151
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Ishiwatari A, Yamaguchi S, Takamori S, Yamahira S, Minamihata K, Nagamune T. Photolytic Protein Aggregates: Versatile Materials for Controlled Release of Active Proteins. Adv Healthc Mater 2016; 5:1002-7. [PMID: 26945901 DOI: 10.1002/adhm.201500957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/18/2016] [Indexed: 01/29/2023]
Abstract
Photolytic protein aggregates are developed as a facile and versatile platform for light-induced release of active proteins. The proteins modified with biotin through a photo-cleavable linker rapidly form aggregates with streptavidin and biotinylated functional molecules simply by mixing. Light irradiation releases active proteins from the aggregates in high yields, and light-induced uptake of drug-modified transferrin into living cells is successfully demonstrated.
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Affiliation(s)
- Akira Ishiwatari
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Satoshi Yamaguchi
- Research Center for Advanced Science and Technology (RCAST); The University of Tokyo; 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
| | - Satoshi Takamori
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinya Yamahira
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kosuke Minamihata
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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152
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Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters. Biophys Rev 2016; 8:121-138. [PMID: 28510054 PMCID: PMC4884202 DOI: 10.1007/s12551-016-0195-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/09/2016] [Indexed: 01/26/2023] Open
Abstract
Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e.g., chloride and calcium), redox indicators, membrane potential, temperature, pressure, and molecular crowding. We demonstrate that these fluroescent protein-based sensors have a shared history of concepts and development strategies, and we highlight the most original concepts used to date. We believe that the understanding and application of these various concepts will pave the road for the development of future GE sensors and lead to new breakthroughs in bioimaging.
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153
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Xu Y, Nan D, Fan J, Bogan JS, Toomre D. Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action. J Cell Sci 2016; 129:2085-95. [PMID: 27076519 DOI: 10.1242/jcs.174805] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 03/31/2016] [Indexed: 12/26/2022] Open
Abstract
Glucose transporter 4 (GLUT4; also known as SLC2A4) resides on intracellular vesicles in muscle and adipose cells, and translocates to the plasma membrane in response to insulin. The phosphoinositide 3-kinase (PI3K)-Akt signaling pathway plays a major role in GLUT4 translocation; however, a challenge has been to unravel the potentially distinct contributions of PI3K and Akt (of which there are three isoforms, Akt1-Akt3) to overall insulin action. Here, we describe new optogenetic tools based on CRY2 and the N-terminus of CIB1 (CIBN). We used these 'Opto' modules to activate PI3K and Akt selectively in time and space in 3T3-L1 adipocytes. We validated these tools using biochemical assays and performed live-cell kinetic analyses of IRAP-pHluorin translocation (IRAP is also known as LNPEP and acts as a surrogate marker for GLUT4 here). Strikingly, Opto-PIP3 largely mimicked the maximal effects of insulin stimulation, whereas Opto-Akt only partially triggered translocation. Conversely, drug-mediated inhibition of Akt only partially dampened the translocation response of Opto-PIP3 In spatial optogenetic studies, focal targeting of Akt to a region of the cell marked the sites where IRAP-pHluorin vesicles fused, supporting the idea that local Akt-mediated signaling regulates exocytosis. Taken together, these results indicate that PI3K and Akt play distinct roles, and that PI3K stimulates Akt-independent pathways that are important for GLUT4 translocation.
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Affiliation(s)
- Yingke Xu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou 310027, China Department of Cell Biology, Yale University School of Medicine, New Haven, 06510, USA
| | - Di Nan
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou 310027, China
| | - Jiannan Fan
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou 310027, China
| | - Jonathan S Bogan
- Department of Cell Biology, Yale University School of Medicine, New Haven, 06510, USA Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520-8020, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, New Haven, 06510, USA
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154
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Jones DC, Mistry IN, Tavassoli A. Post-translational control of protein function with light using a LOV-intein fusion protein. MOLECULAR BIOSYSTEMS 2016; 12:1388-93. [PMID: 26940144 DOI: 10.1039/c6mb00007j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methods for the post-translational control of protein function with light hold much value as tools in cell biology. To this end, we report a fusion protein that consists of DnaE split-inteins, flanking the light sensitive LOV2 domain of Avena sativa. The resulting chimera combines the activities of these two unrelated proteins to enable controlled formation of a functional protein via upregulation of intein splicing with blue light in bacterial and human cells.
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Affiliation(s)
- D C Jones
- Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
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155
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Construction and application of photoresponsive smart nanochannels. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2016. [DOI: 10.1016/j.jphotochemrev.2015.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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156
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Carling CJ, Olejniczak J, Foucault-Collet A, Collet G, Viger ML, Nguyen Huu VA, Duggan BM, Almutairi A. Efficient Red Light Photo-Uncaging of Active Molecules in Water Upon Assembly into Nanoparticles. Chem Sci 2016; 7:2392-2398. [PMID: 27014436 PMCID: PMC4800316 DOI: 10.1039/c5sc03717d] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/08/2015] [Indexed: 12/16/2022] Open
Abstract
We introduce a means of efficiently photo-uncaging active compounds from amino-1,4-benzoquinone in aqueous environments. Aqueous photochemistry of this photocage with one-photon red light is typically not efficient unless the photocaged molecules are allowed to assemble into nanoparticles. A variety of biologically active molecules were functionalized with the photocage and subsequently formulated into water-dispersible nanoparticles. Red light irradiation through various mammalian tissues achieved efficient photo-uncaging. Co-encapsulation of NIR fluorescent dyes and subsequent photomodulation provides a NIR fluorescent tool to assess both particle location and successful photorelease.
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Affiliation(s)
- Carl-Johan Carling
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
| | - Jason Olejniczak
- Department of Chemistry and Biochemistry
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
| | - Alexandra Foucault-Collet
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
| | - Guillaume Collet
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
| | - Mathieu L. Viger
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
| | - Viet Anh Nguyen Huu
- Department of Nanoengineering
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
| | - Adah Almutairi
- Skaggs School of Pharmacy and Pharmaceutical Sciences
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
.
- Department of Nanoengineering
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
- Department of Materials Science and Engineering
, University of California, San Diego
,
9500 Gilman Dr.
, La Jolla
, California 92093
, USA
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157
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Quérard J, Le Saux T, Gautier A, Alcor D, Croquette V, Lemarchand A, Gosse C, Jullien L. Kinetics of Reactive Modules Adds Discriminative Dimensions for Selective Cell Imaging. Chemphyschem 2016; 17:1396-413. [PMID: 26833808 DOI: 10.1002/cphc.201500987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 11/07/2022]
Abstract
Living cells are chemical mixtures of exceptional interest and significance, whose investigation requires the development of powerful analytical tools fulfilling the demanding constraints resulting from their singular features. In particular, multiplexed observation of a large number of molecular targets with high spatiotemporal resolution appears highly desirable. One attractive road to address this analytical challenge relies on engaging the targets in reactions and exploiting the rich kinetic signature of the resulting reactive module, which originates from its topology and its rate constants. This review explores the various facets of this promising strategy. We first emphasize the singularity of the content of a living cell as a chemical mixture and suggest that its multiplexed observation is significant and timely. Then, we show that exploiting the kinetics of analytical processes is relevant to selectively detect a given analyte: upon perturbing the system, the kinetic window associated to response read-out has to be matched with that of the targeted reactive module. Eventually, we introduce the state-of-the-art of cell imaging exploiting protocols based on reaction kinetics and draw some promising perspectives.
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Affiliation(s)
- Jérôme Quérard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Thomas Le Saux
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Arnaud Gautier
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Damien Alcor
- INSERM U1065, C3M; 151 route Saint Antoine de Ginestière, BP 2 3194 F-06204 Nice Cedex 3 France
| | - Vincent Croquette
- Ecole Normale Supérieure; Département de Physique and Département de Biologie, Laboratoire de Physique Statistique UMR CNRS-ENS 8550; 24 rue Lhomond F-75005 Paris France
| | - Annie Lemarchand
- Sorbonne Universités; UPMC Univ Paris 06, Laboratoire de Physique Théorique de la Matière Condensée; 4 place Jussieu, case courrier 121 75252 Paris cedex 05 France
- CNRS, UMR 7600 LPTMC; 75005 Paris France
| | - Charlie Gosse
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS; route de Nozay 91460 Marcoussis France
| | - Ludovic Jullien
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
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158
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Li H, Fan X, Chen X. Near-Infrared Light Activation of Proteins Inside Living Cells Enabled by Carbon Nanotube-Mediated Intracellular Delivery. ACS APPLIED MATERIALS & INTERFACES 2016; 8:4500-4507. [PMID: 26859435 DOI: 10.1021/acsami.6b00323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Light-responsive proteins have been delivered into the cells for controlling intracellular events with high spatial and temporal resolution. However, the choice of wavelength is limited to the UV and visible range; activation of proteins inside the cells using near-infrared (NIR) light, which has better tissue penetration and biocompatibility, remains elusive. Here, we report the development of a single-walled carbon nanotube (SWCNT)-based bifunctional system that enables protein intracellular delivery, followed by NIR activation of the delivered proteins inside the cells. Proteins of interest are conjugated onto SWCNTs via a streptavidin-desthiobiotin (SA-DTB) linkage, where the protein activity is blocked. SWCNTs serve as both a nanocarrier for carrying proteins into the cells and subsequently a NIR sensitizer to photothermally cleave the linkage and release the proteins. The released proteins become active and exert their functions inside the cells. We demonstrated this strategy by intracellular delivery and NIR-triggered nuclear translocation of enhanced green fluorescent protein, and by intracellular delivery and NIR-activation of a therapeutic protein, saporin, in living cells. Furthermore, we showed that proteins conjugated onto SWCNTs via the SA-DTB linkage could be delivered to the tumors, and optically released and activated by using NIR light in living mice.
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Affiliation(s)
- He Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, China
| | - Xinqi Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, China
| | - Xing Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, China
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159
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Animal models of major depression and their clinical implications. Prog Neuropsychopharmacol Biol Psychiatry 2016; 64:293-310. [PMID: 25891248 DOI: 10.1016/j.pnpbp.2015.04.004] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/09/2015] [Accepted: 04/12/2015] [Indexed: 12/12/2022]
Abstract
Major depressive disorder is a common, complex, and potentially life-threatening mental disorder that imposes a severe social and economic burden worldwide. Over the years, numerous animal models have been established to elucidate pathophysiology that underlies depression and to test novel antidepressant treatment strategies. Despite these substantial efforts, the animal models available currently are of limited utility for these purposes, probably because none of the models mimics this complex disorder fully. It is presumable that psychiatric illnesses, such as affective disorders, are related to the complexity of the human brain. Here, we summarize the animal models that are used most commonly for depression, and discuss their advantages and limitations. We discuss genetic models, including the recently developed optogenetic tools and the stress models, such as the social stress, chronic mild stress, learned helplessness, and early-life stress paradigms. Moreover, we summarize briefly the olfactory bulbectomy model, as well as models that are based on pharmacological manipulations and disruption of the circadian rhythm. Finally, we highlight common misinterpretations and often-neglected important issues in this field.
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160
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Wang L, Chen Y, Yin L, Zhang S, Zhou N, Zhang W, Zhu X. Synthesis and characterization of visible-light-activated Azo hyperbranched polymers. Polym Chem 2016. [DOI: 10.1039/c6py01232a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
All visible-light-activated Azo polymer photoswitches were efficiently synthesized via combination of the AuNP-catalyzed photocatalytic method and the A3 monomer strategy.
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Affiliation(s)
- Laibing Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Yang Chen
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Lu Yin
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Shuangshuang Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Nianchen Zhou
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Wei Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
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161
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Abstract
Regulation of protein stability is a fundamental process in eukaryotic cells and pivotal to, e.g., cell cycle progression, faithful chromosome segregation, or protein quality control. Synthetic regulation of protein stability requires conditional degradation sequences (degrons) that induce a stability switch upon a specific signal. Fusion to a selected target protein permits to influence virtually every process in a cell. Light as signal is advantageous due to its precise applicability in time, space, quality, and quantity. Light control of protein stability was achieved by fusing the LOV2 photoreceptor domain of Arabidopsis thaliana phototropin1 with a synthetic degron (cODC1) derived from the carboxy-terminal degron of ornithine decarboxylase to obtain the photosensitive degron (psd) module. The psd module can be attached to the carboxy terminus of target proteins that are localized to the cytosol or nucleus to obtain light control over their stability. Blue light induces structural changes in the LOV2 domain, which in turn lead to activation of the degron and thus proteasomal degradation of the whole fusion protein. Variants of the psd module with diverse characteristics are useful to fine-tune the stability of a selected target at permissive (darkness) and restrictive conditions (blue light).
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162
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Lemoine D, Durand-de Cuttoli R, Mourot A. Optogenetic Control of Mammalian Ion Channels with Chemical Photoswitches. Methods Mol Biol 2016; 1408:177-93. [PMID: 26965123 DOI: 10.1007/978-1-4939-3512-3_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In neurons, ligand-gated ion channels decode the chemical signal of neurotransmitters into an electric response, resulting in a transient excitation or inhibition. Neurotransmitters act on multiple receptor types and subtypes, with spatially and temporally precise patterns. Hence, understanding the neural function of a given receptor requires methods for its targeted, rapid activation/inactivation in defined brain regions. To address this, we have developed a versatile optochemical genetic strategy, which allows the reversible control of defined receptor subtypes in designated cell types, with millisecond and micrometer precision. In this chapter, we describe the engineering of light-activated and -inhibited neuronal nicotinic acetylcholine receptors, as well as their characterization and use in cultured cells.
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Affiliation(s)
- Damien Lemoine
- Sorbonne Universités, UPMC Univ Paris 06, UM 119, 9 Quai St Bernard, 75005, Paris, France.,Neuroscience Paris Seine, CNRS, UMR 8246, 75005, Paris, France.,Neuroscience Paris Seine, INSERM, U1130, 75005, Paris, France
| | - Romain Durand-de Cuttoli
- Sorbonne Universités, UPMC Univ Paris 06, UM 119, 9 Quai St Bernard, 75005, Paris, France.,Neuroscience Paris Seine, CNRS, UMR 8246, 75005, Paris, France.,Neuroscience Paris Seine, INSERM, U1130, 75005, Paris, France
| | - Alexandre Mourot
- Sorbonne Universités, UPMC Univ Paris 06, UM 119, 9 Quai St Bernard, 75005, Paris, France. .,Neuroscience Paris Seine, CNRS, UMR 8246, 75005, Paris, France. .,Neuroscience Paris Seine, INSERM, U1130, 75005, Paris, France.
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163
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Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor. Proc Natl Acad Sci U S A 2015; 113:E91-100. [PMID: 26699507 DOI: 10.1073/pnas.1507355112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Optogenetics provides new ways to activate gene transcription; however, no attempts have been made as yet to modulate mammalian transcription factors. We report the light-mediated regulation of the repressor element 1 (RE1)-silencing transcription factor (REST), a master regulator of neural genes. To tune REST activity, we selected two protein domains that impair REST-DNA binding or recruitment of the cofactor mSin3a. Computational modeling guided the fusion of the inhibitory domains to the light-sensitive Avena sativa light-oxygen-voltage-sensing (LOV) 2-phototrophin 1 (AsLOV2). By expressing AsLOV2 chimeras in Neuro2a cells, we achieved light-dependent modulation of REST target genes that was associated with an improved neural differentiation. In primary neurons, light-mediated REST inhibition increased Na(+)-channel 1.2 and brain-derived neurotrophic factor transcription and boosted Na(+) currents and neuronal firing. This optogenetic approach allows the coordinated expression of a cluster of genes impinging on neuronal activity, providing a tool for studying neuronal physiology and correcting gene expression changes taking place in brain diseases.
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164
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Nadler A, Yushchenko DA, Müller R, Stein F, Feng S, Mulle C, Carta M, Schultz C. Exclusive photorelease of signalling lipids at the plasma membrane. Nat Commun 2015; 6:10056. [PMID: 26686736 PMCID: PMC4703838 DOI: 10.1038/ncomms10056] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 10/28/2015] [Indexed: 12/17/2022] Open
Abstract
Photoactivation of caged biomolecules has become a powerful approach to study cellular signalling events. Here we report a method for anchoring and uncaging biomolecules exclusively at the outer leaflet of the plasma membrane by employing a photocleavable, sulfonated coumarin derivative. The novel caging group allows quantifying the reaction progress and efficiency of uncaging reactions in a live-cell microscopy setup, thereby greatly improving the control of uncaging experiments. We synthesized arachidonic acid derivatives bearing the new negatively charged or a neutral, membrane-permeant coumarin caging group to locally induce signalling either at the plasma membrane or on internal membranes in β-cells and brain slices derived from C57B1/6 mice. Uncaging at the plasma membrane triggers a strong enhancement of calcium oscillations in β-cells and a pronounced potentiation of synaptic transmission while uncaging inside cells blocks calcium oscillations in β-cells and causes a more transient effect on neuronal transmission, respectively. The precise subcellular site of arachidonic acid release is therefore crucial for signalling outcome in two independent systems. Caged signalling intermediates are powerful cell biological tools, however it can be challenging to precisely control where activation occurs. Nadler et al. develop a caging group that specifically targets the plasma membrane, and demonstrate spatially controlled activation of arachidonic acid signalling.
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Affiliation(s)
- André Nadler
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Dmytro A Yushchenko
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Rainer Müller
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Suihan Feng
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christophe Mulle
- Institut Interdisciplinaire de Neurosciences, CNRS UMR 5297 Université Bordeaux 2, 146, rue Léo-Saignat, 33077 Bordeaux, France
| | - Mario Carta
- Institut Interdisciplinaire de Neurosciences, CNRS UMR 5297 Université Bordeaux 2, 146, rue Léo-Saignat, 33077 Bordeaux, France
| | - Carsten Schultz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
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165
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Hanswillemenke A, Kuzdere T, Vogel P, Jékely G, Stafforst T. Site-Directed RNA Editing in Vivo Can Be Triggered by the Light-Driven Assembly of an Artificial Riboprotein. J Am Chem Soc 2015; 137:15875-81. [PMID: 26594902 PMCID: PMC4731850 DOI: 10.1021/jacs.5b10216] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Site-directed
RNA editing allows for the manipulation of RNA and
protein function by reprogramming genetic information at the RNA level.
For this we assemble artificial RNA-guided editases and demonstrate
their transcript repair activity in cells and in developing embryos
of the annelid Platynereis dumerilii. A hallmark
of our assembly strategy is the covalent attachment of guideRNA and
editing enzyme by applying the SNAP-tag technology, a process that
we demonstrate here to be readily triggered by light in vitro, in
mammalian cell culture, and also in P. dumerilii.
Lacking both sophisticated chemistry and extensive genetic engineering,
this technology provides a convenient route for the light-dependent
switching of protein isoforms. The presented strategy may also serve
as a blue-print for the engineering of addressable machineries that
apply tailored nucleic acid analogues to manipulate RNA or DNA site-specifically
in living organisms.
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Affiliation(s)
- Alfred Hanswillemenke
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Tahsin Kuzdere
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Paul Vogel
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Gáspár Jékely
- Max-Planck-Institute for Developmental Biology , Spemannstraße 35, 72076 Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
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166
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Lin WC, Tsai MC, Davenport CM, Smith CM, Veit J, Wilson NM, Adesnik H, Kramer RH. A Comprehensive Optogenetic Pharmacology Toolkit for In Vivo Control of GABA(A) Receptors and Synaptic Inhibition. Neuron 2015; 88:879-891. [PMID: 26606997 DOI: 10.1016/j.neuron.2015.10.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/21/2015] [Accepted: 10/01/2015] [Indexed: 01/27/2023]
Abstract
Exogenously expressed opsins are valuable tools for optogenetic control of neurons in circuits. A deeper understanding of neural function can be gained by bringing control to endogenous neurotransmitter receptors that mediate synaptic transmission. Here we introduce a comprehensive optogenetic toolkit for controlling GABA(A) receptor-mediated inhibition in the brain. We developed a series of photoswitch ligands and the complementary genetically modified GABA(A) receptor subunits. By conjugating the two components, we generated light-sensitive versions of the entire GABA(A) receptor family. We validated these light-sensitive receptors for applications across a broad range of spatial scales, from subcellular receptor mapping to in vivo photo-control of visual responses in the cerebral cortex. Finally, we generated a knockin mouse in which the "photoswitch-ready" version of a GABA(A) receptor subunit genomically replaces its wild-type counterpart, ensuring normal receptor expression. This optogenetic pharmacology toolkit allows scalable interrogation of endogenous GABA(A) receptor function with high spatial, temporal, and biochemical precision.
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Affiliation(s)
- Wan-Chen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ming-Chi Tsai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher M Davenport
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caleb M Smith
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Veit
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Neil M Wilson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hillel Adesnik
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Richard H Kramer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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167
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Jullien L, Gautier A. Fluorogen-based reporters for fluorescence imaging: a review. Methods Appl Fluoresc 2015; 3:042007. [PMID: 29148509 DOI: 10.1088/2050-6120/3/4/042007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescence bioimaging has recently jumped into a new area of spatiotemporal resolution and sensitivity thanks to synergistic advances in both optical physics and probe/biosensor design. This review focuses on the recent development of genetically encodable fluorescent reporters that bind endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activate their fluorescence. We highlight the innovative engineering and design that gave rise to these new natural and synthetic fluorescent reporters, and describe some of the emerging applications in imaging and biosensing.
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Affiliation(s)
- Ludovic Jullien
- École Normale Supérieure-PSL Research University, Department of Chemistry, 24 rue Lhomond, F-75005 Paris, France. Sorbonne Universités, UPMC Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France. CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
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168
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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169
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Hughes RM, Freeman DJ, Lamb KN, Pollet RM, Smith WJ, Lawrence DS. Optogenetic apoptosis: light-triggered cell death. Angew Chem Int Ed Engl 2015; 54:12064-8. [PMID: 26418181 PMCID: PMC4819321 DOI: 10.1002/anie.201506346] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/06/2015] [Indexed: 12/11/2022]
Abstract
An optogenetic Bax has been designed that facilitates light-induced apoptosis. We demonstrate that mitochondrial recruitment of a genetically encoded light-responsive Bax results in the release of mitochondrial proteins, downstream caspase-3 cleavage, changes in cellular morphology, and ultimately cell death. Mutagenesis of a key phosphorylatable residue or modification of the C-terminus mitigates background (dark) levels of apoptosis that result from Bax overexpression. The mechanism of optogenetic Bax-mediated apoptosis was explored using a series of small molecules known to interfere with various steps in programmed cell death. Optogenetic Bax appears to form a mitochondrial apoptosis-induced channel analogous to that of endogenous Bax.
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Affiliation(s)
- Robert M Hughes
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA).
| | - David J Freeman
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Kelsey N Lamb
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Rebecca M Pollet
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Weston J Smith
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - David S Lawrence
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA).
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170
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Dong X, Zhang Z, Zhao D, Liu Y, Meng Y, Zhang Y, Zhang D, Liu C. Ultraviolet light triggers the conversion of Cu2+-bound Aβ42 aggregates into cytotoxic species in a copper chelation-independent manner. Sci Rep 2015; 5:13897. [PMID: 26350232 PMCID: PMC4563556 DOI: 10.1038/srep13897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 07/10/2015] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence indicates that abnormal Cu2+ binding to Aβ peptides are responsible for the formation of soluble Aβ oligomers and ROS that play essential roles in AD pathogenesis. During studying the Cu2+-chelating treatment of Cu2+-bound Aβ42 aggregates, we found that UV light exposure pronouncedly enhances cytotoxicity of the chelator-treated and -untreated Cu2+-bound Aβ42 aggregates. This stimulated us to thoroughly investigate (1) either the chelation treatment or UV light exposure leads to the increased cytotoxicity of the aggregates, and (2) why the chelator-treated and -untreated Cu2+-bound Aβ42 aggregates exhibit the increased cytotoxicity following UV light exposure if the latter is the case. The data indicated that the controlled UV exposure induced the dissociation of Cu2+-free and -bound Aβ42 aggregates into SDS-stable soluble oligomers and the production of ROS including H2O2 in an UV light intensity- and time-dependent, but Cu2+ chelation-independent manner. Although we can't fully understand the meaning of this finding at the current stage, the fact that the UV illuminated Aβ42 aggregates can efficiently kill HeLa cells implies that the aggregates after UV light exposure could be used to decrease the viability of skin cancer cells through skin administration.
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Affiliation(s)
- Xiongwei Dong
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Zhe Zhang
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Dan Zhao
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Yaojing Liu
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Yan Meng
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Yong Zhang
- School of Chemical and Materials Engineering, Hubei Polytechnic University, Huangshi, 435003 Hubei, China
| | - Dan Zhang
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
| | - Changlin Liu
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, and School of Chemistry, Central China Normal University, Wuhan 430079, Hubei
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171
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Hughes RM, Freeman DJ, Lamb KN, Pollet RM, Smith WJ, Lawrence DS. Optogenetic Apoptosis: Light-Triggered Cell Death. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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172
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A light-switchable bidirectional expression module allowing simultaneous regulation of multiple genes. Biochem Biophys Res Commun 2015; 465:769-76. [PMID: 26301633 DOI: 10.1016/j.bbrc.2015.08.085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
Abstract
Several light-regulated genetic circuits have been applied to spatiotemporally control transgene expression in mammalian cells. However, simultaneous regulation of multiple genes using one genetic device by light has not yet been reported. In this study, we engineered a bidirectional expression module based on LightOn system. Our data showed that both reporter genes could be regulated at defined and quantitative levels. Simultaneous regulation of four genes was further achieved in cultured cells and mice. Additionally, we successfully utilized the bidirectional expression module to monitor the expression of a suicide gene, showing potential for photodynamic gene therapy. Collectively, we provide a robust and useful tool to simultaneously control multiple genes expression by light, which will be widely used in biomedical research and biotechnology.
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173
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Delacour Q, Li C, Plamont MA, Billon-Denis E, Aujard I, Le Saux T, Jullien L, Gautier A. Light-Activated Proteolysis for the Spatiotemporal Control of Proteins. ACS Chem Biol 2015; 10:1643-7. [PMID: 25938742 DOI: 10.1021/acschembio.5b00069] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The regulation of proteolysis is an efficient way to control protein function in cells. Here, we present a general strategy enabling to increase the spatiotemporal resolution of conditional proteolysis by using light activation as trigger. Our approach relies on the auxin-inducible degradation system obtained by transposing components of the plant auxin-dependent degradation pathway in mammalian cells. We developed a photoactivatable auxin that acts as a photoactivatable inducer of degradation. Upon local and short light illumination, auxin is released in cells and triggers the degradation of a protein of interest with spatiotemporal control.
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Affiliation(s)
- Quentin Delacour
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Chenge Li
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Marie-Aude Plamont
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Emmanuelle Billon-Denis
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Isabelle Aujard
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Thomas Le Saux
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Ludovic Jullien
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | - Arnaud Gautier
- Department
of Chemistry, École Normale Supérieure−PSL Research University, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC
Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France
- CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
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174
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Kochanowski K, Sauer U, Noor E. Posttranslational regulation of microbial metabolism. Curr Opin Microbiol 2015; 27:10-7. [PMID: 26048423 DOI: 10.1016/j.mib.2015.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/04/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Fluxes in microbial metabolism are controlled by various regulatory layers that alter abundance or activity of metabolic enzymes. Recent studies suggest a division of labor between these layers: transcriptional regulation mostly controls the allocation of protein resources, passive flux regulation by enzyme saturation and thermodynamics allows rapid responses at the expense of higher protein cost, and posttranslational regulation is utilized by cells to directly take control of metabolic decisions. We present recent advances in elucidating the role of these regulatory layers, focusing on posttranslational modifications and allosteric interactions. As the systematic mapping of posttranslational regulatory events has now become possible, the next challenge is to identify those regulatory events that are functionally relevant under a given condition.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland; Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland.
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
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175
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Etoc F, Vicario C, Lisse D, Siaugue JM, Piehler J, Coppey M, Dahan M. Magnetogenetic control of protein gradients inside living cells with high spatial and temporal resolution. NANO LETTERS 2015; 15:3487-94. [PMID: 25895433 DOI: 10.1021/acs.nanolett.5b00851] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Tools for controlling the spatial organization of proteins are a major prerequisite for deciphering mechanisms governing the dynamic architecture of living cells. Here, we have developed a generic approach for inducing and maintaining protein gradients inside living cells by means of biofunctionalized magnetic nanoparticles (MNPs). For this purpose, we tailored the size and surface properties of MNPs in order to ensure unhindered mobility in the cytosol. These MNPs with a core diameter below 50 nm could be rapidly relocalized in living cells by exploiting biased diffusion at weak magnetic forces in the femto-Newton range. In combination with MNP surface functionalization for specific in situ capturing of target proteins as well as efficient delivery into the cytosplasm, we here present a comprehensive technology for controlling intracellular protein gradients with a temporal resolution of a few tens of seconds.
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Affiliation(s)
- Fred Etoc
- †Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Chiara Vicario
- †Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Domenik Lisse
- †Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France
- ‡Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jean-Michel Siaugue
- §Sorbonne Universités, UPMC Univ Paris 06, UMR 8234, PHENIX, F-75005 Paris, France
| | - Jacob Piehler
- ‡Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Mathieu Coppey
- †Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Maxime Dahan
- †Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France
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176
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Hirakawa H, Ishikawa S, Nagamune T. Ca2+ -independent sortase-A exhibits high selective protein ligation activity in the cytoplasm of Escherichia coli. Biotechnol J 2015; 10:1487-92. [PMID: 25864513 DOI: 10.1002/biot.201500012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/10/2015] [Accepted: 04/08/2015] [Indexed: 11/07/2022]
Abstract
A Staphylococcus aureus transpeptidase, sortase A (SrtA), which catalyzes a peptide ligation with high substrate specificity, is a useful tool to site-specifically attach proteinaceous/peptidic functional molecules to target proteins. However, its strong Ca(2+) dependency makes SrtA difficult for use under low Ca(2+) concentrations and in the presence of Ca(2+)-binding substances. To overcome this problem, we designed a SrtA mutant that Ca(2+)-independently demonstrates a high catalytic activity. The heptamutant (P94R/E105K/E108A/D160N/D165A/K190E/K196T), which resulted from a combination of known mutations at the Ca(2+) -binding site and around the substrate-binding site, successfully catalyzed a selective protein-protein ligation in the cytoplasm of Escherichia coli. Selective protein modification in living cells is a promising approach for investigating cellular events and regulating cell functions. This SrtA mutant may prove to be a versatile tool for adding new functionalities to proteins of interest by incorporating functional proteins and chemically modified peptides in living cells, which usually retain low Ca(2+) concentrations.
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Affiliation(s)
- Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Suguru Ishikawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
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177
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Hemphill J, Borchardt EK, Brown K, Asokan A, Deiters A. Optical Control of CRISPR/Cas9 Gene Editing. J Am Chem Soc 2015; 137:5642-5. [PMID: 25905628 DOI: 10.1021/ja512664v] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has emerged as an important tool in biomedical research for a wide range of applications, with significant potential for genome engineering and gene therapy. In order to achieve conditional control of the CRISPR/Cas9 system, a genetically encoded light-activated Cas9 was engineered through the site-specific installation of a caged lysine amino acid. Several potential lysine residues were identified as viable caging sites that can be modified to optically control Cas9 function, as demonstrated through optical activation and deactivation of both exogenous and endogenous gene function.
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Affiliation(s)
- James Hemphill
- †Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Kalyn Brown
- †Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Alexander Deiters
- †Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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178
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Yokoyama C, Onoe H. Positron emission tomography imaging of the social brain of common marmosets. Neurosci Res 2015; 93:82-90. [DOI: 10.1016/j.neures.2014.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 01/07/2023]
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179
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Müller K, Zurbriggen MD, Weber W. An optogenetic upgrade for the Tet-OFF system. Biotechnol Bioeng 2015; 112:1483-7. [DOI: 10.1002/bit.25562] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/28/2015] [Accepted: 02/05/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Konrad Müller
- Faculty of Biology; University of Freiburg; Schänzlestrasse 1, 79104 Freiburg Germany
| | - Matias D. Zurbriggen
- Faculty of Biology; University of Freiburg; Schänzlestrasse 1, 79104 Freiburg Germany
- BIOSS Centre for Biological Signalling Studies; University of Freiburg; Schänzlestrasse 18, 79104 Freiburg Germany
| | - Wilfried Weber
- Faculty of Biology; University of Freiburg; Schänzlestrasse 1, 79104 Freiburg Germany
- BIOSS Centre for Biological Signalling Studies; University of Freiburg; Schänzlestrasse 18, 79104 Freiburg Germany
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180
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Polstein LR, Gersbach CA. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol 2015; 11:198-200. [PMID: 25664691 PMCID: PMC4412021 DOI: 10.1038/nchembio.1753] [Citation(s) in RCA: 469] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Optogenetic systems enable precise spatial and temporal control of cell behavior. We engineered a light-activated CRISPR/Cas9 effector (LACE) system that induces transcription of endogenous genes in the presence of blue light. This was accomplished by fusing the light-inducible heterodimerizing proteins CRY2 and CIB1 to a transactivation domain and the catalytically inactive dCas9, respectively. The versatile LACE system can be easily directed to new DNA sequences for the dynamic regulation of endogenous genes.
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Affiliation(s)
- Lauren R Polstein
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Charles A Gersbach
- 1] Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA. [2] Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA. [3] Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA
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181
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182
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Schmidt D, Cho YK. Natural photoreceptors and their application to synthetic biology. Trends Biotechnol 2015; 33:80-91. [DOI: 10.1016/j.tibtech.2014.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/19/2014] [Accepted: 10/20/2014] [Indexed: 01/22/2023]
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183
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Schelkle KM, Griesbaum T, Ollech D, Becht S, Buckup T, Hamburger M, Wombacher R. Lichtinduzierte Proteindimerisierung in lebenden Zellen durch Ein- und Zweiphotonenaktivierung von Gibberellinsäurederivaten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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184
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Schelkle KM, Griesbaum T, Ollech D, Becht S, Buckup T, Hamburger M, Wombacher R. Light-Induced Protein Dimerization by One- and Two-Photon Activation of Gibberellic Acid Derivatives in Living Cells. Angew Chem Int Ed Engl 2015; 54:2825-9. [DOI: 10.1002/anie.201409196] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Indexed: 01/02/2023]
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185
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Reddington SC, Driezis S, Hartley AM, Watson PD, Rizkallah PJ, Jones DD. Genetically encoded phenyl azide photochemistry drives positive and negative functional modulation of a red fluorescent protein. RSC Adv 2015. [DOI: 10.1039/c5ra13552d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genetically encoded incorporation of phenyl azide chemistry into the autofluorescent protein mCherry can be used to switch on or off fluorescence.
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186
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Hansen MJ, Velema WA, Lerch MM, Szymanski W, Feringa BL. Wavelength-selective cleavage of photoprotecting groups: strategies and applications in dynamic systems. Chem Soc Rev 2015; 44:3358-77. [DOI: 10.1039/c5cs00118h] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wavelength-selective deprotection is an attractive method to control multiple functions in one system using light.
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Affiliation(s)
- Mickel J. Hansen
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Willem A. Velema
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Michael M. Lerch
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Ben L. Feringa
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
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187
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Chevalier A, Renard PY, Romieu A. Straightforward synthesis of bioconjugatable azo dyes. Part 1: Black Hole Quencher-1 (BHQ-1) scaffold. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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188
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Isomura A, Kageyama R. Ultradian oscillations and pulses: coordinating cellular responses and cell fate decisions. Development 2014; 141:3627-36. [PMID: 25249457 PMCID: PMC4197574 DOI: 10.1242/dev.104497] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biological clocks play key roles in organismal development, homeostasis and function. In recent years, much work has focused on circadian clocks, but emerging studies have highlighted the existence of ultradian oscillators – those with a much shorter periodicity than 24 h. Accumulating evidence, together with recently developed optogenetic approaches, suggests that such ultradian oscillators play important roles during cell fate decisions, and analyzing the functional links between ultradian oscillation and cell fate determination will contribute to a deeper understanding of the design principle of developing embryos. In this Review, we discuss the mechanisms of ultradian oscillatory dynamics and introduce examples of ultradian oscillators in various biological contexts. We also discuss how optogenetic technology has been used to elucidate the biological significance of ultradian oscillations.
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Affiliation(s)
- Akihiro Isomura
- Institute for Virus Research, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (CREST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ryoichiro Kageyama
- Institute for Virus Research, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (CREST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan World Premier International Research Initiative-Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
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189
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Schmidl SR, Sheth RU, Wu A, Tabor JJ. Refactoring and optimization of light-switchable Escherichia coli two-component systems. ACS Synth Biol 2014; 3:820-31. [PMID: 25250630 DOI: 10.1021/sb500273n] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light-switchable proteins enable unparalleled control of molecular biological processes in live organisms. Previously, we have engineered red/far-red and green/red photoreversible two-component signal transduction systems (TCSs) with transcriptional outputs in E. coli and used them to characterize and control synthetic gene circuits with exceptional quantitative, temporal, and spatial precision. However, the broad utility of these light sensors is limited by bulky DNA encoding, incompatibility with commonly used ligand-responsive transcription factors, leaky output in deactivating light, and less than 10-fold dynamic range. Here, we compress the four genes required for each TCS onto two streamlined plasmids and replace all chemically inducible and evolved promoters with constitutive, engineered versions. Additionally, we systematically optimize the expression of each sensor histidine kinase and response regulator, and redesign both pathway output promoters, resulting in low leakiness and 72- and 117-fold dynamic range, respectively. These second-generation light sensors can be used to program the expression of more genes over a wider range and can be more easily combined with additional plasmids or moved to different host strains. This work demonstrates that bacterial TCSs can be optimized to function as high-performance sensors for scientific and engineering applications.
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Affiliation(s)
- Sebastian R. Schmidl
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ravi U. Sheth
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Andrew Wu
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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190
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Ballister ER, Aonbangkhen C, Mayo AM, Lampson MA, Chenoweth DM. Localized light-induced protein dimerization in living cells using a photocaged dimerizer. Nat Commun 2014; 5:5475. [PMID: 25400104 PMCID: PMC4308733 DOI: 10.1038/ncomms6475] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein-protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations.
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Affiliation(s)
- Edward R Ballister
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chanat Aonbangkhen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alyssa M Mayo
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David M Chenoweth
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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