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Shkarina K, Broz P. Selective induction of programmed cell death using synthetic biology tools. Semin Cell Dev Biol 2024; 156:74-92. [PMID: 37598045 DOI: 10.1016/j.semcdb.2023.07.012] [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: 05/05/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Regulated cell death (RCD) controls the removal of dispensable, infected or malignant cells, and is thus essential for development, homeostasis and immunity of multicellular organisms. Over the last years different forms of RCD have been described (among them apoptosis, necroptosis, pyroptosis and ferroptosis), and the cellular signaling pathways that control their induction and execution have been characterized at the molecular level. It has also become apparent that different forms of RCD differ in their capacity to elicit inflammation or an immune response, and that RCD pathways show a remarkable plasticity. Biochemical and genetic studies revealed that inhibition of a given pathway often results in the activation of back-up cell death mechanisms, highlighting close interconnectivity based on shared signaling components and the assembly of multivalent signaling platforms that can initiate different forms of RCD. Due to this interconnectivity and the pleiotropic effects of 'classical' cell death inducers, it is challenging to study RCD pathways in isolation. This has led to the development of tools based on synthetic biology that allow the targeted induction of RCD using chemogenetic or optogenetic methods. Here we discuss recent advances in the development of such toolset, highlighting their advantages and limitations, and their application for the study of RCD in cells and animals.
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Affiliation(s)
- Kateryna Shkarina
- Institute of Innate Immunity, University Hospital Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Petr Broz
- Department of Immunobiology, University of Lausanne, Switzerland.
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2
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Nano M, Montell DJ. Apoptotic signaling: Beyond cell death. Semin Cell Dev Biol 2024; 156:22-34. [PMID: 37988794 DOI: 10.1016/j.semcdb.2023.11.002] [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: 06/26/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Apoptosis is the best described form of regulated cell death, and was, until relatively recently, considered irreversible once particular biochemical points-of-no-return were activated. In this manuscript, we examine the mechanisms cells use to escape from a self-amplifying death signaling module. We discuss the role of feedback, dynamics, propagation, and noise in apoptotic signaling. We conclude with a revised model for the role of apoptosis in animal development, homeostasis, and disease.
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Affiliation(s)
- Maddalena Nano
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
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3
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Cumming T, Levayer R. Toward a predictive understanding of epithelial cell death. Semin Cell Dev Biol 2024; 156:44-57. [PMID: 37400292 DOI: 10.1016/j.semcdb.2023.06.008] [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: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Epithelial cell death is highly prevalent during development and tissue homeostasis. While we have a rather good understanding of the molecular regulators of programmed cell death, especially for apoptosis, we still fail to predict when, where, how many and which specific cells will die in a tissue. This likely relies on the much more complex picture of apoptosis regulation in a tissular and epithelial context, which entails cell autonomous but also non-cell autonomous factors, diverse feedback and multiple layers of regulation of the commitment to apoptosis. In this review, we illustrate this complexity of epithelial apoptosis regulation by describing these different layers of control, all demonstrating that local cell death probability is a complex emerging feature. We first focus on non-cell autonomous factors that can locally modulate the rate of cell death, including cell competition, mechanical input and geometry as well as systemic effects. We then describe the multiple feedback mechanisms generated by cell death itself. We also outline the multiple layers of regulation of epithelial cell death, including the coordination of extrusion and regulation occurring downstream of effector caspases. Eventually, we propose a roadmap to reach a more predictive understanding of cell death regulation in an epithelial context.
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Affiliation(s)
- Tom Cumming
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France; Sorbonne Université, Collège Doctoral, F75005 Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France.
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4
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Mo W, Su S, Shang R, Yang L, Zhao X, Wu C, Yang Z, Zhang H, Wu L, Liu Y, He Y, Zhang R, Zuo Z. Optogenetic induction of caspase-8 mediated apoptosis by employing Arabidopsis cryptochrome 2. Sci Rep 2023; 13:23067. [PMID: 38155283 PMCID: PMC10754905 DOI: 10.1038/s41598-023-50561-y] [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: 04/20/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023] Open
Abstract
Apoptosis, a programmed cell death mechanism, is a regulatory process controlling cell proliferation as cells undergo demise. Caspase-8 serves as a pivotal apoptosis-inducing factor that initiates the death receptor-mediated apoptosis pathway. In this investigation, we have devised an optogenetic method to swiftly modulate caspase-8 activation in response to blue light. The cornerstone of our optogenetic tool relies on the PHR domain of Arabidopsis thaliana cryptochrome 2, which self-oligomerizes upon exposure to blue light. In this study, we have developed two optogenetic approaches for rapidly controlling caspase-8 activation in response to blue light in cellular systems. The first strategy, denoted as Opto-Casp8-V1, entails the fusion expression of the Arabidopsis blue light receptor CRY2 N-terminal PHR domain with caspase-8. The second strategy, referred to as Opto-Casp8-V2, involves the independent fusion expression of caspase-8 with the PHR domain and the CRY2 blue light-interacting protein CIB1 N-terminal CIB1N. Upon induction with blue light, PHR undergoes aggregation, leading to caspase-8 aggregation. Additionally, the blue light-dependent interaction between PHR and CIB1N also results in caspase-8 aggregation. We have validated these strategies in both HEK293T and HeLa cells. The findings reveal that both strategies are capable of inducing apoptosis, with Opto-Casp8-V2 demonstrating significantly superior efficiency compared to Opto-Casp8-V1.
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Affiliation(s)
- Weiliang Mo
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shengzhong Su
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ruige Shang
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Liang Yang
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Xuelai Zhao
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Chengfeng Wu
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Zhenming Yang
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - He Zhang
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Liuming Wu
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yibo Liu
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yun He
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ruipeng Zhang
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Zecheng Zuo
- Jlin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China.
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Baker M, Kang S, Hong SI, Song M, Yang MA, Peyton L, Essa H, Lee SW, Choi DS. External globus pallidus input to the dorsal striatum regulates habitual seeking behavior in male mice. Nat Commun 2023; 14:4085. [PMID: 37438336 PMCID: PMC10338526 DOI: 10.1038/s41467-023-39545-8] [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: 10/27/2022] [Accepted: 06/16/2023] [Indexed: 07/14/2023] Open
Abstract
The external globus pallidus (GPe) coordinates action-selection through GABAergic projections throughout the basal ganglia. GPe arkypallidal (arky) neurons project exclusively to the dorsal striatum, which regulates goal-directed and habitual seeking. However, the role of GPe arky neurons in reward-seeking remains unknown. Here, we identified that a majority of arky neurons target the dorsolateral striatum (DLS). Using fiber photometry, we found that arky activities were higher during random interval (RI; habit) compared to random ratio (RR; goal) operant conditioning. Support vector machine analysis demonstrated that arky neuron activities have sufficient information to distinguish between RR and RI behavior. Genetic ablation of this arkyGPe→DLS circuit facilitated a shift from goal-directed to habitual behavior. Conversely, chemogenetic activation globally reduced seeking behaviors, which was blocked by systemic D1R agonism. Our findings reveal a role of this arkyGPe→DLS circuit in constraining habitual seeking in male mice, which is relevant to addictive behaviors and other compulsive disorders.
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Affiliation(s)
- Matthew Baker
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Seungwoo Kang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Sa-Ik Hong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Minryung Song
- Department of Brain and Cognitive Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Minsu Abel Yang
- Department of Brain and Cognitive Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Lee Peyton
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hesham Essa
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sang Wan Lee
- Department of Brain and Cognitive Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doo-Sup Choi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Psychiatry and Psychology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
- Neuroscience Program, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
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6
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Nagasawa Y, Ueda HH, Kawabata H, Murakoshi H. LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics. Biophys Physicobiol 2023; 20:e200027. [PMID: 38496236 PMCID: PMC10941968 DOI: 10.2142/biophysico.bppb-v20.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/02/2023] [Indexed: 03/19/2024] Open
Abstract
Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the "high spatial resolution" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as "Local Optogenetics", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.
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Affiliation(s)
- Yutaro Nagasawa
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hiromi H Ueda
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Haruka Kawabata
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hideji Murakoshi
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
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7
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Nano M, Mondo JA, Harwood J, Balasanyan V, Montell DJ. Cell survival following direct executioner-caspase activation. Proc Natl Acad Sci U S A 2023; 120:e2216531120. [PMID: 36669100 PMCID: PMC9942801 DOI: 10.1073/pnas.2216531120] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/17/2022] [Indexed: 01/21/2023] Open
Abstract
Executioner-caspase activation has been considered a point-of-no-return in apoptosis. However, numerous studies report survival from caspase activation after treatment with drugs or radiation. An open question is whether cells can recover from direct caspase activation without pro-survival stress responses induced by drugs. To address this question, we engineered a HeLa cell line to express caspase-3 inducibly and combined it with a quantitative caspase activity reporter. While high caspase activity levels killed all cells and very low levels allowed all cells to live, doses of caspase activity sufficient to kill 15 to 30% of cells nevertheless allowed 70 to 85% to survive. At these doses, neither the rate, nor the peak level, nor the total amount of caspase activity could accurately predict cell death versus survival. Thus, cells can survive direct executioner-caspase activation, and variations in cellular state modify the outcome of potentially lethal caspase activity. Such heterogeneities may underlie incomplete tumor cell killing in response to apoptosis-inducing cancer treatments.
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Affiliation(s)
- Maddalena Nano
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA93106
- Neuroscience Research Institute, University of California, Santa Barbara, CA93106
| | - James A. Mondo
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA93106
| | - Jacob Harwood
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA93106
| | - Varuzhan Balasanyan
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA93106
| | - Denise J. Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA93106
- Neuroscience Research Institute, University of California, Santa Barbara, CA93106
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8
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Fan H, Barnes C, Hwang H, Zhang K, Yang J. Precise modulation of embryonic development through optogenetics. Genesis 2022; 60:e23505. [PMID: 36478118 PMCID: PMC9847014 DOI: 10.1002/dvg.23505] [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: 09/06/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed enormous progress in optogenetics, which uses photo-sensitive proteins to control signal transduction in live cells and animals. The ever-increasing amount of optogenetic tools, however, could overwhelm the selection of appropriate optogenetic strategies. In this work, we summarize recent progress in this emerging field and highlight the application of opsin-free optogenetics in studying embryonic development, focusing on new insights gained into optical induction of morphogenesis, cell polarity, cell fate determination, tissue differentiation, neuronal regeneration, synaptic plasticity, and removal of cells during development.
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Affiliation(s)
- Huaxun Fan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin Barnes
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
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9
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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.
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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
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10
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Soleymani F, Paquet E, Viktor H, Michalowski W, Spinello D. Protein-protein interaction prediction with deep learning: A comprehensive review. Comput Struct Biotechnol J 2022; 20:5316-5341. [PMID: 36212542 PMCID: PMC9520216 DOI: 10.1016/j.csbj.2022.08.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022] Open
Abstract
Most proteins perform their biological function by interacting with themselves or other molecules. Thus, one may obtain biological insights into protein functions, disease prevalence, and therapy development by identifying protein-protein interactions (PPI). However, finding the interacting and non-interacting protein pairs through experimental approaches is labour-intensive and time-consuming, owing to the variety of proteins. Hence, protein-protein interaction and protein-ligand binding problems have drawn attention in the fields of bioinformatics and computer-aided drug discovery. Deep learning methods paved the way for scientists to predict the 3-D structure of proteins from genomes, predict the functions and attributes of a protein, and modify and design new proteins to provide desired functions. This review focuses on recent deep learning methods applied to problems including predicting protein functions, protein-protein interaction and their sites, protein-ligand binding, and protein design.
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Affiliation(s)
- Farzan Soleymani
- Department of Mechanical Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Eric Paquet
- National Research Council, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada
| | - Herna Viktor
- School of Electrical Engineering and Computer Science, University of Ottawa, ON, Canada
| | | | - Davide Spinello
- Department of Mechanical Engineering, University of Ottawa, Ottawa, ON, Canada
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11
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A photo-switchable assay system for dendrite degeneration and repair in Drosophila melanogaster. Proc Natl Acad Sci U S A 2022; 119:e2204577119. [PMID: 35969739 PMCID: PMC9407391 DOI: 10.1073/pnas.2204577119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurodegeneration arising from aging, injury, or diseases has devastating health consequences. Whereas neuronal survival and axon degeneration have been studied extensively, much less is known about how neurodegeneration affects dendrites, in part due to the limited assay systems available. To develop an assay for dendrite degeneration and repair, we used photo-switchable caspase-3 (caspase-Light-Oxygen-Voltage-sensing [caspase-LOV]) in peripheral class 4 dendrite arborization (c4da) neurons to induce graded neurodegeneration by adjusting illumination duration during development and adulthood in Drosophila melanogaster. We found that both developing and mature c4da neurons were able to survive while sustaining mild neurodegeneration induced by moderate caspase-LOV activation. Further, we observed active dendrite addition and dendrite regeneration in developing and mature c4da neurons, respectively. Using this assay, we found that the mouse Wallerian degeneration slow (WldS) protein can protect c4da neurons from caspase-LOV-induced dendrite degeneration and cell death. Furthermore, our data show that WldS can reduce dendrite elimination without affecting dendrite addition. In summary, we successfully established a photo-switchable assay system in both developing and mature neurons and used WldS as a test case to study the mechanisms underlying dendrite regeneration and repair.
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12
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Shkarina K, Hasel de Carvalho E, Santos JC, Ramos S, Leptin M, Broz P. Optogenetic activators of apoptosis, necroptosis, and pyroptosis. J Cell Biol 2022; 221:213145. [PMID: 35420640 DOI: 10.1083/jcb.202109038] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/16/2022] [Accepted: 03/18/2022] [Indexed: 12/20/2022] Open
Abstract
Targeted and specific induction of cell death in an individual or groups of cells hold the potential for new insights into the response of tissues or organisms to different forms of death. Here, we report the development of optogenetically controlled cell death effectors (optoCDEs), a novel class of optogenetic tools that enables light-mediated induction of three types of programmed cell death (PCD)-apoptosis, pyroptosis, and necroptosis-using Arabidopsis thaliana photosensitive protein Cryptochrome-2. OptoCDEs enable a rapid and highly specific induction of PCD in human, mouse, and zebrafish cells and are suitable for a wide range of applications, such as sub-lethal cell death induction or precise elimination of single cells or cell populations in vitro and in vivo. As the proof-of-concept, we utilize optoCDEs to assess the differences in neighboring cell responses to apoptotic or necrotic PCD, revealing a new role for shingosine-1-phosphate signaling in regulating the efferocytosis of the apoptotic cell by epithelia.
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Affiliation(s)
- Kateryna Shkarina
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - José Carlos Santos
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Saray Ramos
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Maria Leptin
- Director's Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Petr Broz
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
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13
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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14
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Abstract
Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
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15
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Lehtinen K, Nokia MS, Takala H. Red Light Optogenetics in Neuroscience. Front Cell Neurosci 2022; 15:778900. [PMID: 35046775 PMCID: PMC8761848 DOI: 10.3389/fncel.2021.778900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.
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Affiliation(s)
- Kimmo Lehtinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Miriam S. Nokia
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
- Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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16
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Han Y, Lu X, Li Y, Qiu Y, Dong X, Li X, Si X, Liu Q, Ni JQ. CRISPR-Based Transcriptional Activation in Drosophila. Methods Mol Biol 2022; 2540:177-199. [PMID: 35980578 DOI: 10.1007/978-1-0716-2541-5_8] [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] [Indexed: 06/15/2023]
Abstract
Overexpression is one of the classical approaches to study pleiotropic functions of genes of interest. To achieve overexpression, we often increase the transcription by introducing genes on exogenous vectors or by using the CRISPR/dCas9-based transcriptional activation system. To date, the most efficient CRISPR/dCas9-based transcriptional activator is the Synergistic Activation Mediator (SAM) system whereby three different transcriptional activation domains are directly fused to dCas9 and MS2 phage Coat Protein (MCP), respectively, and the system in Drosophila is named flySAM. Here we describe the effective and convenient transcriptional activation system, flySAM, starting from vector construction, microinjection, and transgenic fly selection to the phenotypic analysis.
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Affiliation(s)
- Yuting Han
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xinyi Lu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Yutong Li
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Yuhao Qiu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xizhi Dong
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaochen Li
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xu Si
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Qingfei Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.
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17
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Asadi M, Taghizadeh S, Kaviani E, Vakili O, Taheri-Anganeh M, Tahamtan M, Savardashtaki A. Caspase-3: Structure, function, and biotechnological aspects. Biotechnol Appl Biochem 2021; 69:1633-1645. [PMID: 34342377 DOI: 10.1002/bab.2233] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/01/2021] [Indexed: 12/16/2022]
Abstract
Caspase-3, a cysteine-aspartic acid protease, has recently attracted much attention because of its incredible roles in tissue differentiation, regeneration, and neural development. This enzyme is a key zymogen in cell apoptosis and is not activated until it is cleaved by initiator caspases during apoptotic flux. Since caspase-3 has represented valuable capabilities in the field of medical research, biotechnological aspects of this enzyme, including the production of recombinant type, protein engineering, and designing delivery systems, have been considered as emerging therapeutic strategies in treating the apoptosis-related disorders. To date, several advances have been made in the therapeutic use of caspase-3 in the management of some diseases such as cancers, heart failure, and neurodegenerative disorders. In the current review, we intend to discuss the caspase-3's structure, functions, therapeutic applications, as well as its molecular cloning, protein engineering, and relevant delivery systems.
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Affiliation(s)
- Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Taghizadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elina Kaviani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahshid Tahamtan
- Department of Neuroscience, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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18
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Oh TJ, Fan H, Skeeters SS, Zhang K. Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives. Adv Biol (Weinh) 2021; 5:e2000180. [PMID: 34028216 PMCID: PMC8218620 DOI: 10.1002/adbi.202000180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Optogenetics utilizes photosensitive proteins to manipulate the localization and interaction of molecules in living cells. Because light can be rapidly switched and conveniently confined to the sub-micrometer scale, optogenetics allows for controlling cellular events with an unprecedented resolution in time and space. The past decade has witnessed an enormous progress in the field of optogenetics within the biological sciences. The ever-increasing amount of optogenetic tools, however, can overwhelm the selection of appropriate optogenetic strategies. Considering that each optogenetic tool may have a distinct mode of action, a comparative analysis of the current optogenetic toolbox can promote the further use of optogenetics, especially by researchers new to this field. This review provides such a compilation that highlights the spatiotemporal accuracy of current optogenetic systems. Recent advances of optogenetics in live cells and animal models are summarized, the emerging work that interlinks optogenetics with other research fields is presented, and exciting clinical and industrial efforts to employ optogenetic strategy toward disease intervention are reported.
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Affiliation(s)
- Teak-Jung Oh
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Huaxun Fan
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Savanna S Skeeters
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Kai Zhang
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
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19
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Seong J, Lin MZ. Optobiochemistry: Genetically Encoded Control of Protein Activity by Light. Annu Rev Biochem 2021; 90:475-501. [PMID: 33781076 DOI: 10.1146/annurev-biochem-072420-112431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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20
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Morstein J, Kol M, Novak AJE, Feng S, Khayyo S, Hinnah K, Li-Purcell N, Pan G, Williams BM, Riezman H, Atilla-Gokcumen GE, Holthuis JCM, Trauner D. Short Photoswitchable Ceramides Enable Optical Control of Apoptosis. ACS Chem Biol 2021; 16:452-456. [PMID: 33586946 DOI: 10.1021/acschembio.0c00823] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report short ceramide analogs that can be activated with light and further functionalized using azide-alkyne click chemistry. These molecules, termed scaCers, exhibit increased cell permeability compared to their long-chain analogs as demonstrated using mass spectrometry and imaging. Notably, scaCers enable optical control of apoptosis, which is not observed with long-chain variants. Additionally, they function as photoswitchable substrates for sphingomyelin synthase 2 (SMS2), exhibiting inverted light-dependence compared to their extended analogs.
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Affiliation(s)
- Johannes Morstein
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Matthijs Kol
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Alexander J. E. Novak
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Suihan Feng
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Shadi Khayyo
- Department of Chemistry, University of Buffalo, The State University of New York (SUNY), Buffalo, New York, United States
| | - Konstantin Hinnah
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nasi Li-Purcell
- Department of Chemistry, University of Buffalo, The State University of New York (SUNY), Buffalo, New York, United States
| | - Grace Pan
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Benjamin M. Williams
- Department of Chemistry and Center for Integrated Protein Science, Ludwig Maximilians University Munich, 81377 Munich, Germany
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - G. Ekin Atilla-Gokcumen
- Department of Chemistry, University of Buffalo, The State University of New York (SUNY), Buffalo, New York, United States
| | | | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York 10003, United States
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21
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Dokholyan NV. Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming. NPJ Syst Biol Appl 2021; 7:15. [PMID: 33707429 PMCID: PMC7952909 DOI: 10.1038/s41540-021-00176-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
The advent of protein design in recent years has brought us within reach of developing a "nanoscale programing language," in which molecules serve as operands with their conformational states functioning as logic gates. Combining these operands into a set of operations will result in a functional program, which is executed using nanoscale computing agents (NCAs). These agents would respond to any given input and return the desired output signal. The ability to utilize natural evolutionary processes would allow code to "evolve" in the course of computation, thus enabling radically new algorithmic developments. NCAs will revolutionize the studies of biological systems, enable a deeper understanding of human biology and disease, and facilitate the development of in situ precision therapeutics. Since NCAs can be extended to novel reactions and processes not seen in biological systems, the growth of this field will spark the growth of biotechnological applications with wide-ranging impacts, including fields not typically considered relevant to biology. Unlike traditional approaches in synthetic biology that are based on the rewiring of signaling pathways in cells, NCAs are autonomous vehicles based on single-chain proteins. In this perspective, I will introduce and discuss this new field of biological computing, as well as challenges and the future of the NCA. Addressing these challenges will provide a significant leap in technology for programming living cells.
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Affiliation(s)
- Nikolay V Dokholyan
- Departments of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA.
- Departments of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA.
- Departments of Chemistry, and Biomedical Engineering, Penn State University, University Park, PA, 16802, USA.
- Departments of Biomedical Engineering, Penn State University, University Park, PA, 16802, USA.
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22
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Mathony J, Niopek D. Enlightening Allostery: Designing Switchable Proteins by Photoreceptor Fusion. Adv Biol (Weinh) 2020; 5:e2000181. [PMID: 33107225 DOI: 10.1002/adbi.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Indexed: 11/05/2022]
Abstract
Optogenetics harnesses natural photoreceptors to non-invasively control selected processes in cells with previously unmet spatiotemporal precision. Linking the activity of a protein of choice to the conformational state of a photosensor domain through allosteric coupling represents a powerful method for engineering light-responsive proteins. It enables the design of compact and highly potent single-component optogenetic systems with fast on- and off-switching kinetics. However, designing protein-photoreceptor chimeras, in which structural changes of the photoreceptor are effectively propagated to the fused effector protein, is a challenging engineering problem and often relies on trial and error. Here, recent advances in the design and application of optogenetic allosteric switches are reviewed. First, an overview of existing optogenetic tools based on inducible allostery is provided and their utility for cell biology applications is highlighted. Focusing on light-oxygen-voltage domains, a widely applied class of small blue light sensors, the available strategies for engineering light-dependent allostery are presented and their individual advantages and limitations are highlighted. Finally, high-throughput screening technologies based on comprehensive insertion libraries, which could accelerate the creation of stimulus-responsive receptor-protein chimeras for use in optogenetics and beyond, are discussed.
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Affiliation(s)
- Jan Mathony
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany.,BZH graduate school, Heidelberg University, Im Neuheimer Feld 328, Heidelberg, 69120, Germany
| | - Dominik Niopek
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany
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23
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Gräwe A, Ranglack J, Weber W, Stein V. Engineering artificial signalling functions with proteases. Curr Opin Biotechnol 2020; 63:1-7. [DOI: 10.1016/j.copbio.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023]
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24
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Zhang Y, Zhang W, Zeng K, Ao Y, Wang M, Yu Z, Qi F, Yu W, Mao H, Tao L, Zhang C, Tan TTY, Yang X, Pu K, Gao S. Upconversion Nanoparticles-Based Multiplex Protein Activation to Neuron Ablation for Locomotion Regulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906797. [PMID: 32003923 DOI: 10.1002/smll.201906797] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/06/2020] [Indexed: 05/24/2023]
Abstract
The optogenetic neuron ablation approach enables noninvasive remote decoding of specific neuron function within a complex living organism in high spatiotemporal resolution. However, it suffers from shallow tissue penetration of visible light with low ablation efficiency. This study reports a upconversion nanoparticle (UCNP)-based multiplex proteins activation tool to ablate deep-tissue neurons for locomotion modulation. By optimizing the dopant contents and nanoarchitecure, over 300-fold enhancement of blue (450-470 nm) and red (590-610 nm) emissions from UCNPs is achieved upon 808 nm irradiation. Such emissions simultaneously activate mini singlet oxygen generator and Chrimson, leading to boosted near infrared (NIR) light-induced neuronal ablation efficiency due to the synergism between singlet oxygen generation and intracellular Ca2+ elevation. The loss of neurons severely inhibits reverse locomotion, revealing the instructive role of neurons in controlling motor activity. The deep penetrance NIR light makes the current system feasible for in vivo deep-tissue neuron elimination. The results not only provide a rapidly adoptable platform to efficient photoablate single- and multiple-cells, but also define the neural circuits underlying behavior, with potential for development of remote therapy in diseases.
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Affiliation(s)
- Yan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Wanmei Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Kanghua Zeng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yanxiao Ao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Mengdie Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, P. R. China
| | - Zhongzheng Yu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Fukang Qi
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Weiwei Yu
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Heng Mao
- LMAM, School of Mathematical Sciences, Peking University, Beijing, 100871, P. R. China
| | - Louis Tao
- Center for Quantitative Biology, Peking University, Beijing, 100871, P. R. China
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Timothy Thatt Yang Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Xiangliang Yang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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25
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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26
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27
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Kim S, Shin J, Oh H, Ahn S, Kim N, Heo WD. An inducible system for in vitro and in vivo Fas activation using FKBP-FRB-rapamycin complex. Biochem Biophys Res Commun 2019; 523:473-480. [PMID: 31882118 DOI: 10.1016/j.bbrc.2019.12.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/15/2019] [Indexed: 11/16/2022]
Abstract
The inducible activation system is valuable for investigating spatiotemporal roles of molecules. A chemically inducible activation system for Fas (CD95/APO-1), which works efficiently to induce apoptosis and leads non-apoptotic pathways, has not yet been developed. Here, we engineered a rapamycin-induced dimerization system of Fas consisting of FKBP and FRB proteins. Treatment of rapamycin specifically induces cellular apoptosis. In neurons and cells with high c-FLIP expression, rapamycin-induced Fas activation triggered the activation of the non-apoptotic pathway components instead of cell death. Intracranial delivery of the system could be utilized to induce apoptosis of tumor cells upon rapamycin treatment. Our results demonstrate a novel inducible Fas activation system which operates with high efficiency and temporal precision in vitro and in vivo promising a potential therapeutic strategy.
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Affiliation(s)
- Seokhwi Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jongpil Shin
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Hyunsik Oh
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Sangphil Ahn
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Nury Kim
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea; Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, Republic of Korea; KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea.
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28
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 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.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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29
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Directed evolution improves the catalytic efficiency of TEV protease. Nat Methods 2019; 17:167-174. [PMID: 31819267 PMCID: PMC7004888 DOI: 10.1038/s41592-019-0665-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022]
Abstract
Tobacco etch virus protease (TEV) is one of the most widely used proteases in biotechnology because of its exquisite sequence specificity. A limitation, however, is its slow catalytic rate. We developed a generalizable yeast-based platform for directed evolution of protease catalytic properties. Protease activity is read out via proteolytic release of a membrane-anchored transcription factor, and we temporally regulate access to TEV's cleavage substrate using a photosensory LOV domain. By gradually decreasing light exposure time, we enriched faster variants of TEV over multiple rounds of selection. Our TEV-S153N mutant (uTEV1Δ), when incorporated into the calcium integrator FLARE, improved the signal/background ratio by 27-fold, and enabled recording of neuronal activity in culture with 60-s temporal resolution. Given the widespread use of TEV in biotechnology, both our evolved TEV mutants and the directed-evolution platform used to generate them could be beneficial across a wide range of applications.
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Liu F, Dai S, Feng D, Peng X, Qin Z, Kearns AC, Huang W, Chen Y, Ergün S, Wang H, Rappaport J, Bryda EC, Chandrasekhar A, Aktas B, Hu H, Chang SL, Gao B, Qin X. Versatile cell ablation tools and their applications to study loss of cell functions. Cell Mol Life Sci 2019; 76:4725-4743. [PMID: 31359086 PMCID: PMC6858955 DOI: 10.1007/s00018-019-03243-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022]
Abstract
Targeted cell ablation is a powerful approach for studying the role of specific cell populations in a variety of organotypic functions, including cell differentiation, and organ generation and regeneration. Emerging tools for permanently or conditionally ablating targeted cell populations and transiently inhibiting neuronal activities exhibit a diversity of application and utility. Each tool has distinct features, and none can be universally applied to study different cell types in various tissue compartments. Although these tools have been developed for over 30 years, they require additional improvement. Currently, there is no consensus on how to select the tools to answer the specific scientific questions of interest. Selecting the appropriate cell ablation technique to study the function of a targeted cell population is less straightforward than selecting the method to study a gene's functions. In this review, we discuss the features of the various tools for targeted cell ablation and provide recommendations for optimal application of specific approaches.
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Affiliation(s)
- Fengming Liu
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Shen Dai
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Dechun Feng
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiao Peng
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Zhongnan Qin
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Alison C Kearns
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Wenfei Huang
- Institute of NeuroImmune Pharmacology, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Yong Chen
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
- Key Lab for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, 261053, Weifang, People's Republic of China
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius-Maximillan University, 97070, Wurzburg, Germany
| | - Hong Wang
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA
| | - Jay Rappaport
- Division of Pathology, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Elizabeth C Bryda
- Rat Resource and Research Center, University of Missouri, 4011 Discovery Drive, Columbia, MO, 65201, USA
| | - Anand Chandrasekhar
- Division of Biological Sciences, 340D Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, USA
| | - Bertal Aktas
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Hongzhen Hu
- Department of Anesthesiology, Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuebin Qin
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA, 19140, USA.
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, 70433, USA.
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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31
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Boudreau MW, Peh J, Hergenrother PJ. Procaspase-3 Overexpression in Cancer: A Paradoxical Observation with Therapeutic Potential. ACS Chem Biol 2019; 14:2335-2348. [PMID: 31260254 PMCID: PMC6858495 DOI: 10.1021/acschembio.9b00338] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many anticancer strategies rely on the promotion of apoptosis in cancer cells as a means to shrink tumors. Crucial for apoptotic function are executioner caspases, most notably caspase-3, that proteolyze a variety of proteins, inducing cell death. Paradoxically, overexpression of procaspase-3 (PC-3), the low-activity zymogen precursor to caspase-3, has been reported in a variety of cancer types. Until recently, this counterintuitive overexpression of a pro-apoptotic protein in cancer has been puzzling. Recent studies suggest subapoptotic caspase-3 activity may promote oncogenic transformation, a possible explanation for the enigmatic overexpression of PC-3. Herein, the overexpression of PC-3 in cancer and its mechanistic basis is reviewed; collectively, the data suggest the potential for exploitation of PC-3 overexpression with PC-3 activators as a targeted anticancer strategy.
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Affiliation(s)
- Matthew W. Boudreau
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois, United States
| | - Jessie Peh
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois, United States
| | - Paul J. Hergenrother
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois, United States
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Yue J, Liang C, Wu K, Hou Z, Wang L, Zhang C, Liu S, Yang H. Upregulated SHP-2 expression in the epileptogenic zone of temporal lobe epilepsy and various effects of SHP099 treatment on a pilocarpine model. Brain Pathol 2019; 30:373-385. [PMID: 31398269 DOI: 10.1111/bpa.12777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
Temporal lobe epilepsy (TLE) is defined as the sporadic occurrence of spontaneous recurrent seizures, and its pathogenesis is complex. SHP-2 (Src homology 2-containing protein tyrosine phosphatase 2) is a widely expressed cytosolic tyrosine phosphatase protein that participates in the regulation of inflammation, angiogenesis, gliosis, neurogenesis and apoptosis, suggesting a potential role of SHP-2 in TLE. Therefore, we investigated the expression patterns of SHP-2 in the epileptogenic brain tissue of intractable TLE patients and the various effects of treatment with the SHP-2-specific inhibitor SHP099 on a pilocarpine model. Western blotting and immunohistochemistry results confirmed that SHP-2 expression was upregulated in the temporal neocortex of patients with TLE. Double-labeling experiments revealed that SHP-2 was highly expressed in neurons, astrocytes, microglia and vascular endothelial cells in the epileptic foci of TLE patients. In the pilocarpine-induced C57BL/6 mouse model, SHP-2 upregulation in the hippocampus began one day after status epilepticus, reached a peak at 21 days and then maintained a significantly high level until day 60. Similarly, we found a remarkable increase in SHP-2 expression at 1, 7, 21 and 60 days post-SE in the temporal neocortex. In addition, we also showed that SHP099 increased reactive gliosis, the release of IL-1β, neuronal apoptosis and neuronal loss, while reduced neurogenesis and albumin leakage. Taken together, the increased expression of SHP-2 in the epileptic zone may be involved in the process of TLE.
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Affiliation(s)
- Jiong Yue
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Chao Liang
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Kefu Wu
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhi Hou
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lukang Wang
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Chunqing Zhang
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shiyong Liu
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Hui Yang
- Epilepsy research center of PLA, Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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Ciriachi C, Svane‐Petersen D, Rickhag M. Genetic tools to study complexity of striatal function. J Neurosci Res 2019; 97:1181-1193. [DOI: 10.1002/jnr.24479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Chiara Ciriachi
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - David Svane‐Petersen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Mattias Rickhag
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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Wagner HJ, Weber W. Design of a Human Rhinovirus-14 3C Protease-Inducible Caspase-3. Molecules 2019; 24:E1945. [PMID: 31117169 PMCID: PMC6571611 DOI: 10.3390/molecules24101945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 11/16/2022] Open
Abstract
The engineering of enzymes for the purpose of controlling their activity represents a valuable approach to address challenges in both fundamental and applied research. Here, we describe and compare different design strategies for the generation of a human rhinovirus-14 (HRV14) 3C protease-inducible caspase-3 (CASP3). We exemplify the application potential of the resulting protease by controlling the activity of a synthetic enzyme cascade, which represents an important motif for the design of artificial signal transduction networks. In addition, we use our engineered CASP3 to characterize the effect of aspartate mutations on enzymatic activity. Besides the identification of mutations that render the enzyme inactive, we find the CASP3-D192E mutant (aspartate-to-glutamate exchange at position 192) to be inaccessible for 3C protease-mediated cleavage. This indicates a structural change of CASP3 that goes beyond a slight misalignment of the catalytic triad. This study could inspire the design of additional engineered proteases that could be used to unravel fundamental research questions or to expand the collection of biological parts for the design of synthetic signaling pathways.
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Affiliation(s)
- Hanna J Wagner
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
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35
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Zhao W, Li H, Hou Y, Jin Y, Zhang L. Combined Administration of Poly-ADP-Ribose Polymerase-1 and Caspase-3 Inhibitors Alleviates Neuronal Apoptosis After Spinal Cord Injury in Rats. World Neurosurg 2019; 127:e346-e352. [PMID: 30904799 DOI: 10.1016/j.wneu.2019.03.116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Neuronal apoptosis plays a pivotal role in spinal cord injury (SCI)-induced secondary cellular events. Caspase-dependent and -independent pathways are involved in neuronal apoptosis. Caspase-3 is the final effector of caspase-dependent apoptosis, whereas poly-ADP-ribose polymerase-1 (PARP-1) and apoptosis-inducing factor (AIF) are key executors of caspase-independent apoptosis. However, it remains unclear whether simultaneous inhibition of the 2 apoptosis pathways will be more beneficial for neuronal survival. Therefore, this study investigated the ability of coadministration of the PARP-1 inhibitor 3-aminobenzamide (3-AB) and caspase-3 inhibitor z-DEVD-fmk to attenuate apoptosis in a rat SCI model. METHODS The rats were subjected to moderate contusive SCI. Locomotor function was measured using the Basso, Beattie, and Bresnahan rating scales; neuronal apoptosis was detected using transferase-mediated deoxyuridine triphosphate-biotin nick end labeling; and immunohistochemistry and Western blotting were used to measure protein expression. RESULTS We found the locomotor function of rats was weakened within 7 days post-SCI. At day 7 post-SCI, neuronal apoptosis dramatically increased and the expression of PARP-1, AIF, and cleaved caspase-3 was significantly upregulated. Further, Bcl-2 expression was significantly downregulated. The highest locomotor function recovery was recorded after the combined administration of 3-AB and z-DEVD-fmk for 7 days post-SCI when compared with 3-AB or z-DEVD-fmk administered alone. In addition, this combination therapy significantly reduced neuronal apoptosis by preventing upregulation of PARP-1 and AIF, inhibiting caspase-3 activation, and elevating Bcl-2 expression. CONCLUSIONS These results suggest that combination therapy is beneficial for neuronal function recovery in rats with SCI. The underlying mechanism may be associated with cosuppression of caspase-dependent and caspase-independent apoptosis pathways.
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Affiliation(s)
- Wei Zhao
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Hongxing Li
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Yun Hou
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Yinchuan Jin
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Lianshuang Zhang
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China.
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36
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Cao W, Qi J, Qian K, Tian L, Cheng Z, Wang Y. Structure−activity relationships of 2‑quinolinecarboxaldehyde thiosemicarbazone gallium(III) complexes with potent and selective anticancer activity. J Inorg Biochem 2019; 191:174-182. [DOI: 10.1016/j.jinorgbio.2018.11.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/23/2018] [Accepted: 11/25/2018] [Indexed: 12/22/2022]
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Mansouri M, Strittmatter T, Fussenegger M. Light-Controlled Mammalian Cells and Their Therapeutic Applications in Synthetic Biology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800952. [PMID: 30643713 PMCID: PMC6325585 DOI: 10.1002/advs.201800952] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Indexed: 05/12/2023]
Abstract
The ability to remote control the expression of therapeutic genes in mammalian cells in order to treat disease is a central goal of synthetic biology-inspired therapeutic strategies. Furthermore, optogenetics, a combination of light and genetic sciences, provides an unprecedented ability to use light for precise control of various cellular activities with high spatiotemporal resolution. Recent work to combine optogenetics and therapeutic synthetic biology has led to the engineering of light-controllable designer cells, whose behavior can be regulated precisely and noninvasively. This Review focuses mainly on non-neural optogenetic systems, which are often used in synthetic biology, and their applications in genetic programing of mammalian cells. Here, a brief overview of the optogenetic tool kit that is available to build light-sensitive mammalian cells is provided. Then, recently developed strategies for the control of designer cells with specific biological functions are summarized. Recent translational applications of optogenetically engineered cells are also highlighted, ranging from in vitro basic research to in vivo light-controlled gene therapy. Finally, current bottlenecks, possible solutions, and future prospects for optogenetics in synthetic biology are discussed.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
- Faculty of ScienceUniversity of BaselMattenstrasse 26CH‐4058BaselSwitzerland
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38
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Goglia AG, Toettcher JE. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr Opin Chem Biol 2018; 48:106-113. [PMID: 30529586 DOI: 10.1016/j.cbpa.2018.11.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
Abstract
Cells sense, process, and respond to extracellular information using signaling networks: collections of proteins that act as precise biochemical sensors. These protein networks are characterized by both complex temporal organization, such as pulses of signaling activity, and by complex spatial organization, where proteins assemble structures at particular locations and times within the cell. Yet despite their ubiquity, studying these spatial and temporal properties has remained challenging because they emerge from the entire protein network rather than a single node, and cannot be easily tuned by drugs or mutations. These challenges are being met by a new generation of optogenetic tools capable of directly controlling the activity of individual signaling nodes over time and the assembly of protein complexes in space. Here, we outline how these recent innovations are being used in conjunction with engineering-influenced experimental design to address longstanding questions in signaling biology.
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Affiliation(s)
- Alexander G Goglia
- Department of Molecular Biology, Princeton University, Princeton NJ 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton NJ 08544, United States.
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Abstract
Understanding how activity patterns in specific neural circuits coordinate an animal’s behavior remains a key area of neuroscience research. Genetic tools and a brain of tractable complexity make Drosophila a premier model organism for these studies. Here, we review the wealth of reagents available to map and manipulate neuronal activity with light.
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40
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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41
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Affiliation(s)
- Mareike Daniela Hoffmann
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Felix Bubeck
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Roland Eils
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
- Digital Health Center; Berlin Institute of Health (BIH) and Charité-University Medicine Berlin; 10117 Berlin Germany
- Health Data Science Unit; University Hospital Heidelberg; 10117 Heidelberg Germany
| | - Dominik Niopek
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
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Ueda Y, Sato M. Induction of Signal Transduction by Using Non-Channelrhodopsin-Type Optogenetic Tools. Chembiochem 2018; 19:1217-1231. [PMID: 29577530 DOI: 10.1002/cbic.201700635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 12/24/2022]
Abstract
Signal transductions are the basis for all cellular functions. Previous studies investigating signal transductions mainly relied on pharmacological inhibition, RNA interference, and constitutive active/dominant negative protein expression systems. However, such studies do not allow the modulation of protein activity with high spatial and temporal precision in cells, tissues, and organs in animals. Recently, non-channelrhodopsin-type optogenetic tools for regulating signal transduction have emerged. These photoswitches address several disadvantages of previous techniques, and allow us to control a variety of signal transductions such as cell membrane dynamics, calcium signaling, lipid signaling, and apoptosis. In this review we summarize recent advances in the development of such photoswitches and in how these optotools are applied to signaling processes.
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Affiliation(s)
- Yoshibumi Ueda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- AMED-PRIME (Japan), Agency for Medical Research and Development, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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Near-infrared light-controlled systems for gene transcription regulation, protein targeting and spectral multiplexing. Nat Protoc 2018; 13:1121-1136. [PMID: 29700485 DOI: 10.1038/nprot.2018.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Near-infrared (NIR, 740-780 nm) optogenetic systems are well-suited to spectral multiplexing with blue-light-controlled tools. Here, we present two protocols, one for regulation of gene transcription and another for control of protein localization, that use a NIR-responsive bacterial phytochrome BphP1-QPAS1 optogenetic pair. In the first protocol, cells are transfected with the optogenetic constructs for independently controlling gene transcription by NIR (BphP1-QPAS1) and blue (LightOn) light. The NIR and blue-light-controlled gene transcription systems show minimal spectral crosstalk and induce a 35- to 40-fold increase in reporter gene expression. In the second protocol, the BphP1-QPAS1 pair is combined with a light-oxygen-voltage-sensing (LOV) domain-based construct into a single optogenetic tool, termed iRIS. This dual-light-controllable protein localization tool allows tridirectional protein translocation among the cytoplasm, nucleus and plasma membrane. Both procedures can be performed within 3-5 d. Use of NIR light-controlled optogenetic systems should advance basic and biomedical research.
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