1
|
Wang Y, Bi Z, Song Y, Duan L, Chen SC. Selective activation of photoactivatable fluorescent protein based on binary holography. BIOMEDICAL OPTICS EXPRESS 2024; 15:3382-3393. [PMID: 38855656 PMCID: PMC11161383 DOI: 10.1364/boe.519531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/11/2024]
Abstract
The ability to deliver laser doses to different target locations with high spatial and temporal resolution has been a long-sought goal in photo-stimulation and optogenetics research via, for example, photoactivatable proteins. These light-sensitive proteins undergo conformational changes upon photoactivation, serving functions such as triggering fluorescence, modulating ion channel activities, or initiating biochemical reactions within cells. Conventionally, photo-stimulation on light-sensitive proteins is performed by serially scanning a laser focus or via 2D projection, which is limited by relatively low spatiotemporal resolution. In this work, we present a programmable two-photon stimulation method based on a digital micromirror device (DMD) and binary holography to perform the activation of photoactivatable green fluorescent protein (PAGFP) in live cells. This method achieved grayscale and 3D selective PAGFP activation with subcellular resolution. In the experiments, we demonstrated the 3D activation capability and investigated the diffusion dynamics of activated PAGFP on the cell membrane. A regional difference in cell membrane diffusivity was observed, indicating the great potential of our approach in interrogating the spatiotemporal dynamics of cellular processes inside living cells.
Collapse
Affiliation(s)
- Yintao Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
- Centre for Perceptual and Interactive Intelligence (CPII), Hong Kong Science Park, N.T., Hong Kong SAR, China
| | - Zhenyu Bi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Yutong Song
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Liting Duan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
- Centre for Perceptual and Interactive Intelligence (CPII), Hong Kong Science Park, N.T., Hong Kong SAR, China
| |
Collapse
|
2
|
Pang B, Wu X, Chen H, Yan Y, Du Z, Yu Z, Yang X, Wang W, Lu K. Exploring the memory: existing activity-dependent tools to tag and manipulate engram cells. Front Cell Neurosci 2024; 17:1279032. [PMID: 38259503 PMCID: PMC10800721 DOI: 10.3389/fncel.2023.1279032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/17/2023] [Indexed: 01/24/2024] Open
Abstract
The theory of engrams, proposed several years ago, is highly crucial to understanding the progress of memory. Although it significantly contributes to identifying new treatments for cognitive disorders, it is limited by a lack of technology. Several scientists have attempted to validate this theory but failed. With the increasing availability of activity-dependent tools, several researchers have found traces of engram cells. Activity-dependent tools are based on the mechanisms underlying neuronal activity and use a combination of emerging molecular biological and genetic technology. Scientists have used these tools to tag and manipulate engram neurons and identified numerous internal connections between engram neurons and memory. In this review, we provide the background, principles, and selected examples of applications of existing activity-dependent tools. Using a combination of traditional definitions and concepts of engram cells, we discuss the applications and limitations of these tools and propose certain developmental directions to further explore the functions of engram cells.
Collapse
Affiliation(s)
- Bo Pang
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Xiaoyan Wu
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Hailun Chen
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Yiwen Yan
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Zibo Du
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zihan Yu
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Xiai Yang
- Department of Neurology, Ankang Central Hospital, Ankang, China
| | - Wanshan Wang
- Laboratory Animal Management Center, Southern Medical University, Guangzhou, China
- Guangzhou Southern Medical Laboratory Animal Sci. and Tech. Co., Ltd., Guangzhou, China
| | - Kangrong Lu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Southern Medical University, Guangzhou, China
| |
Collapse
|
3
|
Kocaoglan EG, Radhakrishnan D, Nakayama N. Synthetic developmental biology: molecular tools to re-design plant shoots and roots. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3864-3876. [PMID: 37155965 PMCID: PMC10826796 DOI: 10.1093/jxb/erad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
Collapse
Affiliation(s)
- Elif Gediz Kocaoglan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Dhanya Radhakrishnan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Naomi Nakayama
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
4
|
Gligorovski V, Sadeghi A, Rahi SJ. Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor. Nat Commun 2023; 14:3810. [PMID: 37369667 DOI: 10.1038/s41467-023-38959-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z3EV, blue-light inducible optogenetic systems El222-LIP, El222-GLIP, and red-light inducible PhyB-PIF3. We report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of each system using an intuitive unit, maxGAL1. We uncover disadvantages of widely used tools, e.g., nonmonotonic activity of MET3pr and GALL, slow off kinetics of the doxycycline- and estradiol-inducible systems tetOpr and Z3EV, and high variability of PHO5pr and red-light activated PhyB-PIF3 system. We introduce two previously uncharacterized systems: strongLOV, a more light-sensitive El222 mutant, and ARG3pr, which is induced in the absence of arginine or presence of methionine. To demonstrate fine control over gene circuits, we experimentally tune the time between cell cycle Start and mitosis, artificially simulating near-wild-type timing. All strains, constructs, code, and data ( https://promoter-benchmark.epfl.ch/ ) are made available.
Collapse
Affiliation(s)
- Vojislav Gligorovski
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ahmad Sadeghi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sahand Jamal Rahi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
5
|
Kiyota N, Namekata K, Nishijima E, Guo X, Kimura A, Harada C, Nakazawa T, Harada T. Effects of constitutively active K-Ras on axon regeneration after optic nerve injury. Neurosci Lett 2023; 799:137124. [PMID: 36780941 DOI: 10.1016/j.neulet.2023.137124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
Visual disturbance after optic nerve injury is a serious problem. Attempts have been made to enhance the intrinsic ability of retinal ganglion cells (RGCs) to regenerate their axons, and the importance of PI3K/Akt and RAF/MEK/ERK signal activation has been suggested. Since these signals are shared with oncogenic signaling cascades, in this study, we focused on a constitutively active form of K-Ras, K-RasV12, to determine if overexpression of this molecule could stimulate axon regeneration. We confirmed that K-RasV12 phosphorylated Akt and ERK in vitro. Intravitreal delivery of AAV2-K-RasV12 increased the number of surviving RGCs and promoted 1.0 mm of axon regeneration one week after optic nerve injury without inducing abnormal proliferative effects in the RGCs. In addition, AAV2-K-RasV12 induced robust RGC axon regeneration, reaching as far as approximately 2.5 mm from the injury site, in eight weeks. Our findings suggest that AAV2-K-RasV12 could provide a good model for speedy and efficient analysis of the mechanism underlying axon regeneration in vivo.
Collapse
Affiliation(s)
- Naoki Kiyota
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuhiko Namekata
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
| | - Euido Nishijima
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Xiaoli Guo
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Atsuko Kimura
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Chikako Harada
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takayuki Harada
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| |
Collapse
|
6
|
Crellin HA, Buckley CE. Using Optogenetics to Investigate the Shared Mechanisms of Apical-Basal Polarity and Mitosis. Cells Tissues Organs 2023; 213:161-180. [PMID: 36599311 DOI: 10.1159/000528796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/18/2022] [Indexed: 01/05/2023] Open
Abstract
The initiation of apical-basal (AB) polarity and the process of mitotic cell division are both characterised by the generation of specialised plasma membrane and cortical domains. These are generated using shared mechanisms, such as asymmetric protein accumulation, Rho GTPase signalling, cytoskeletal reorganisation, vesicle trafficking, and asymmetric phosphoinositide distribution. In epithelial tissue, the coordination of AB polarity and mitosis in space and time is important both during initial epithelial development and to maintain tissue integrity and ensure appropriate cell differentiation at later stages. Whilst significant progress has been made in understanding the mechanisms underlying cell division and AB polarity, it has so far been challenging to fully unpick the complex interrelationship between polarity, signalling, morphogenesis, and cell division. However, the recent emergence of optogenetic protein localisation techniques is now allowing researchers to reversibly control protein activation, localisation, and signalling with high spatiotemporal resolution. This has the potential to revolutionise our understanding of how subcellular processes such as AB polarity are integrated with cell behaviours such as mitosis and how these processes impact whole tissue morphogenesis. So far, these techniques have been used to investigate processes such as cleavage furrow ingression, mitotic spindle positioning, and in vivo epithelial morphogenesis. This review describes some of the key shared mechanisms of cell division and AB polarity establishment, how they are coordinated during development and how the advance of optogenetic techniques is furthering this research field.
Collapse
Affiliation(s)
- Helena A Crellin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Clare E Buckley
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| |
Collapse
|
7
|
Lan TH, He L, Huang Y, Zhou Y. Optogenetics for transcriptional programming and genetic engineering. Trends Genet 2022; 38:1253-1270. [PMID: 35738948 PMCID: PMC10484296 DOI: 10.1016/j.tig.2022.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 01/24/2023]
Abstract
Optogenetics combines genetics and biophotonics to enable noninvasive control of biological processes with high spatiotemporal precision. When engineered into protein machineries that govern the cellular information flow as depicted in the central dogma, multiple genetically encoded non-opsin photosensory modules have been harnessed to modulate gene transcription, DNA or RNA modifications, DNA recombination, and genome engineering by utilizing photons emitting in the wide range of 200-1000 nm. We present herein generally applicable modular strategies for optogenetic engineering and highlight latest advances in the broad applications of opsin-free optogenetics to program transcriptional outputs and precisely manipulate the mammalian genome, epigenome, and epitranscriptome. We also discuss current challenges and future trends in opsin-free optogenetics, which has been rapidly evolving to meet the growing needs in synthetic biology and genetics research.
Collapse
Affiliation(s)
- Tien-Hung Lan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA; Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX 77030, USA.
| |
Collapse
|
8
|
Sharfstein ST. Bio-hybrid electronic and photonic devices. Exp Biol Med (Maywood) 2022; 247:2128-2141. [PMID: 36533579 PMCID: PMC9837307 DOI: 10.1177/15353702221144087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bio-hybrid devices, combining electronic and photonic components with cells, tissues, and organs, hold potential for advancing our understanding of biology, physiology, and pathologies and for treating a wide range of conditions and diseases. In this review, I describe the devices, materials, and technologies that enable bio-hybrid devices and provide examples of their utilization at multiple biological scales ranging from the subcellular to whole organs. Finally, I describe the outcomes of a National Science Foundation (NSF)-funded workshop envisioning potential applications of these technologies to improve health outcomes and quality of life.
Collapse
|
9
|
Khamaru M, Nath D, Mitra D, Roy S. Assessing Combinatorial Diversity of Aureochrome Basic Leucine Zippers through Genome-Wide Screening. Cells Tissues Organs 2022; 213:133-146. [PMID: 36261029 DOI: 10.1159/000527593] [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: 06/06/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Aureochromes are unique blue light-responsive light-oxygen-voltage (LOV) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in these brown photosynthetic algae. Both the LOV sensor and the bZIP effector show overall sequence-structure conservation. The structurally similar LOV + bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles - though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.
Collapse
Affiliation(s)
| | - Deep Nath
- Department of Physics, Bose Institute, Kolkata, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Soumen Roy
- Department of Physics, Bose Institute, Kolkata, India
| |
Collapse
|
10
|
Ribeiro IMA, Eßbauer W, Kutlesa R, Borst A. Spatial and temporal control of expression with light-gated LOV-LexA. G3 GENES|GENOMES|GENETICS 2022; 12:6649684. [PMID: 35876796 PMCID: PMC9526042 DOI: 10.1093/g3journal/jkac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022]
Abstract
The ability to drive expression of exogenous genes in different tissues and cell types, under the control of specific enhancers, has been crucial for discovery in biology. While many enhancers drive expression broadly, several genetic tools were developed to obtain access to isolated cell types. Studies of spatially organized neuropiles in the central nervous system of fruit flies have raised the need for a system that targets subsets of cells within a single neuronal type, a feat currently dependent on stochastic flip-out methods. To access the same cells within a given expression pattern consistently across fruit flies, we developed the light-gated expression system LOV-LexA. We combined the bacterial LexA transcription factor with the plant-derived light, oxygen, or voltage photosensitive domain and a fluorescent protein. Exposure to blue light uncages a nuclear localizing signal in the C-terminal of the light, oxygen, or voltage domain and leads to the translocation of LOV-LexA to the nucleus, with the subsequent initiation of transcription. LOV-LexA enables spatial and temporal control of expression of transgenes under LexAop sequences in larval fat body and pupal and adult neurons with blue light. The LOV-LexA tool is ready to use with GAL4 and Split-GAL4 drivers in its current form and constitutes another layer of intersectional genetics that provides light-controlled genetic access to specific cells across flies.
Collapse
Affiliation(s)
- Inês M A Ribeiro
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Wolfgang Eßbauer
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Romina Kutlesa
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Alexander Borst
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| |
Collapse
|
11
|
Shin W, Jeong S, Lee JU, Jeong SY, Shin J, Kim HH, Cheon J, Lee JH. Magnetogenetics with Piezo1 Mechanosensitive Ion Channel for CRISPR Gene Editing. NANO LETTERS 2022; 22:7415-7422. [PMID: 36069378 DOI: 10.1021/acs.nanolett.2c02314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Regulation of genetic activity in single cells and tissues is pivotal to determine key cellular functions in current biomedicine, yet the conventional biochemical activators lack spatiotemporal precision due to the diffusion-mediated slow kinetics and nonselectivity. Here, we describe a magnetogenetic method for target-specific activation of a clustered regularly interspaced short palindromic repeats (CRISPR) system for the regulation of intracellular proteins. We used magnetomechanical force generated by the magnetic nanostructure to activate pre-encoded Piezo1, the mechanosensitive ion channel, on the target cell. The activated Piezo1 further triggers the intracellular Ca2+ signaling pathway, inducing the pre-encoded genes to express genes of interest (GOIs), which is Cas9 protein for the CRISPR regulation of the target proteins. We demonstrated that this magnetogenetic CRISPR system successfully edits the target genome for both in vitro and pseudo-in vivo environments, providing a versatile magnetic platform for remote gene editing of animals with various size scales.
Collapse
Affiliation(s)
- Wookjin Shin
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Sumin Jeong
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-Uk Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Soo Yeun Jeong
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Jeonghong Shin
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyongbum Henry Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Jae-Hyun Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
12
|
Li H, Liu T, Yang H. Amplifying Intermolecular Events by Streptavidin-Induced Proximity. J Am Chem Soc 2022; 144:11377-11385. [PMID: 35715211 DOI: 10.1021/jacs.2c03666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Weak interactions between biomolecules play important roles in many cellular functions. Structural and kinetic analyses of these interactions, however, have been hindered by the transient nature of such events. Here, we pointed out a general approach to overcome this obstacle─anchoring the molecular partners to streptavidin hosts─and achieved constrained proximity and stoichiometry for the sought-after molecular coupling. We elaborated this idea through a series of DNA hybridization reactions and quantitatively characterized them using single-molecule experiments. Compared to a nominally 1 μM solution, for example, the streptavidin-induced proximity (SIP) amounted to an effective molarity of ∼10-30 μM for the binding partners. There was also a significantly increased proportion of molecular association, manifested in both ensemble population and single-molecule residence time. As an application example, we showed how SIP enabled the observation and quantitative characterization of an unstable complex between Cas9-RNA and noncognate DNA substrates, interactions that had been challenging to characterize previously. Conceptually simple and implementationally robust, SIP was shown to considerably enhance the efficacy in capturing weak interactions and, as demonstrated here, could empower scientists to see the otherwise unseeable.
Collapse
Affiliation(s)
- Hao Li
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Tao Liu
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Haw Yang
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| |
Collapse
|
13
|
Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
Collapse
Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|
14
|
Synthetic RNA-based post-transcriptional expression control methods and genetic circuits. Adv Drug Deliv Rev 2022; 184:114196. [PMID: 35288218 DOI: 10.1016/j.addr.2022.114196] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022]
Abstract
RNA-based synthetic genetic circuits provide an alternative for traditional transcription-based circuits in applications where genomic integration is to be avoided. Incorporating various post-transcriptional control methods into such circuits allows for controlling the behaviour of the circuit through the detection of certain biomolecular inputs or reconstituting defined circuit behaviours, thus manipulating cellular functions. In this review, recent developments of various types of post-transcriptional control methods in mammalian cells are discussed as well as auxiliary components that allow for the creation and development of mRNA-based switches. How such post-transcriptional switches are combined into synthetic circuits as well as their applications in biomedical and preclinical settings are also described. Finally, we examine the challenges that need to be surmounted before RNA-based synthetic circuits can be reliably deployed into clinical settings.
Collapse
|
15
|
Singh AP, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher JE. Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. Cell Rep 2022; 38:110543. [PMID: 35320726 PMCID: PMC9019726 DOI: 10.1016/j.celrep.2022.110543] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Developmental patterning networks are regulated by multiple inputs and feedback connections that rapidly reshape gene expression, limiting the information that can be gained solely from slow genetic perturbations. Here we show that fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background can be combined to reveal the kinetics of gene expression downstream of a developmental transcription factor in vivo. We engineer light-controlled versions of the Bicoid transcription factor and study their effects on downstream gap genes in embryos. Our results recapitulate known relationships, including rapid Bicoid-dependent transcription of giant and hunchback and delayed repression of Krüppel. In addition, we find that the posterior pattern of knirps exhibits a quick but inverted response to Bicoid perturbation, suggesting a noncanonical role for Bicoid in directly suppressing knirps transcription. Acute modulation of transcription factor concentration while recording output gene activity represents a powerful approach for studying developmental gene networks in vivo.
Collapse
Affiliation(s)
- Anand P Singh
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ping Wu
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sergey Ryabichko
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - João Raimundo
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michael Swan
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eric Wieschaus
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Thomas Gregor
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA.
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
16
|
Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
Collapse
Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| |
Collapse
|
17
|
Rah JC, Choi JH. Finding Needles in a Haystack with Light: Resolving the Microcircuitry of the Brain with Fluorescence Microscopy. Mol Cells 2022; 45:84-92. [PMID: 35236783 PMCID: PMC8907002 DOI: 10.14348/molcells.2022.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022] Open
Abstract
To understand the microcircuitry of the brain, the anatomical and functional connectivity among neurons must be resolved. One of the technical hurdles to achieving this goal is that the anatomical connections, or synapses, are often smaller than the diffraction limit of light and thus are difficult to resolve by conventional microscopy, while the microcircuitry of the brain is on the scale of 1 mm or larger. To date, the gold standard method for microcircuit reconstruction has been electron microscopy (EM). However, despite its rapid development, EM has clear shortcomings as a method for microcircuit reconstruction. The greatest weakness of this method is arguably its incompatibility with functional and molecular analysis. Fluorescence microscopy, on the other hand, is readily compatible with numerous physiological and molecular analyses. We believe that recent advances in various fluorescence microscopy techniques offer a new possibility for reliable synapse detection in large volumes of neural circuits. In this minireview, we summarize recent advances in fluorescence-based microcircuit reconstruction. In the same vein as these studies, we introduce our recent efforts to analyze the long-range connectivity among brain areas and the subcellular distribution of synapses of interest in relatively large volumes of cortical tissue with array tomography and superresolution microscopy.
Collapse
Affiliation(s)
- Jong-Cheol Rah
- Laboratory of Neurophysiology, Korea Brain Research Institute, Daegu 41062, Korea
- Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea
| | - Joon Ho Choi
- Laboratory of Neurophysiology, Korea Brain Research Institute, Daegu 41062, Korea
| |
Collapse
|
18
|
Wang S, Luo Y, Jiang W, Li X, Qi Q, Liang Q. Development of Optogenetic Dual-Switch System for Rewiring Metabolic Flux for Polyhydroxybutyrate Production. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030617. [PMID: 35163885 PMCID: PMC8838604 DOI: 10.3390/molecules27030617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022]
Abstract
Several strategies, including inducer addition and biosensor use, have been developed for dynamical regulation. However, the toxicity, cost, and inflexibility of existing strategies have created a demand for superior technology. In this study, we designed an optogenetic dual-switch system and applied it to increase polyhydroxybutyrate (PHB) production. First, an optimized chromatic acclimation sensor/regulator (RBS10–CcaS#10–CcaR) system (comprising an optimized ribosomal binding site (RBS), light sensory protein CcaS, and response regulator CcaR) was selected for a wide sensing range of approximately 10-fold between green-light activation and red-light repression. The RBS10–CcaS#10–CcaR system was combined with a blue light-activated YF1–FixJ–PhlF system (containing histidine kinase YF1, response regulator FixJ, and repressor PhlF) engineered with reduced crosstalk. Finally, the optogenetic dual-switch system was used to rewire the metabolic flux for PHB production by regulating the sequences and intervals of the citrate synthase gene (gltA) and PHB synthesis gene (phbCAB) expression. Consequently, the strain RBS34, which has high gltA expression and a time lag of 3 h, achieved the highest PHB content of 16.6 wt%, which was approximately 3-fold that of F34 (expressed at 0 h). The results indicate that the optogenetic dual-switch system was verified as a practical and convenient tool for increasing PHB production.
Collapse
Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Yue Luo
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Xiaomeng Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Correspondence: (Q.Q.); (Q.L.)
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
- Correspondence: (Q.Q.); (Q.L.)
| |
Collapse
|
19
|
Dwijayanti A, Zhang C, Poh CL, Lautier T. Toward Multiplexed Optogenetic Circuits. Front Bioeng Biotechnol 2022; 9:804563. [PMID: 35071213 PMCID: PMC8766309 DOI: 10.3389/fbioe.2021.804563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits. Progressively, more complex systems have been designed in which multiple photoreceptors, each sensing its dedicated wavelength, are combined to simultaneously coordinate cellular responses in a single cell. In this review, we highlight recent works and challenges on multiplexed optogenetic circuits in natural and engineered systems for a dynamic regulation breakthrough in biotechnological applications.
Collapse
Affiliation(s)
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Thomas Lautier
- CNRS@CREATE, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| |
Collapse
|
20
|
di Pietro F, Herszterg S, Huang A, Bosveld F, Alexandre C, Sancéré L, Pelletier S, Joudat A, Kapoor V, Vincent JP, Bellaïche Y. Rapid and robust optogenetic control of gene expression in Drosophila. Dev Cell 2021; 56:3393-3404.e7. [PMID: 34879263 PMCID: PMC8693864 DOI: 10.1016/j.devcel.2021.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/13/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022]
Abstract
Deciphering gene function requires the ability to control gene expression in space and time. Binary systems such as the Gal4/UAS provide a powerful means to modulate gene expression and to induce loss or gain of function. This is best exemplified in Drosophila, where the Gal4/UAS system has been critical to discover conserved mechanisms in development, physiology, neurobiology, and metabolism, to cite a few. Here we describe a transgenic light-inducible Gal4/UAS system (ShineGal4/UAS) based on Magnet photoswitches. We show that it allows efficient, rapid, and robust activation of UAS-driven transgenes in different tissues and at various developmental stages in Drosophila. Furthermore, we illustrate how ShineGal4 enables the generation of gain and loss-of-function phenotypes at animal, organ, and cellular levels. Thanks to the large repertoire of UAS-driven transgenes, ShineGal4 enriches the Drosophila genetic toolkit by allowing in vivo control of gene expression with high temporal and spatial resolutions.
Collapse
Affiliation(s)
- Florencia di Pietro
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | | | - Anqi Huang
- Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Floris Bosveld
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | | | - Lucas Sancéré
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Stéphane Pelletier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Amina Joudat
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Varun Kapoor
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | | | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France.
| |
Collapse
|
21
|
Müllenbroich MC, Kelly A, Acker C, Bub G, Bruegmann T, Di Bona A, Entcheva E, Ferrantini C, Kohl P, Lehnart SE, Mongillo M, Parmeggiani C, Richter C, Sasse P, Zaglia T, Sacconi L, Smith GL. Novel Optics-Based Approaches for Cardiac Electrophysiology: A Review. Front Physiol 2021; 12:769586. [PMID: 34867476 PMCID: PMC8637189 DOI: 10.3389/fphys.2021.769586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 12/31/2022] Open
Abstract
Optical techniques for recording and manipulating cellular electrophysiology have advanced rapidly in just a few decades. These developments allow for the analysis of cardiac cellular dynamics at multiple scales while largely overcoming the drawbacks associated with the use of electrodes. The recent advent of optogenetics opens up new possibilities for regional and tissue-level electrophysiological control and hold promise for future novel clinical applications. This article, which emerged from the international NOTICE workshop in 2018, reviews the state-of-the-art optical techniques used for cardiac electrophysiological research and the underlying biophysics. The design and performance of optical reporters and optogenetic actuators are reviewed along with limitations of current probes. The physics of light interaction with cardiac tissue is detailed and associated challenges with the use of optical sensors and actuators are presented. Case studies include the use of fluorescence recovery after photobleaching and super-resolution microscopy to explore the micro-structure of cardiac cells and a review of two photon and light sheet technologies applied to cardiac tissue. The emergence of cardiac optogenetics is reviewed and the current work exploring the potential clinical use of optogenetics is also described. Approaches which combine optogenetic manipulation and optical voltage measurement are discussed, in terms of platforms that allow real-time manipulation of whole heart electrophysiology in open and closed-loop systems to study optimal ways to terminate spiral arrhythmias. The design and operation of optics-based approaches that allow high-throughput cardiac electrophysiological assays is presented. Finally, emerging techniques of photo-acoustic imaging and stress sensors are described along with strategies for future development and establishment of these techniques in mainstream electrophysiological research.
Collapse
Affiliation(s)
| | - Allen Kelly
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Corey Acker
- Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, United States
| | - Gil Bub
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Tobias Bruegmann
- Institute for Cardiovascular Physiology, University Medical Center Goettingen, Goettingen, Germany
| | - Anna Di Bona
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington, DC, United States
| | | | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Center and Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Stephan E. Lehnart
- Heart Research Center Göttingen, University Medical Center Göttingen, Göttingen, Germany
- Department of Cardiology and Pneumology, Georg-August University Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Marco Mongillo
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
| | | | - Claudia Richter
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Philipp Sasse
- Institute of Physiology I, Medical Faculty, University of Bonn, Bonn, Germany
| | - Tania Zaglia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
| | - Leonardo Sacconi
- European Laboratory for Nonlinear Spectroscopy, Sesto Fiorentino, Italy
- Institute for Experimental Cardiovascular Medicine, University Heart Center and Medical Faculty, University of Freiburg, Freiburg, Germany
- National Institute of Optics, National Research Council, Florence, Italy
| | - Godfrey L. Smith
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
22
|
Biological signal processing filters via engineering allosteric transcription factors. Proc Natl Acad Sci U S A 2021; 118:2111450118. [PMID: 34772815 PMCID: PMC8609624 DOI: 10.1073/pnas.2111450118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
As the size and complexity of genetic circuits increases, scientists and engineers need to find solutions to rapidly optimize flux and reduce the metabolic burden imposed on chassis cells. In this study, we report synthetic biology tools that imbue chassis cells with advanced signal processing functions akin to electrical devices commonly used in wireless transmitters and receivers (i.e., biological BANDPASS and BANDSTOP devices) that can simultaneously reduce metabolic burden. Moreover, this study presents a set of granular and more complete design rules for engineering allosteric transcription factors in the broader LacI/GalR topology. In addition, this study has improved our fundamental understanding of the plasticity and continuum of allosteric communication from the binding pocket to the protein–DNA interaction. Signal processing is critical to a myriad of biological phenomena (natural and engineered) that involve gene regulation. Biological signal processing can be achieved by way of allosteric transcription factors. In canonical regulatory systems (e.g., the lactose repressor), an INPUT signal results in the induction of a given transcription factor and objectively switches gene expression from an OFF state to an ON state. In such biological systems, to revert the gene expression back to the OFF state requires the aggressive dilution of the input signal, which can take 1 or more d to achieve in a typical biotic system. In this study, we present a class of engineered allosteric transcription factors capable of processing two-signal INPUTS, such that a sequence of INPUTS can rapidly transition gene expression between alternating OFF and ON states. Here, we present two fundamental biological signal processing filters, BANDPASS and BANDSTOP, that are regulated by D-fucose and isopropyl-β-D-1-thiogalactopyranoside. BANDPASS signal processing filters facilitate OFF–ON–OFF gene regulation. Whereas, BANDSTOP filters facilitate the antithetical gene regulation, ON–OFF–ON. Engineered signal processing filters can be directed to seven orthogonal promoters via adaptive modular DNA binding design. This collection of signal processing filters can be used in collaboration with our established transcriptional programming structure. Kinetic studies show that our collection of signal processing filters can switch between states of gene expression within a few minutes with minimal metabolic burden—representing a paradigm shift in general gene regulation.
Collapse
|
23
|
Pérez ALA, Piva LC, Fulber JPC, de Moraes LMP, De Marco JL, Vieira HLA, Coelho CM, Reis VCB, Torres FAG. Optogenetic strategies for the control of gene expression in yeasts. Biotechnol Adv 2021; 54:107839. [PMID: 34592347 DOI: 10.1016/j.biotechadv.2021.107839] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/18/2022]
Abstract
Optogenetics involves the use of light to control cellular functions and has become increasingly popular in various areas of research, especially in the precise control of gene expression. While this technology is already well established in neurobiology and basic research, its use in bioprocess development is still emerging. Some optogenetic switches have been implemented in yeasts for different purposes, taking advantage of a wide repertoire of biological parts and relatively easy genetic manipulation. In this review, we cover the current strategies used for the construction of yeast strains to be used in optogenetically controlled protein or metabolite production, as well as the operational aspects to be considered for the scale-up of this type of process. Finally, we discuss the main applications of optogenetic switches in yeast systems and highlight the main advantages and challenges of bioprocess development considering future directions for this field.
Collapse
Affiliation(s)
- Ana Laura A Pérez
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Luiza C Piva
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Julia P C Fulber
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Lidia M P de Moraes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Janice L De Marco
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Hugo L A Vieira
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Cintia M Coelho
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Viviane C B Reis
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Fernando A G Torres
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil.
| |
Collapse
|
24
|
Dowbaj AM, Jenkins RP, Williamson D, Heddleston JM, Ciccarelli A, Fallesen T, Hahn KM, O'Dea RD, King JR, Montagner M, Sahai E. An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling. J Cell Sci 2021; 134:jcs253484. [PMID: 34060624 PMCID: PMC8313864 DOI: 10.1242/jcs.253484] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
The shuttling of transcription factors and transcriptional regulators into and out of the nucleus is central to the regulation of many biological processes. Here we describe a new method for studying the rates of nuclear entry and exit of transcriptional regulators. A photo-responsive LOV (light-oxygen-voltage) domain from Avena sativa is used to sequester fluorescently labelled transcriptional regulators YAP1 and TAZ (also known as WWTR1) on the surface of mitochondria and to reversibly release them upon blue light illumination. After dissociation, fluorescent signals from the mitochondria, cytoplasm and nucleus are extracted by a bespoke app and used to generate rates of nuclear entry and exit. Using this method, we demonstrate that phosphorylation of YAP1 on canonical sites enhances its rate of nuclear export. Moreover, we provide evidence that, despite high intercellular variability, YAP1 import and export rates correlate within the same cell. By simultaneously releasing YAP1 and TAZ from sequestration, we show that their rates of entry and exit are correlated. Furthermore, combining the optogenetic release of YAP1 with lattice light-sheet microscopy reveals high heterogeneity of YAP1 dynamics within different cytoplasmic regions, demonstrating the utility and versatility of our tool to study protein dynamics. This article has an associated First Person interview with Anna M. Dowbaj, joint first author of the paper.
Collapse
Affiliation(s)
- Anna M. Dowbaj
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Robert P. Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Daniel Williamson
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - John M. Heddleston
- Advanced Imaging Center, Janelia Research Campus, HHMI, Ashburn, VA 20147, USA
| | - Alessandro Ciccarelli
- Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Todd Fallesen
- Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Klaus M. Hahn
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599-7365, USA
| | - Reuben D. O'Dea
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - John R. King
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marco Montagner
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Molecular Medicine, University of Padova, Viale G. Colombo 3, 35126 Padova, Italy
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| |
Collapse
|
25
|
Zhao EM, Lalwani MA, Chen JM, Orillac P, Toettcher JE, Avalos JL. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol 2021; 10:1143-1154. [PMID: 33835777 DOI: 10.1021/acssynbio.0c00642] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dynamic control of microbial metabolism is an effective strategy to improve chemical production in fermentations. While dynamic control is most often implemented using chemical inducers, optogenetics offers an attractive alternative due to the high tunability and reversibility afforded by light. However, a major concern of applying optogenetics in metabolic engineering is the risk of insufficient light penetration at high cell densities, especially in large bioreactors. Here, we present a new series of optogenetic circuits we call OptoAMP, which amplify the transcriptional response to blue light by as much as 23-fold compared to the basal circuit (OptoEXP). These circuits show as much as a 41-fold induction between dark and light conditions, efficient activation at light duty cycles as low as ∼1%, and strong homogeneous light-induction in bioreactors of at least 5 L, with limited illumination at cell densities above 40 OD600. We demonstrate the ability of OptoAMP circuits to control engineered metabolic pathways in novel three-phase fermentations using different light schedules to control enzyme expression and improve production of lactic acid, isobutanol, and naringenin. These circuits expand the applicability of optogenetics to metabolic engineering.
Collapse
Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jhong-Min Chen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Paulina Orillac
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
26
|
Duplus-Bottin H, Spichty M, Triqueneaux G, Place C, Mangeot PE, Ohlmann T, Vittoz F, Yvert G. A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch. eLife 2021; 10:61268. [PMID: 33620312 PMCID: PMC7997657 DOI: 10.7554/elife.61268] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
Optogenetics enables genome manipulations with high spatiotemporal resolution, opening exciting possibilities for fundamental and applied biological research. Here, we report the development of LiCre, a novel light-inducible Cre recombinase. LiCre is made of a single flavin-containing protein comprising the AsLOV2 photoreceptor domain of Avena sativa fused to a Cre variant carrying destabilizing mutations in its N-terminal and C-terminal domains. LiCre can be activated within minutes of illumination with blue light without the need of additional chemicals. When compared to existing photoactivatable Cre recombinases based on two split units, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark. LiCre was efficient both in yeast, where it allowed us to control the production of β-carotene with light, and human cells. Given its simplicity and performances, LiCre is particularly suited for fundamental and biomedical research, as well as for controlling industrial bioprocesses. In a biologist’s toolkit, the Cre protein holds a special place. Naturally found in certain viruses, this enzyme recognises and modifies specific genetic sequences, creating changes that switch on or off whatever gene is close by. Genetically engineering cells or organisms so that they carry Cre and its target sequences allows scientists to control the activation of a given gene, often in a single tissue or organ. However, this relies on the ability to activate the Cre protein ‘on demand’ once it is in the cells of interest. One way to do so is to split the enzyme into two pieces, which can then reassemble when exposed to blue light. Yet, this involves the challenging step of introducing both parts separately into a tissue. Instead, Duplus-Bottin et al. engineered LiCre, a new system where a large section of the Cre protein is fused to a light sensor used by oats to detect their environment. LiCre is off in the dark, but it starts to recognize and modify Cre target sequences when exposed to blue light. Duplus-Bottin et al. then assessed how LiCre compares to the two-part Cre system in baker's yeast and human kidney cells. This showed that the new protein is less ‘incorrectly’ active in the dark, and can switch on faster under blue light. The improved approach could give scientists a better tool to study the role of certain genes at precise locations and time points, but also help them to harness genetic sequences for industry or during gene therapy.
Collapse
Affiliation(s)
- Hélène Duplus-Bottin
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gérard Triqueneaux
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Christophe Place
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Philippe Emmanuel Mangeot
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Théophile Ohlmann
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Franck Vittoz
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| |
Collapse
|
27
|
Forro C, Caron D, Angotzi GN, Gallo V, Berdondini L, Santoro F, Palazzolo G, Panuccio G. Electrophysiology Read-Out Tools for Brain-on-Chip Biotechnology. MICROMACHINES 2021; 12:124. [PMID: 33498905 PMCID: PMC7912435 DOI: 10.3390/mi12020124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023]
Abstract
Brain-on-Chip (BoC) biotechnology is emerging as a promising tool for biomedical and pharmaceutical research applied to the neurosciences. At the convergence between lab-on-chip and cell biology, BoC couples in vitro three-dimensional brain-like systems to an engineered microfluidics platform designed to provide an in vivo-like extrinsic microenvironment with the aim of replicating tissue- or organ-level physiological functions. BoC therefore offers the advantage of an in vitro reproduction of brain structures that is more faithful to the native correlate than what is obtained with conventional cell culture techniques. As brain function ultimately results in the generation of electrical signals, electrophysiology techniques are paramount for studying brain activity in health and disease. However, as BoC is still in its infancy, the availability of combined BoC-electrophysiology platforms is still limited. Here, we summarize the available biological substrates for BoC, starting with a historical perspective. We then describe the available tools enabling BoC electrophysiology studies, detailing their fabrication process and technical features, along with their advantages and limitations. We discuss the current and future applications of BoC electrophysiology, also expanding to complementary approaches. We conclude with an evaluation of the potential translational applications and prospective technology developments.
Collapse
Affiliation(s)
- Csaba Forro
- Tissue Electronics, Fondazione Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci, 53-80125 Naples, Italy; (C.F.); (F.S.)
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Davide Caron
- Enhanced Regenerative Medicine, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (D.C.); (V.G.)
| | - Gian Nicola Angotzi
- Microtechnology for Neuroelectronics, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (G.N.A.); (L.B.)
| | - Vincenzo Gallo
- Enhanced Regenerative Medicine, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (D.C.); (V.G.)
| | - Luca Berdondini
- Microtechnology for Neuroelectronics, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (G.N.A.); (L.B.)
| | - Francesca Santoro
- Tissue Electronics, Fondazione Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci, 53-80125 Naples, Italy; (C.F.); (F.S.)
| | - Gemma Palazzolo
- Enhanced Regenerative Medicine, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (D.C.); (V.G.)
| | - Gabriella Panuccio
- Enhanced Regenerative Medicine, Fondazione Istituto Italiano di Tecnologia, Via Morego, 30-16163 Genova, Italy; (D.C.); (V.G.)
| |
Collapse
|
28
|
Dixon TA, Williams TC, Pretorius IS. Sensing the future of bio-informational engineering. Nat Commun 2021; 12:388. [PMID: 33452260 PMCID: PMC7810845 DOI: 10.1038/s41467-020-20764-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
The practices of synthetic biology are being integrated into 'multiscale' designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of 'bio-informational' engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.
Collapse
Affiliation(s)
- Thomas A Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
| | | |
Collapse
|
29
|
Zhang J, Firestone E, Elattma A. Animal Models of Tinnitus Treatment: Cochlear and Brain Stimulation. Curr Top Behav Neurosci 2021; 51:83-129. [PMID: 34282563 DOI: 10.1007/7854_2021_227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Neuromodulation, via stimulation of a variety of peripheral and central structures, is used to suppress tinnitus. However, investigative limitations in humans due to ethical reasons have made it difficult to decipher the mechanisms underlying treatment-induced tinnitus relief, so a number of animal models have arisen to address these unknowns. This chapter reviews animal models of cochlear and brain stimulation and assesses their modulatory effects on behavioral evidence of tinnitus and its related neural correlates. When a structure is stimulated, localized modulation, often presenting as downregulation of spontaneous neuronal spike firing rate, bursting and neurosynchrony, occurs within the brain area. Through anatomical projections and transmitter pathways, the interventions activate both auditory- and non-auditory structures by taking bottom-up ascending and top-down descending modes to influence their target brain structures. Furthermore, it is the brain oscillations that cochlear or brain stimulation evoke and connect the prefrontal cortex, striatal systems, and other limbic structures to refresh neural networks and relieve auditory, attentive, conscious, as well as emotional reactive aspects of tinnitus. This oscillatory neural network connectivity is achieved via the thalamocorticothalamic circuitry including the lemniscal and non-lemniscal auditory brain structures. Beyond existing technologies, the review also reveals opportunities for developing advanced animal models using new modalities to achieve precision neuromodulation and tinnitus abatement, such as optogenetic cochlear and/or brain stimulation.
Collapse
Affiliation(s)
- Jinsheng Zhang
- Department of Otolaryngology-Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Communication Sciences and Disorders, Wayne State University College of Liberal Arts and Sciences, Detroit, MI, USA.
| | - Ethan Firestone
- Department of Otolaryngology-Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ahmed Elattma
- Department of Otolaryngology-Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI, USA
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
Collapse
Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| |
Collapse
|
32
|
Carrasco-López C, García-Echauri SA, Kichuk T, Avalos JL. Optogenetics and biosensors set the stage for metabolic cybergenetics. Curr Opin Biotechnol 2020; 65:296-309. [DOI: 10.1016/j.copbio.2020.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
|
33
|
Hartmann D, Smith JM, Mazzotti G, Chowdhry R, Booth MJ. Controlling gene expression with light: a multidisciplinary endeavour. Biochem Soc Trans 2020; 48:1645-1659. [PMID: 32657338 PMCID: PMC7458398 DOI: 10.1042/bst20200014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.
Collapse
Affiliation(s)
- Denis Hartmann
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Jefferson M. Smith
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Giacomo Mazzotti
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| |
Collapse
|
34
|
de Mena L, Rincon-Limas DE. PhotoGal4: A Versatile Light-Dependent Switch for Spatiotemporal Control of Gene Expression in Drosophila Explants. iScience 2020; 23:101308. [PMID: 32652492 PMCID: PMC7347995 DOI: 10.1016/j.isci.2020.101308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/15/2020] [Accepted: 06/19/2020] [Indexed: 12/04/2022] Open
Abstract
We present here PhotoGal4, a phytochrome B-based optogenetic switch for fine-tuned spatiotemporal control of gene expression in Drosophila explants. This switch integrates the light-dependent interaction between phytochrome B and PIF6 from plants with regulatory elements from the yeast Gal4/UAS system. We found that PhotoGal4 efficiently activates and deactivates gene expression upon red- or far-red-light irradiation, respectively. In addition, this optogenetic tool reacts to different illumination conditions, allowing for fine modulation of the light-dependent response. Importantly, by simply focusing a laser beam, PhotoGal4 induces intricate patterns of expression in a customized manner. For instance, we successfully sketched personalized patterns of GFP fluorescence such as emoji-like shapes or letterform logos in Drosophila explants, which illustrates the exquisite precision and versatility of this tool. Hence, we anticipate that PhotoGal4 will expand the powerful Drosophila toolbox and will provide a new avenue to investigate intricate and complex problems in biomedical research.
Collapse
Affiliation(s)
- Lorena de Mena
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA.
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA; Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
35
|
McCormick JW, Pincus D, Resnekov O, Reynolds KA. Strategies for Engineering and Rewiring Kinase Regulation. Trends Biochem Sci 2019; 45:259-271. [PMID: 31866305 DOI: 10.1016/j.tibs.2019.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic protein kinases (EPKs) catalyze the transfer of a phosphate group onto another protein in response to appropriate regulatory cues. In doing so, they provide a primary means for cellular information transfer. Consequently, EPKs play crucial roles in cell differentiation and cell-cycle progression, and kinase dysregulation is associated with numerous disease phenotypes including cancer. Nonnative cues for synthetically regulating kinases are thus much sought after, both for dissecting cell signaling pathways and for pharmaceutical development. In recent years advances in protein engineering and sequence analysis have led to new approaches for manipulating kinase activity, localization, and in some instances specificity. These tools have revealed fundamental principles of intracellular signaling and suggest paths forward for the design of therapeutic allosteric kinase regulators.
Collapse
Affiliation(s)
- James W McCormick
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | | | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
36
|
Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
Collapse
Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
| |
Collapse
|
37
|
Shiri Z, Simorgh S, Naderi S, Baharvand H. Optogenetics in the Era of Cerebral Organoids. Trends Biotechnol 2019; 37:1282-1294. [PMID: 31227305 DOI: 10.1016/j.tibtech.2019.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/18/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
The human brain has been deemed the most complex organ and has captivated neuroscientists for decades. Most studies of this organ have relied on reductionist model systems. Although all model systems are essentially wrong, cerebral organoids so far represent the closest recapitulation of human brain development and disease both in terms of cell diversity and organization. The optogenetic technique can be used in this context to study the functional neuroanatomy of the brain, to examine the neural circuits, and to determine the etiology of neurological disorders. In this opinion article, we suggest ways in which optogenetics can be combined with cerebral organoids to allow unprecedented precision and accuracy in studying normal and aberrant neurodevelopmental processes and, as well, neurodegenerative diseases.
Collapse
Affiliation(s)
- Zahra Shiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Susan Simorgh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Somayeh Naderi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
| |
Collapse
|
38
|
Hernández-Candia CN, Wysoczynski CL, Tucker CL. Advances in optogenetic regulation of gene expression in mammalian cells using cryptochrome 2 (CRY2). Methods 2019; 164-165:81-90. [PMID: 30905749 DOI: 10.1016/j.ymeth.2019.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Synthetic regulation of gene expression provides a powerful approach to reprogram molecular and cellular processes and test the function of specific genes and gene products. In the last decade, optogenetic systems that allow light-dependent gene regulation have become valuable tools, providing tight spatiotemporal control of protein levels. Here we discuss and build on recent optogenetic approaches for regulating gene expression in mammalian cells using cryptochrome 2 (CRY2), a photoreceptor protein from Arabidopsis. We provide detailed protocols for using light to manipulate activity of a CRY2-based engineered photoactivatable Cre DNA recombinase, and to induce or disrupt transcription factor function. In addition, we provide instructions and software for building an inexpensive Rasberry-Pi-based programable LED device for optogenetic experiments, delivering pulsed light with customized control of illumination duration, frequency, and intensity.
Collapse
Affiliation(s)
| | - Christina L Wysoczynski
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| |
Collapse
|
39
|
DiGuiseppi J, Zuo J. The awesome power of optogenetics in hearing research. Neurosci Lett 2019; 701:175-179. [PMID: 30822439 DOI: 10.1016/j.neulet.2019.02.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022]
Abstract
The use of light as a tool to manipulate cellular processes or optogenetics has developed rapidly in various biological fields over the past decade. Through the addition of photosensitive proteins, light can be used to control intracellular mechanisms, map neuronal pathways, and alter variables that would be difficult to control using other mechanisms. Photons of a specific wavelength affect these light sensitive targets for in vitro or in vivo experiments. Optogenetics is beneficial because it gives the investigator spatial and temporal control over experimental variables. Precise control is achieved by sequential activation of different ion channels and the ability to non-invasively control membrane potential. In this review, we will discuss the recent use of optogenetics in biological fields to understand the role of different cell types in hearing and creating a new cochlear implant, as well as future uses such as light controlled drug delivery and gene expression.
Collapse
Affiliation(s)
- Joseph DiGuiseppi
- Dept. of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA
| | - Jian Zuo
- Dept. of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA.
| |
Collapse
|