systems, 13 273Marseille, France
| | - Renaud Vincentelli
- Aix Marseille Université, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, 13 288Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, 13 288Marseille, France
| | - Julien Gigan
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Morgane Thépaut
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rémy Char
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Maud Boussand
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Mathias Lechelon
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rafael J. Argüello
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Didier Marguet
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Hai-Tao He
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rémi Lasserre
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
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3
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Konrad KR, Gao S, Zurbriggen MD, Nagel G. Optogenetic Methods in Plant Biology. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:313-339. [PMID: 37216203 DOI: 10.1146/annurev-arplant-071122-094840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.
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Affiliation(s)
- Kai R Konrad
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany;
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany;
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
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4
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Cao M, Peng B, Chen H, Yang M, Chen P, Ye L, Wang H, Ren L, Xie J, Zhu J, Xu X, Xu W, Geng L, Gong S. miR-34a induces neutrophil apoptosis by regulating Cdc42-WASP-Arp2/3 pathway-mediated F-actin remodeling and ROS production. Redox Rep 2022; 27:167-175. [PMID: 35938579 PMCID: PMC9364709 DOI: 10.1080/13510002.2022.2102843] [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] [Indexed: 11/25/2022] Open
Abstract
Background The number of neutrophils is significantly reduced in myelodysplastic syndrome (MDS), but the molecular basis remains unclear. We recently found that miR-34a was significantly increased in MDS neutrophils. Therefore, this study aims to clarify the effects of aberrant miR-34a expression on neutrophil counts. Methods miR-34a mimics/inhibitor transfection were performed in neutrophil-like differentiated HL60 (dHL60) cells, and a FACSCalibur flow cytometer was used to measure ROS production and apoptosis. In addition, the Cdc42-WASP-Arp2/3 pathway inhibitor (ML141) and activator (CN02) treated the dHL60 cells, and then ROS production, apoptosis and related proteins expression were detected. And, luciferase reporter assay to verify the relationship of miR-34a and the Cdc42-WASP-Arp2/3 pathway. Results overexpression of miR-34a could induce ROS production and apoptosis, decrease the expression levels of DOCK8, p-WASP, WASP, Arp2, Arp3, and increase F-actin’s expression. Meanwhile, knockdown of miR-34a could decrease ROS production and apoptosis, increase the expression of DOCK8, p-WASP, WASP, Arp2, Arp3, and decrease F-actin’s expression. Immunofluorescence staining showed aberrant miR-34a and Cdc42-WASP-Arp2/3 pathway could induce F-actin membrane transfer. Luciferase reporter assay indicated that DOCK8 was a direct target gene of miR-34a. Conclusion These data indicates miR-34a may induce neutrophil apoptosis by regulating Cdc42-WASP-Arp2/3 pathway-mediated F-actin remodeling and ROS production.
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Affiliation(s)
- Meiwan Cao
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Baoling Peng
- Center for child health and mental health, Shenzhen Childen’s Hospital, Shenzhen, People’s Republic of China
| | - Huan Chen
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Min Yang
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Peiyu Chen
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Liping Ye
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Hongli Wang
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lu Ren
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jing Xie
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jingnan Zhu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiangye Xu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wanfu Xu
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lanlan Geng
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Sitang Gong
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
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5
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Küllmer F, Vepřek NA, Borowiak M, Nasufović V, Barutzki S, Thorn-Seshold O, Arndt HD, Trauner D. Next Generation Opto-Jasplakinolides Enable Local Remodeling of Actin Networks. Angew Chem Int Ed Engl 2022; 61:e202210220. [PMID: 36048143 PMCID: PMC11256906 DOI: 10.1002/anie.202210220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Indexed: 11/12/2022]
Abstract
The natural product jasplakinolide is widely used to stabilize F-actin. Based on extensive structure-activity relationship studies, we have developed a new generation of photoswitchable jasplakinolides that feature rationally designed red-shifted azobenzene photoswitches. Our lead compound, nOJ, can be activated with longer wavelengths in the visible range (e.g. 440-475 nm) and rapidly returns to its inactive state through thermal relaxation. nOJ enables the reversible control of F-actin dynamics, as shown through live-cell imaging, cell migration, and cell proliferation assays. Short, local irradiation with blue light resulted in highly localized and reversible actin aggregation with subcellular precision. Our optical tool can be useful in diverse fields to study actin dynamics with excellent spatiotemporal resolution.
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Affiliation(s)
- Florian Küllmer
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Nynke A Vepřek
- New York University, Department of Chemistry, 100 Washington Square East, New York, NY 10003, USA
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Malgorzata Borowiak
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Veselin Nasufović
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Sebastian Barutzki
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Hans-Dieter Arndt
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Dirk Trauner
- New York University, Department of Chemistry, 100 Washington Square East, New York, NY 10003, USA
- Department of Chemistry University of Pennsylvania, 231 South 34th St., Philadelphia, PA 19104-6323, USA
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6
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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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7
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Wichert N, Witt M, Blume C, Scheper T. Clinical applicability of optogenetic gene regulation. Biotechnol Bioeng 2021; 118:4168-4185. [PMID: 34287844 DOI: 10.1002/bit.27895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/27/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022]
Abstract
The field of optogenetics is rapidly growing in relevance and number of developed tools. Among other things, the optogenetic repertoire includes light-responsive ion channels and methods for gene regulation. This review will be confined to the optogenetic control of gene expression in mammalian cells as suitable models for clinical applications. Here optogenetic gene regulation might offer an excellent method for spatially and timely regulated gene and protein expression in cell therapeutic approaches. Well-known systems for gene regulation, such as the LOV-, CRY2/CIB-, PhyB/PIF-systems, as well as other, in mammalian cells not yet fully established systems, will be described. Advantages and disadvantages with regard to clinical applications are outlined in detail. Among the many unanswered questions concerning the application of optogenetics, we discuss items such as the use of exogenous chromophores and their effects on the biology of the cells and methods for a gentle, but effective gene transfection method for optogenetic tools for in vivo applications.
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Affiliation(s)
- Nina Wichert
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Martin Witt
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Cornelia Blume
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Thomas Scheper
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
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8
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Lim WK, Kaur P, Huang H, Jo RS, Ramamoorthy A, Ng LF, Suresh J, Maisha FI, Mathuru AS, Tolwinski NS. Optogenetic approaches for understanding homeostatic and degenerative processes in Drosophila. Cell Mol Life Sci 2021; 78:5865-5880. [PMID: 34232330 PMCID: PMC8260576 DOI: 10.1007/s00018-021-03836-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/22/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022]
Abstract
Many organs and tissues have an intrinsic ability to regenerate from a dedicated, tissue-specific stem cell pool. As organisms age, the process of self-regulation or homeostasis begins to slow down with fewer stem cells available for tissue repair. Tissues become more fragile and organs less efficient. This slowdown of homeostatic processes leads to the development of cellular and neurodegenerative diseases. In this review, we highlight the recent use and future potential of optogenetic approaches to study homeostasis. Optogenetics uses photosensitive molecules and genetic engineering to modulate cellular activity in vivo, allowing precise experiments with spatiotemporal control. We look at applications of this technology for understanding the mechanisms governing homeostasis and degeneration as applied to widely used model organisms, such as Drosophila melanogaster, where other common tools are less effective or unavailable.
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Affiliation(s)
- Wen Kin Lim
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Prameet Kaur
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Huanyan Huang
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | | | - Li Fang Ng
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Jahnavi Suresh
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | - Ajay S Mathuru
- Science Division, Yale-NUS College, Singapore, Singapore
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9
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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10
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The effects of the M2a macrophage-induced axonal regeneration of neurons by arginase 1. Biosci Rep 2021; 40:221966. [PMID: 31994698 PMCID: PMC7012653 DOI: 10.1042/bsr20193031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Spinal cord injury (SCI) is a challenge worldwide, but there are no effective treatments or therapeutic methods in the clinic. Recent studies have shown that type I arginase (Arginase1, Arg1) is closely associated with the treatment of SCI. The classical treatment for SCI involves filling the local area of SCI with activated M2a macrophages to allow the repair and regeneration of some synapses, but the specific mechanism of action of Arg1 is not clear. METHOD In the present study, we first induced the polarization of RAW264.7 macrophages to M2a-type cells using IL-4 and constructed an Arg1 knockout cell line through the use of shRNA; we used these cells to treat a rat model of SCI. Finally, the present study explored the mechanism and pathway by which Arginase 1 regulates spinal repair by immunoblotting and immunohistochemistry. RESULT Suspended M2a (Arg1-/+) macrophages were transplanted into the injury site in a rat model of contusion SCI. Compared with the model group and the shArg1 group, the shScramble (shSc) group exhibited higher Basso, Beattie, Bresnahan motor function scores, more compact structures and more Nissl bodies. Immunohistochemical results showed that the shSc group expressed higher levels of NeuN (a neuronal marker) and tau (an axonal marker), as well as the up-regulation of Cdc42, N-WASP, Arp2/3 and tau, as determined by Western blot. CONCLUSION The study found that the polarization of M2a macrophages promoted the expression of Arginase 1, which restored axonal regeneration, promoted axonal regeneration, and promoted the structural and functional recovery of the contused spinal cord.
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11
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Shaaya M, Fauser J, Karginov AV. Optogenetics: The Art of Illuminating Complex Signaling Pathways. Physiology (Bethesda) 2021; 36:52-60. [PMID: 33325819 DOI: 10.1152/physiol.00022.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dissection of cell signaling requires tools that can mimic spatiotemporal dynamics of individual pathways in living cells. Optogenetic methods enable manipulation of signaling processes with precise timing and local control. In this review, we describe recent optogenetic approaches for regulation of cell signaling, highlight their advantages and limitations, and discuss examples of their application.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois.,University of Illinois Cancer Center, The University of Illinois at Chicago, Chicago, Illinois
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12
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Abstract
Cyanobacteriochromes (CBCRs) are photoswitchable linear tetrapyrrole (bilin)-based light sensors in the phytochrome superfamily with a broad spectral range from the near UV through the far red (330 to 760 nm). The recent discovery of far-red absorbing CBCRs (frCBCRs) has garnered considerable interest from the optogenetic and imaging communities because of the deep penetrance of far-red light into mammalian tissue and the small size of the CBCR protein scaffold. The present studies were undertaken to determine the structural basis for far-red absorption by JSC1_58120g3, a frCBCR from the thermophilic cyanobacterium Leptolyngbya sp. JSC-1 that is a representative member of a phylogenetically distinct class. Unlike most CBCRs that bind phycocyanobilin (PCB), a phycobilin naturally occurring in cyanobacteria and only a few eukaryotic phototrophs, JSC1_58120g3's far-red absorption arises from incorporation of the PCB biosynthetic intermediate 181,182-dihydrobiliverdin (181,182-DHBV) rather than the more reduced and more abundant PCB. JSC1_58120g3 can also yield a far-red-absorbing adduct with the more widespread linear tetrapyrrole biliverdin IXα (BV), thus circumventing the need to coproduce or supplement optogenetic cell lines with PCB. Using high-resolution X-ray crystal structures of 181,182-DHBV and BV adducts of JSC1_58120g3 along with structure-guided mutagenesis, we have defined residues critical for its verdin-binding preference and far-red absorption. Far-red sensing and verdin incorporation make this frCBCR lineage an attractive template for developing robust optogenetic and imaging reagents for deep tissue applications.
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Hörner M, Yousefi OS, Schamel WWA, Weber W. Production, Purification and Characterization of Recombinant Biotinylated Phytochrome B for Extracellular Optogenetics. Bio Protoc 2020; 10:e3541. [PMID: 33659515 PMCID: PMC7842835 DOI: 10.21769/bioprotoc.3541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
In the field of extracellular optogenetics, photoreceptors are applied outside of cells to obtain systems with a desired functionality. Among the diverse applied photoreceptors, phytochromes are the only ones that can be actively and reversibly switched between the active and inactive photostate by the illumination with cell-compatible red and far-red light. In this protocol, we describe the production of a biotinylated variant of the photosensory domain of A. thaliana phytochrome B (PhyB-AviTag) in E. coli with a single, optimized expression plasmid. We give detailed instructions for the purification of the protein by immobilized metal affinity chromatography and the characterization of the protein in terms of purity, biotinylation, spectral photoswitching and the light-dependent interaction with its interaction partner PIF6. In comparison to previous studies applying PhyB-AviTag, the optimized expression plasmid used in this protocol simplifies the production process and shows an increased yield and purity.
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Affiliation(s)
- Maximilian Hörner
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - O. Sascha Yousefi
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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14
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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15
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Teets FD, Watanabe T, Hahn KM, Kuhlman B. A Computational Protocol for Regulating Protein Binding Reactions with a Light-Sensitive Protein Dimer. J Mol Biol 2019; 432:805-814. [PMID: 31887287 DOI: 10.1016/j.jmb.2019.12.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Light-sensitive proteins can be used to perturb signaling networks in living cells and animals with high spatiotemporal resolution. We recently engineered a protein heterodimer that dissociates when irradiated with blue light and demonstrated that by fusing each half of the dimer to termini of a protein that it is possible to selectively block binding surfaces on the protein when in the dark. On activation with light, the dimer dissociates and exposes the binding surface, allowing the protein to bind its partner. Critical to the success of this system, called Z-lock, is that the linkers connecting the dimer components to the termini are engineered so that the dimer forms over the appropriate binding surface. Here, we develop and test a protocol in the Rosetta molecular modeling program for designing linkers for Z-lock. We show that the protocol can predict the most effective linker sets for three different light-sensitive switches, including a newly designed switch that binds the Rho-family GTPase Cdc42 on stimulation with blue light. This protocol represents a generalized computational approach to placing a wide variety of proteins under optogenetic control with Z-lock.
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Affiliation(s)
- Frank D Teets
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, United States.
| | - Takashi Watanabe
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Dr, Chapel Hill, NC 27514, USA.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Dr, Chapel Hill, NC 27514, USA.
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16
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He M, Wang Y, Chen X, Zhao Y, Lou K, Wang Y, Huang L, Hou X, Xu J, Cai X, Cheng Y, Lan M, Yang Y, Gao F. Spatiotemporally controllable diphtheria toxin expression using a light-switchable transgene system combining multifunctional nanoparticle delivery system for targeted melanoma therapy. J Control Release 2019; 319:1-14. [PMID: 31838205 DOI: 10.1016/j.jconrel.2019.12.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022]
Abstract
Gene therapy with external gene insertion (e. g. a suicide gene) and expression specifically in mutated tumor cells has shown to be a promising strategy in treatment of tumors. However, current tumor gene therapy often suffered from low efficiency in gene expression and off-target effects which may cause damage to normal tissues. To address these issues, in this study, a light-switchable transgene nanoparticle delivery system loaded with a diphtheria toxin A (DTA) segment encoded gene, a suicide gene for tumor cells, was developed. The nanoparticles contained vitamin E succinate-grafted polyethyleneimine core and arginylglycylaspartic acid (RGD)-modified pegylated hyaluronic acid shell for targeted delivery of the loaded gene to tumor cells via receptor-mediated (CD44 and αvβ3) endocytosis. Notably, the expression of target proteins in tumor cells could be conveniently regulated by adjusting the blue light intensity in the Light-On system. In in-vitro studies in cultured B16-F10 cells, the pG-DTA-loaded nano-micelles showed greatly improved inhibitory rate compared with the pG-DTA group. Moreover, in the tumor-bearing C57BL/6 mice model, the pG-DTA-loaded nanoparticle exhibited greatly improved efficacy and reduced systemic toxicity with significantly increased survival rate after 21 days. Significantly suppressed tumor angiogenesis was also identified in the nanoparticle-treated group likely due to the targeting ability of the RGD-modified nanoparticle. All the above results indicated that the combination of a light-switchable transgene system with a nanoparticle-based targeted delivery system have great potentials in gene therapy of malignant tumors with improved precision and efficacy.
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Affiliation(s)
- Muye He
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China; Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Wang
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xianjun Chen
- Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Yuzheng Zhao
- Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Kaiyan Lou
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yujie Wang
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lei Huang
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyu Hou
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiajun Xu
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoran Cai
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Cheng
- Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Yang
- Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Optogenetics & Molecular Imaging Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Feng Gao
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China; Department of Pharmaceutics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China.
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Using Tools from Optogenetics to Create Light-Responsive Biomaterials: LOVTRAP-PEG Hydrogels for Dynamic Peptide Immobilization. Ann Biomed Eng 2019; 48:1885-1894. [PMID: 31720906 DOI: 10.1007/s10439-019-02407-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
Hydrogel materials have become a versatile platform for in vitro cell culture due to their ability to simulate many aspects of native tissues. However, precise spatiotemporal presentation of peptides and other biomolecules has remained challenging. Here we report the use of light-sensing proteins (LSPs), more commonly used in optogenetics research, as light-activated reversible binding sites within synthetic poly(ethylene glycol) (PEG) hydrogels. We used LOVTRAP, a two component LSP system consisting of LOV2, a protein domain that can cycle reversibly between "light" and "dark" conformations in response to blue light, and a z-affibody, Zdark (Zdk), that binds the dark state of LOV2, to spatiotemporally control the presentation of a recombinant protein within PEG hydrogels. By immobilizing LOV2 within PEG gels, we were able to capture a recombinant fluorescent protein (used as a model biomolecule) containing a Zdk domain, and then release the Zdk fusion protein using blue light. Zdk was removed from LOV2-containing PEG gels using focused blue light, resulting in a 30% reduction of fluorescence compared to unexposed regions of the gel. Additionally, the reversible binding capability of LOVTRAP was observed in our system, enabling our LOV2 gels to capture and release Zdk at least three times. By adding a Zdk domain to a recombinant peptide or protein, dynamic, spatially constrained displays of non-diffusing ligands within a PEG gel could feasibly be achieved using LOV2.
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18
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Hörner M, Gerhardt K, Salavei P, Hoess P, Härrer D, Kaiser J, Tabor JJ, Weber W. Production of Phytochromes by High-Cell-Density E. coli Fermentation. ACS Synth Biol 2019; 8:2442-2450. [PMID: 31526004 DOI: 10.1021/acssynbio.9b00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phytochromes are important photoreceptors of plants, bacteria, and fungi responsive to light in the red and far-red spectrum. For increasing applications in basic research, synthetic biology, and materials sciences, it is required to recombinantly produce and purify phytochromes in high amounts. An ideal host organism for this purpose is E. coli due to its widespread use, fast growth, and ability for high-cell-density fermentation. Here, we describe the development of a generic platform for the production of phytochromes in E. coli that is compatible with high-cell-density fermentation. We exemplify our approach by the production of the photosensory domains of phytochrome B (PhyB) from A. thaliana and of the cyanobacterial phytochrome 1 (Cph1) from Synechocystis PCC 6803 in the multigram scale per 10 L fermentation run.
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19
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Photodimerization systems for regulating protein-protein interactions with light. Curr Opin Struct Biol 2019; 57:1-8. [PMID: 30818200 DOI: 10.1016/j.sbi.2019.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/28/2019] [Indexed: 12/17/2022]
Abstract
Optogenetic dimerizers are modular domains that can be utilized in a variety of versatile ways to modulate cellular biochemistry. Because of their modularity, many applications using these tools can be easily transferred to new targets without extensive engineering. While a number of photodimerizer systems are currently available, the field remains nascent, with new optimizations for existing systems and new approaches to regulating biological function continuing to be introduced at a steady pace.
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20
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From membrane receptors to protein synthesis and actin cytoskeleton: Mechanisms underlying long lasting forms of synaptic plasticity. Semin Cell Dev Biol 2019; 95:120-129. [PMID: 30634048 DOI: 10.1016/j.semcdb.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/13/2022]
Abstract
Synaptic plasticity, the activity dependent change in synaptic strength, forms the molecular foundation of learning and memory. Synaptic plasticity includes structural changes, with spines changing their size to accomodate insertion and removal of postynaptic receptors, which are correlated with functional changes. Of particular relevance for memory storage are the long lasting forms of synaptic plasticity which are protein synthesis dependent. Due to the importance of spine structural plasticity and protein synthesis, this review focuses on the signaling pathways that connect synaptic stimulation with regulation of protein synthesis and remodeling of the actin cytoskeleton. We also review computational models that implement novel aspects of molecular signaling in synaptic plasticity, such as the role of neuromodulators and spatial microdomains, as well as highlight the need for computational models that connect activation of memory kinases with spine actin dynamics.
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21
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Jia H, Kai L, Heymann M, García-Soriano DA, Härtel T, Schwille P. Light-Induced Printing of Protein Structures on Membranes in Vitro. NANO LETTERS 2018; 18:7133-7140. [PMID: 30295028 DOI: 10.1021/acs.nanolett.8b03187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Reconstituting functional modules of biological systems in vitro is an important yet challenging goal of bottom-up synthetic biology, in particular with respect to their precise spatiotemporal regulation. One of the most desirable external control parameters for the engineering of biological systems is visible light, owing to its specificity and ease of defined application in space and time. Here we engineered the PhyB-PIF6 system to spatiotemporally target proteins by light onto model membranes and thus sequentially guide protein pattern formation and structural assembly in vitro from the bottom up. We show that complex micrometer-sized protein patterns can be printed on time scales of seconds, and the pattern density can be precisely controlled by protein concentration, laser power, and activation time. Moreover, when printing self-assembling proteins such as the bacterial cytoskeleton protein FtsZ, the targeted assembly into filaments and large-scale structures such as artificial rings can be accomplished. Thus, light mediated sequential protein assembly in cell-free systems represents a promising approach to hierarchically building up the next level of complexity toward a minimal cell.
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Affiliation(s)
- Haiyang Jia
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Lei Kai
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Michael Heymann
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Daniela A García-Soriano
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
- Graduate School for Quantitative Biosciences (QBM) , Ludwig-Maximillians-University , Munich , Germany
| | - Tobias Härtel
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
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22
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Visualizing Viral Infection In Vivo by Multi-Photon Intravital Microscopy. Viruses 2018; 10:v10060337. [PMID: 29925766 PMCID: PMC6024644 DOI: 10.3390/v10060337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 12/11/2022] Open
Abstract
Viral pathogens have adapted to the host organism to exploit the cellular machinery for virus replication and to modulate the host cells for efficient systemic dissemination and immune evasion. Much of our knowledge of the effects that virus infections have on cells originates from in vitro imaging studies using experimental culture systems consisting of cell lines and primary cells. Recently, intravital microscopy using multi-photon excitation of fluorophores has been applied to observe virus dissemination and pathogenesis in real-time under physiological conditions in living organisms. Critical steps during viral infection and pathogenesis could be studied by direct visualization of fluorescent virus particles, virus-infected cells, and the immune response to viral infection. In this review, I summarize the latest research on in vivo studies of viral infections using multi-photon intravital microscopy (MP-IVM). Initially, the underlying principle of multi-photon microscopy is introduced and experimental challenges during microsurgical animal preparation and fluorescent labeling strategies for intravital imaging are discussed. I will further highlight recent studies that combine MP-IVM with optogenetic tools and transcriptional analysis as a powerful approach to extend the significance of in vivo imaging studies of viral pathogens.
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23
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Ueda Y, Sato M. Induction of Signal Transduction by Using Non-Channelrhodopsin-Type Optogenetic Tools. Chembiochem 2018; 19:1217-1231. [PMID: 29577530 DOI: 10.1002/cbic.201700635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 12/24/2022]
Abstract
Signal transductions are the basis for all cellular functions. Previous studies investigating signal transductions mainly relied on pharmacological inhibition, RNA interference, and constitutive active/dominant negative protein expression systems. However, such studies do not allow the modulation of protein activity with high spatial and temporal precision in cells, tissues, and organs in animals. Recently, non-channelrhodopsin-type optogenetic tools for regulating signal transduction have emerged. These photoswitches address several disadvantages of previous techniques, and allow us to control a variety of signal transductions such as cell membrane dynamics, calcium signaling, lipid signaling, and apoptosis. In this review we summarize recent advances in the development of such photoswitches and in how these optotools are applied to signaling processes.
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Affiliation(s)
- Yoshibumi Ueda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- AMED-PRIME (Japan), Agency for Medical Research and Development, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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24
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O'Banion CP, Lawrence DS. Optogenetics: A Primer for Chemists. Chembiochem 2018; 19:1201-1216. [DOI: 10.1002/cbic.201800013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Colin P. O'Banion
- Department of Chemistry; Division of Chemical Biology and Medicinal Chemistry and; Department of Pharmacology; University of North Carolina; Chapel Hill NC 27599 USA
| | - David S. Lawrence
- Department of Chemistry; Division of Chemical Biology and Medicinal Chemistry and; Department of Pharmacology; University of North Carolina; Chapel Hill NC 27599 USA
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25
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A simple optogenetic MAPK inhibitor design reveals resonance between transcription-regulating circuitry and temporally-encoded inputs. Nat Commun 2017; 8:15017. [PMID: 28497795 PMCID: PMC5437309 DOI: 10.1038/ncomms15017] [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: 06/19/2016] [Accepted: 02/20/2017] [Indexed: 12/31/2022] Open
Abstract
Engineering light-sensitive protein regulators has been a tremendous multidisciplinary challenge. Optogenetic regulators of MAPKs, central nodes of cellular regulation, have not previously been described. Here we present OptoJNKi, a light-regulated JNK inhibitor based on the AsLOV2 light-sensor domain using the ubiquitous FMN chromophore. OptoJNKi gene-transfer allows optogenetic applications, whereas protein delivery allows optopharmacology. Development of OptoJNKi suggests a design principle for other optically regulated inhibitors. From this, we generate Optop38i, which inhibits p38MAPK in intact illuminated cells. Neurons are known for interpreting temporally-encoded inputs via interplay between ion channels, membrane potential and intracellular calcium. However, the consequences of temporal variation of JNK-regulating trophic inputs, potentially resulting from synaptic activity and reversible cellular protrusions, on downstream targets are unknown. Using OptoJNKi, we reveal maximal regulation of c-Jun transactivation can occur at unexpectedly slow periodicities of inhibition depending on the inhibitor's subcellular location. This provides evidence for resonance in metazoan JNK-signalling circuits. Light-sensitive regulators of protein kinases could offer valuable insights into intracellular signalling. Here the authors design an optogenetic inhibitor of c-Jun N-terminal kinase (JNK) and show evidence for resonance in JNK signalling circuits in neurons, and use the same design principle to develop an inhibitor for p38MAPK.
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26
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Endo M, Ozawa T. Strategies for development of optogenetic systems and their applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Han T, Chen Q, Liu H. Engineered Photoactivatable Genetic Switches Based on the Bacterium Phage T7 RNA Polymerase. ACS Synth Biol 2017; 6:357-366. [PMID: 27794600 DOI: 10.1021/acssynbio.6b00248] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Genetic switches in which the activity of T7 RNA polymerase (RNAP) is directly regulated by external signals are obtained with an engineering strategy of splitting the protein into fragments and using regulatory domains to modulate their reconstitutions. Robust switchable systems with excellent dark-off/light-on properties are obtained with the light-activatable VVD domain and its variants as regulatory domains. For the best split position found, working switches exploit either the light-induced interactions between the VVD domains or allosteric effects. The split fragments show high modularity when they are combined with different regulatory domains such as those with chemically inducible interaction, enabling chemically controlled switches. To summarize, the T7 RNA polymerase-based switches are powerful tools to implement light-activated gene expression in different contexts. Moreover, results about the studied split positions and domain organizations may facilitate future engineering studies on this and on related proteins.
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Affiliation(s)
| | | | - Haiyan Liu
- Hefei
Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
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28
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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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29
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Goglia AG, Wilson MZ, DiGiorno DB, Toettcher JE. Optogenetic Control of Ras/Erk Signaling Using the Phy-PIF System. Methods Mol Biol 2017; 1636:3-20. [PMID: 28730469 DOI: 10.1007/978-1-4939-7154-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Ras/Erk signaling pathway plays a central role in diverse cellular processes ranging from development to immune cell activation to neural plasticity to cancer. In recent years, this pathway has been widely studied using live-cell fluorescent biosensors, revealing complex Erk dynamics that arise in many cellular contexts. Yet despite these high-resolution tools for measurement, the field has lacked analogous tools for control over Ras/Erk signaling in live cells. Here, we provide detailed methods for one such tool based on the optical control of Ras activity, which we call "Opto-SOS." Expression of the Opto-SOS constructs can be coupled with a live-cell reporter of Erk activity to reveal highly quantitative input-to-output maps of the pathway. Detailed herein are protocols for expressing the Opto-SOS system in cultured cells, purifying the small molecule cofactor necessary for optical stimulation, imaging Erk responses using live-cell microscopy, and processing the imaging data to quantify Ras/Erk signaling dynamics.
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Affiliation(s)
- Alexander G Goglia
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory Room 140, Washington Road, Princeton, NJ, 08544, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory Room 140, Washington Road, Princeton, NJ, 08544, USA
| | - Daniel B DiGiorno
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory Room 140, Washington Road, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory Room 140, Washington Road, Princeton, NJ, 08544, USA.
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Actin-Dependent Alterations of Dendritic Spine Morphology in Shankopathies. Neural Plast 2016; 2016:8051861. [PMID: 27795858 PMCID: PMC5067329 DOI: 10.1155/2016/8051861] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022] Open
Abstract
Shank proteins (Shank1, Shank2, and Shank3) act as scaffolding molecules in the postsynaptic density of many excitatory neurons. Mutations in SHANK genes, in particular SHANK2 and SHANK3, lead to autism spectrum disorders (ASD) in both human and mouse models. Shank3 proteins are made of several domains-the Shank/ProSAP N-terminal (SPN) domain, ankyrin repeats, SH3 domain, PDZ domain, a proline-rich region, and the sterile alpha motif (SAM) domain. Via various binding partners of these domains, Shank3 is able to bind and interact with a wide range of proteins including modulators of small GTPases such as RICH2, a RhoGAP protein, and βPIX, a RhoGEF protein for Rac1 and Cdc42, actin binding proteins and actin modulators. Dysregulation of all isoforms of Shank proteins, but especially Shank3, leads to alterations in spine morphogenesis, shape, and activity of the synapse via altering actin dynamics. Therefore, here, we highlight the role of Shank proteins as modulators of small GTPases and, ultimately, actin dynamics, as found in multiple in vitro and in vivo models. The failure to mediate this regulatory role might present a shared mechanism in the pathophysiology of autism-associated mutations, which leads to dysregulation of spine morphogenesis and synaptic signaling.
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31
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Aper SJ, Merkx M. Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn(2+) Sensor into a Light-Responsive Zn(2+) Binding Protein. ACS Synth Biol 2016; 5:698-709. [PMID: 27031076 DOI: 10.1021/acssynbio.6b00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein-based sensors and switches provide attractive tools for the real-time monitoring and control of molecular processes in complex biological environments. Fluorescent sensor proteins have been developed for a wide variety of small molecules, but the construction of genetically encoded light-responsive ligand binding proteins remains mostly unexplored. Here we present a generic approach to reengineer a previously developed FRET-based Zn(2+) sensor into a light-activatable Zn(2+) binding protein using a design strategy based on mutually exclusive domain interactions. These so-called VividZn proteins consist of two light-responsive Vivid domains that homodimerize upon illumination with blue light, thus preventing the binding of Zn(2+) between two Zn(2+) binding domains, Atox1 and WD4. Following optimization of the linker between WD4 and the N-terminus of one of the Vivid domains, VividZn variants were obtained that show a 9- to 55-fold decrease in Zn(2+) affinity upon illumination, which is fully reversible following dark adaptation. The Zn(2+) affinities of the switch could be rationally tuned between 1 pM and 2 nM by systematic variation of linker length and mutation of one of the Zn(2+) binding residues. Similarly, introduction of mutations in the Vivid domains allowed tuning of the switching kinetics between 10 min and 7 h. Low expression levels in mammalian cells precluded the demonstration of light-induced perturbation of cytosolic Zn(2+) levels. Nonetheless, our results firmly establish the use of intramolecular Vivid dimerization as an attractive light-sensitive input module to rationally engineer light-responsive protein switches based on mutually exclusive domain interactions.
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Affiliation(s)
- Stijn J.A. Aper
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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32
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Rockwell NC, Martin SS, Lagarias JC. Identification of Cyanobacteriochromes Detecting Far-Red Light. Biochemistry 2016; 55:3907-19. [DOI: 10.1021/acs.biochem.6b00299] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
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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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Gomez EJ, Gerhardt K, Judd J, Tabor JJ, Suh J. Light-Activated Nuclear Translocation of Adeno-Associated Virus Nanoparticles Using Phytochrome B for Enhanced, Tunable, and Spatially Programmable Gene Delivery. ACS NANO 2016; 10:225-237. [PMID: 26618393 DOI: 10.1021/acsnano.5b05558] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gene delivery vectors that are activated by external stimuli may allow improved control over the location and the degree of gene expression in target populations of cells. Light is an attractive stimulus because it does not cross-react with cellular signaling networks, has negligible toxicity, is noninvasive, and can be applied in space and time with unparalleled precision. We used the previously engineered red (R)/far-red (FR) light-switchable protein phytochrome B (PhyB) and its R light dependent interaction partner phytochrome interacting factor 6 (PIF6) from Arabidopsis thaliana to engineer an adeno-associated virus (AAV) platform whose gene delivery efficiency is controlled by light. Upon exposure to R light, AAV engineered to display PIF6 motifs on the capsid bind to PhyB tagged with a nuclear localization sequence (NLS), resulting in significantly increased translocation of viruses into the host cell nucleus and overall gene delivery efficiency. By modulating the ratio of R to FR light, the gene delivery efficiency can be tuned to as little as 35% or over 600% of the unengineered AAV. We also demonstrate spatial control of gene delivery using projected patterns of codelivered R and FR light. Overall, our successful use of light-switchable proteins in virus capsid engineering extends these important optogenetic tools into the adjacent realm of nucleic acid delivery and enables enhanced, tunable, and spatially controllable regulation of viral gene delivery. Our current light-triggered viral gene delivery prototype may be broadly useful for genetic manipulation of cells ex vivo or in vivo in transgenic model organisms, with the ultimate prospect of achieving dose- and site-specific gene expression profiles for either therapeutic (e.g., regenerative medicine) or fundamental discovery research efforts.
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Affiliation(s)
- Eric J Gomez
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Karl Gerhardt
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Justin Judd
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Junghae Suh
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
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35
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O'Neill PR, Gautam N. Optimizing optogenetic constructs for control over signaling and cell behaviours. Photochem Photobiol Sci 2015; 14:1578-85. [PMID: 26135203 DOI: 10.1039/c5pp00171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Optogenetic tools have recently been developed that enable dynamic control over the activities of select signaling proteins. They provide the unique ability to rapidly turn signaling events on or off with subcellular control in living cells and organisms. This capability is leading to new insights into how the spatial and temporal coordination of signaling events governs dynamic cell behaviours such as migration and neurite outgrowth. These tools can also be used to dissect a protein's signaling functions at different organelles. Here we review the properties of photoreceptors from diverse organisms that have been leveraged to control signaling in mammalian cells. We emphasize recent engineering approaches that have been used to create optogenetic constructs with optimized spectral, kinetic, and signaling properties for controlling cell behaviours.
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Affiliation(s)
- P R O'Neill
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Abstract
The early mouse embryo is an excellent system to study how a small group of initially rounded cells start to change shape and establish the first forms of adhesion-based cell-cell interactions in mammals in vivo. In addition to its critical role in the structural integrity of the embryo, we discuss here how adhesion is important to regulate cell polarity and cell fate. Recent evidence suggests that adherens junctions participate in signaling pathways by localizing key proteins to subcellular microdomains. E-cadherin has been identified as the main player required for the establishment of adhesion but other mechanisms involving additional proteins or physical forces acting in the embryo may also contribute. Application of new technologies that enable high-resolution quantitative imaging of adhesion protein dynamics and measurements of biomechanical forces will provide a greater understanding of how adhesion patterns the early mammalian embryo.
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Affiliation(s)
- Melanie D White
- European Molecular Biology Laboratory (EMBL) Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Nicolas Plachta
- European Molecular Biology Laboratory (EMBL) Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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37
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Narikawa R, Nakajima T, Aono Y, Fushimi K, Enomoto G, Ni-Ni-Win, Itoh S, Sato M, Ikeuchi M. A biliverdin-binding cyanobacteriochrome from the chlorophyll d-bearing cyanobacterium Acaryochloris marina. Sci Rep 2015; 5:7950. [PMID: 25609645 PMCID: PMC4302295 DOI: 10.1038/srep07950] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole-binding photoreceptors in cyanobacteria that absorb visible and near-ultraviolet light. CBCRs are divided into two types based on the type of chromophore they contain: phycocyanobilin (PCB) or phycoviolobilin (PVB). PCB-binding CBCRs reversibly photoconvert at relatively long wavelengths, i.e., the blue-to-red region, whereas PVB-binding CBCRs reversibly photoconvert at shorter wavelengths, i.e., the near-ultraviolet to green region. Notably, prior to this report, CBCRs containing biliverdin (BV), which absorbs at longer wavelengths than do PCB and PVB, have not been found. Herein, we report that the typical red/green CBCR AM1_1557 from the chlorophyll d–bearing cyanobacterium Acaryochloris marina can bind BV almost comparable to PCB. This BV-bound holoprotein reversibly photoconverts between a far red light–absorbing form (Pfr, λmax = 697 nm) and an orange light–absorbing form (Po, λmax = 622 nm). At room temperature, Pfr fluoresces with a maximum at 730 nm. These spectral features are red-shifted by 48~77 nm compared with those of the PCB-bound domain. Because the absorbance of chlorophyll d is red-shifted compared with that of chlorophyll a, the BV-bound AM1_1557 may be a physiologically relevant feature of A. marina and is potentially useful as an optogenetic switch and/or fluorescence imager.
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Affiliation(s)
- Rei Narikawa
- 1] Department of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku, Shizuoka 422-8529, Japan [2] Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan [3] Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
| | - Takahiro Nakajima
- Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Yuki Aono
- Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Gen Enomoto
- Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Ni-Ni-Win
- Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Shigeru Itoh
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Moritoshi Sato
- Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Masahiko Ikeuchi
- 1] Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan [2] Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
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38
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Weitzman M, Hahn KM. Optogenetic approaches to cell migration and beyond. Curr Opin Cell Biol 2014; 30:112-20. [PMID: 25216352 DOI: 10.1016/j.ceb.2014.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 07/29/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
Optogenetics, the use of genetically encoded tools to control protein function with light, can generate localized changes in signaling within living cells and animals. For years it has been focused on channel proteins for neurobiology, but has recently expanded to cover many different types of proteins, using a broad array of different protein engineering approaches. These methods have largely been directed at proteins involved in motility, cytoskeletal regulation and gene expression. This review provides a survey of non-channel proteins that have been engineered for optogenetics. Existing molecules are used to illustrate the advantages and disadvantages of the many imaginative new approaches that the reader can use to create light-controlled proteins.
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Affiliation(s)
- Matthew Weitzman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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39
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Abstract
The light-based control of ion channels has been transformative for the neurosciences, but the optogenetic toolkit does not stop there. An expanding number of proteins and cellular functions have been shown to be controlled by light, and the practical considerations in deciding between reversible optogenetic systems (such as systems that use light-oxygen-voltage domains, phytochrome proteins, cryptochrome proteins and the fluorescent protein Dronpa) are well defined. The field is moving beyond proof of concept to answering real biological questions, such as how cell signalling is regulated in space and time, that were difficult or impossible to address with previous tools.
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40
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How to control proteins with light in living systems. Nat Chem Biol 2014; 10:533-41. [DOI: 10.1038/nchembio.1534] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/21/2014] [Indexed: 11/08/2022]
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41
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Kianianmomeni A, Hallmann A. Algal photoreceptors: in vivo functions and potential applications. PLANTA 2014; 239:1-26. [PMID: 24081482 DOI: 10.1007/s00425-013-1962-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/09/2013] [Indexed: 06/02/2023]
Abstract
Many algae, particularly microalgae, possess a sophisticated light-sensing system including photoreceptors and light-modulated signaling pathways to sense environmental information and secure the survival in a rapidly changing environment. Over the last couple of years, the multifaceted world of algal photobiology has enriched our understanding of the light absorption mechanisms and in vivo function of photoreceptors. Moreover, specific light-sensitive modules have already paved the way for the development of optogenetic tools to generate light switches for precise and spatial control of signaling pathways in individual cells and even in complex biological systems.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany,
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42
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Beyeler A, Eckhardt CA, Tye KM. Deciphering Memory Function with Optogenetics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 122:341-90. [DOI: 10.1016/b978-0-12-420170-5.00012-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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43
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Ma Z, Du Z, Chen X, Wang X, Yang Y. Fine tuning the LightOn light-switchable transgene expression system. Biochem Biophys Res Commun 2013; 440:419-23. [PMID: 24095689 DOI: 10.1016/j.bbrc.2013.09.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Spatiotemporal control of transgene expression in living cells provides new opportunities for the characterization of gene function in complex biological processes. We previously reported a synthetic, light-switchable transgene expression system called LightOn that can be used to control gene expression using blue light. In the present study, we modified the different promoter segments of the light switchable transcription factor GAVPO and the target gene, and assayed their effects on protein expression under dark or light conditions. The results showed that the LightOn system maintained its high on/off ratio under most modifications, but its induction efficiency and background gene expression level can be fine-tuned by modifying the core promoter, the UASG sequence number, the length of the spacer between UASG and the core promoter of the target protein, and the expression level of the GAVPO transcription factor. Thus, the LightOn gene expression system can be adapted to a large range of applications according to the requirements of the background and the induced gene expression.
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Affiliation(s)
- Zhengcai Ma
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Mei Long Road, Shanghai 200237, China
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44
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Piatkevich KD, Subach FV, Verkhusha VV. Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals. Chem Soc Rev 2013; 42:3441-52. [PMID: 23361376 PMCID: PMC3618476 DOI: 10.1039/c3cs35458j] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Near-infrared light is favourable for imaging in mammalian tissues due to low absorbance of hemoglobin, melanin, and water. Therefore, fluorescent proteins, biosensors and optogenetic constructs for optimal imaging, optical readout and light manipulation in mammals should have fluorescence and action spectra within the near-infrared window. Interestingly, natural Bacterial Phytochrome Photoreceptors (BphPs) utilize the low molecular weight biliverdin, found in most mammalian tissues, as a photoreactive chromophore. Due to their near-infrared absorbance BphPs are preferred templates for designing optical molecular tools for applications in mammals. Moreover, BphPs spectrally complement existing genetically-encoded probes. Several BphPs were already developed into the near-infrared fluorescent variants. Based on the analysis of the photochemistry and structure of BphPs we suggest a variety of possible BphP-based fluorescent proteins, biosensors, and optogenetic tools. Putative design strategies and experimental considerations for such probes are discussed.
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Affiliation(s)
- Kiryl D. Piatkevich
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
| | - Fedor V. Subach
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
| | - Vladislav V. Verkhusha
- Gruss-Lipper Biophotonics Center and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Fax: +1 (718) 430-8996; Tel: +1 (718) 430-8591
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45
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Analysis and regulation of amoeboid-like cell motility using synthetic Ca2+-sensitive proteins. Cell Calcium 2013; 53:231-40. [DOI: 10.1016/j.ceca.2012.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/18/2012] [Accepted: 12/24/2012] [Indexed: 11/19/2022]
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46
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Yin T, Wu YI. Guiding lights: recent developments in optogenetic control of biochemical signals. Pflugers Arch 2013; 465:397-408. [PMID: 23417571 DOI: 10.1007/s00424-013-1244-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
Optogenetics arises from the innovative application of microbial opsins in mammalian neurons and has since been a powerful technology that fuels the advance of our knowledge in neuroscience. In recent years, there has been growing interest in designing optogenetic tools extendable to broader cell types and biochemical signals. To date, a variety of photoactivatable proteins (refers to induction of protein activity in contrast to fluorescence) have been developed based on the understanding of plant and microbial photoreceptors including phototropins, blue light sensors using flavin adenine dinucleotide proteins, cryptochromes, and phytochromes. Such tools offered researchers reversible, quantitative, and precise spatiotemporal control of enzymatic activity, protein-protein interaction, protein translocation, as well as gene transcription in cells and in whole animals. In this review, we will briefly introduce these photosensory proteins, describe recent developments in optogenetics, and compare and contrast different methods based on their advantages and limitations.
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Affiliation(s)
- Taofei Yin
- Robert D. Berlin Center for Cell Analysis & Modeling, Department of Genetics & Developmental Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
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47
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Müller K, Engesser R, Metzger S, Schulz S, Kämpf MM, Busacker M, Steinberg T, Tomakidi P, Ehrbar M, Nagy F, Timmer J, Zubriggen MD, Weber W. A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Res 2013; 41:e77. [PMID: 23355611 PMCID: PMC3627562 DOI: 10.1093/nar/gkt002] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Growth and differentiation of multicellular systems is orchestrated by spatially restricted gene expression programs in specialized subpopulations. The targeted manipulation of such processes by synthetic tools with high-spatiotemporal resolution could, therefore, enable a deepened understanding of developmental processes and open new opportunities in tissue engineering. Here, we describe the first red/far-red light-triggered gene switch for mammalian cells for achieving gene expression control in time and space. We show that the system can reversibly be toggled between stable on- and off-states using short light pulses at 660 or 740 nm. Red light-induced gene expression was shown to correlate with the applied photon number and was compatible with different mammalian cell lines, including human primary cells. The light-induced expression kinetics were quantitatively analyzed by a mathematical model. We apply the system for the spatially controlled engineering of angiogenesis in chicken embryos. The system’s performance combined with cell- and tissue-compatible regulating red light will enable unprecedented spatiotemporally controlled molecular interventions in mammalian cells, tissues and organisms.
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Affiliation(s)
- Konrad Müller
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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48
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Shaw SL, Ehrhardt DW. Smaller, faster, brighter: advances in optical imaging of living plant cells. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:351-75. [PMID: 23506334 DOI: 10.1146/annurev-arplant-042110-103843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The advent of fluorescent proteins and access to modern imaging technologies have dramatically accelerated the pace of discovery in plant cell biology. Remarkable new insights into such diverse areas as plant pathogenesis, cytoskeletal dynamics, sugar transport, cell wall synthesis, secretory control, and hormone signaling have come from careful examination of living cells using advanced optical probes. New technologies, both commercially available and on the horizon, promise a continued march toward more quantitative methods for imaging and for extending the optical exploration of biological structure and activity to molecular scales. In this review, we lay out fundamental issues in imaging plant specimens and look ahead to several technological innovations in molecular tools, instrumentation, imaging methods, and specimen handling that show promise for shaping the coming era of plant cell biology.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Müller K, Weber W. Optogenetic tools for mammalian systems. MOLECULAR BIOSYSTEMS 2013; 9:596-608. [DOI: 10.1039/c3mb25590e] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Pathak GP, Vrana JD, Tucker CL. Optogenetic control of cell function using engineered photoreceptors. Biol Cell 2012; 105:59-72. [PMID: 23157573 DOI: 10.1111/boc.201200056] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
Abstract
Over the past decades, there has been growing recognition that light can provide a powerful stimulus for biological interrogation. Light-actuated tools allow manipulation of molecular events with ultra-fine spatial and fast temporal resolution, as light can be rapidly delivered and focused with sub-micrometre precision within cells. While light-actuated chemicals such as photolabile 'caged' compounds have been in existence for decades, the use of genetically encoded natural photoreceptors for optical control of biological processes has recently emerged as a powerful new approach with several advantages over traditional methods. Here, we review recent advances using light to control basic cellular functions and discuss the engineering challenges that lie ahead for improving and expanding the ever-growing optogenetic toolkit.
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Affiliation(s)
- Gopal P Pathak
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 90045, USA
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