101
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Lee S, Sohn KC, Choi DK, Won M, Park KA, Ju SK, Kang K, Bae YK, Hur GM, Ro H. Ecdysone Receptor-based Singular Gene Switches for Regulated Transgene Expression in Cells and Adult Rodent Tissues. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e367. [PMID: 27673563 PMCID: PMC5056996 DOI: 10.1038/mtna.2016.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]
Abstract
Controlled gene expression is an indispensable technique in biomedical research. Here, we report a convenient, straightforward, and reliable way to induce expression of a gene of interest with negligible background expression compared to the most widely used tetracycline (Tet)-regulated system. Exploiting a Drosophila ecdysone receptor (EcR)-based gene regulatory system, we generated nonviral and adenoviral singular vectors designated as pEUI(+) and pENTR-EUI, respectively, which contain all the required elements to guarantee regulated transgene expression (GAL4-miniVP16-EcR, termed GvEcR hereafter, and 10 tandem repeats of an upstream activation sequence promoter followed by a multiple cloning site). Through the transient and stable transfection of mammalian cell lines with reporter genes, we validated that tebufenozide, an ecdysone agonist, reversibly induced gene expression, in a dose- and time-dependent manner, with negligible background expression. In addition, we created an adenovirus derived from the pENTR-EUI vector that readily infected not only cultured cells but also rodent tissues and was sensitive to tebufenozide treatment for regulated transgene expression. These results suggest that EcR-based singular gene regulatory switches would be convenient tools for the induction of gene expression in cells and tissues in a tightly controlled fashion.
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Affiliation(s)
- Seoghyun Lee
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Kyung-Cheol Sohn
- Department of Dermatology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Dae-Kyoung Choi
- Department of Dermatology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Minho Won
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyeong Ah Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Sung-Kyu Ju
- Affiliated Research (and Development) Institute, Daejeon, Republic of Korea
| | - Kidong Kang
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Young-Ki Bae
- Comparative Biomedical Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Gang Min Hur
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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102
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Ross B, Mehta S, Zhang J. Molecular tools for acute spatiotemporal manipulation of signal transduction. Curr Opin Chem Biol 2016; 34:135-142. [PMID: 27639090 DOI: 10.1016/j.cbpa.2016.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 01/14/2023]
Abstract
The biochemical activities involved in signal transduction in cells are under tight spatiotemporal regulation. To study the effects of the spatial patterning and temporal dynamics of biochemical activities on downstream signaling, researchers require methods to manipulate signaling pathways acutely and rapidly. In this review, we summarize recent developments in the design of three broad classes of molecular tools for perturbing signal transduction, classified by their type of input signal: chemically induced, optically induced, and magnetically induced.
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Affiliation(s)
- Brian Ross
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA.
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103
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Frank JA, Yushchenko DA, Hodson DJ, Lipstein N, Nagpal J, Rutter GA, Rhee JS, Gottschalk A, Brose N, Schultz C, Trauner D. Photoswitchable diacylglycerols enable optical control of protein kinase C. Nat Chem Biol 2016; 12:755-62. [PMID: 27454932 PMCID: PMC6101201 DOI: 10.1038/nchembio.2141] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/16/2016] [Indexed: 01/02/2023]
Abstract
Increased levels of the second messenger lipid diacylglycerol (DAG) induce downstream signaling events including the translocation of C1-domain-containing proteins toward the plasma membrane. Here, we introduce three light-sensitive DAGs, termed PhoDAGs, which feature a photoswitchable acyl chain. The PhoDAGs are inactive in the dark and promote the translocation of proteins that feature C1 domains toward the plasma membrane upon a flash of UV-A light. This effect is quickly reversed after the termination of photostimulation or by irradiation with blue light, permitting the generation of oscillation patterns. Both protein kinase C and Munc13 can thus be put under optical control. PhoDAGs control vesicle release in excitable cells, such as mouse pancreatic islets and hippocampal neurons, and modulate synaptic transmission in Caenorhabditis elegans. As such, the PhoDAGs afford an unprecedented degree of spatiotemporal control and are broadly applicable tools to study DAG signaling.
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Affiliation(s)
- James Allen Frank
- Department of Chemistry and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Munich, Germany
| | - Dmytro A Yushchenko
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David J Hodson
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, ICTEM, Hammersmith Hospital, London, UK
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, UK
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Jatin Nagpal
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biochemistry, Department for Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, ICTEM, Hammersmith Hospital, London, UK
| | - Jeong-Seop Rhee
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biochemistry, Department for Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Carsten Schultz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Dirk Trauner
- Department of Chemistry and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Munich, Germany
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104
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Lee SY, Lee H, Lee HK, Lee SW, Ha SC, Kwon T, Seo JK, Lee C, Rhee HW. Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells. ACS CENTRAL SCIENCE 2016; 2:506-16. [PMID: 27610411 PMCID: PMC4999972 DOI: 10.1021/acscentsci.6b00137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 05/23/2023]
Abstract
Mammalian target of rapamycin (mTOR) signaling is a core pathway in cellular metabolism, and control of the mTOR pathway by rapamycin shows potential for the treatment of metabolic diseases. In this study, we employed a new proximity biotin-labeling method using promiscuous biotin ligase (pBirA) to identify unknown elements in the rapamycin-induced interactome on the FK506-rapamycin binding (FRB) domain in living cells. FKBP25 showed the strongest biotin labeling by FRB-pBirA in the presence of rapamycin. Immunoprecipitation and immunofluorescence experiments confirmed that endogenous FKBP25 has a rapamycin-induced physical interaction with the FRB domain. Furthermore, the crystal structure of the ternary complex of FRB-rapamycin-FKBP25 was determined at 1.67-Å resolution. In this crystal structure we found that the conformational changes of FRB generate a hole where there is a methionine-rich space, and covalent metalloid coordination was observed at C2085 of FRB located at the bottom of the hole. Our results imply that FKBP25 might have a unique physiological role related to metallomics in mTOR signaling.
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Affiliation(s)
- Song-Yi Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hakbong Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hye-Kyeong Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Seung-Won Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Sung Chul Ha
- Pohang
Accelerator Laboratory, Pohang University
of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Taejoon Kwon
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jeong Kon Seo
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Changwook Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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105
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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106
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Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P. A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications. PLoS One 2016; 11:e0159277. [PMID: 27500400 PMCID: PMC4976983 DOI: 10.1371/journal.pone.0159277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022] Open
Abstract
Recombination-based cloning is a quick and efficient way to generate expression vectors. Recent advancements have provided powerful recombinant DNA methods for molecular manipulations. Here, we describe a novel collection of three-fragment MultiSite Gateway cloning system-compatible vectors providing expanded molecular tools for vertebrate research. The components of this toolkit encompass a broad range of uses such as fluorescent imaging, dual gene expression, RNA interference, tandem affinity purification, chemically-inducible dimerization and lentiviral production. We demonstrate examples highlighting the utility of this toolkit for producing multi-component vertebrate expression vectors with diverse primary research applications. The vectors presented here are compatible with other Gateway toolkits and collections, facilitating the rapid generation of a broad range of innovative DNA constructs for biological research.
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Affiliation(s)
- Daniel K. Fowler
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott Stewart
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Steve Seredick
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (PW); (KS)
| | - Philip Washbourne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (PW); (KS)
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107
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Luo J, Liu Q, Morihiro K, Deiters A. Small-molecule control of protein function through Staudinger reduction. Nat Chem 2016; 8:1027-1034. [PMID: 27768095 PMCID: PMC5119652 DOI: 10.1038/nchem.2573] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/13/2016] [Indexed: 01/08/2023]
Abstract
Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl tRNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active, wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (EGFP), protein translocation (nuclear localization sequence), DNA recombination (Cre), and gene editing (Cas9).
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Affiliation(s)
- Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Qingyang Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Kunihiko Morihiro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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108
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Rapamycin-induced oligomer formation system of FRB–FKBP fusion proteins. J Biosci Bioeng 2016; 122:40-6. [DOI: 10.1016/j.jbiosc.2015.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/25/2015] [Accepted: 12/03/2015] [Indexed: 11/20/2022]
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109
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Di Ventura B, Kuhlman B. Go in! Go out! Inducible control of nuclear localization. Curr Opin Chem Biol 2016; 34:62-71. [PMID: 27372352 DOI: 10.1016/j.cbpa.2016.06.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/19/2022]
Abstract
Cells have evolved a variety of mechanisms to regulate the enormous complexity of processes taking place inside them. One mechanism consists in tightly controlling the localization of macromolecules, keeping them away from their place of action until needed. Since a large fraction of the cellular response to external stimuli is mediated by gene expression, it is not surprising that transcriptional regulators are often subject to stimulus-induced nuclear import or export. Here we review recent methods in chemical biology and optogenetics for controlling the nuclear localization of proteins of interest inside living cells. These methods allow researchers to regulate protein activity with exquisite spatiotemporal control, and open up new possibilities for studying the roles of proteins in a broad array of cellular processes and biological functions.
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Affiliation(s)
- Barbara Di Ventura
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg, Germany.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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110
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Andersen TG, Nintemann SJ, Marek M, Halkier BA, Schulz A, Burow M. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization. Sci Rep 2016; 6:27766. [PMID: 27282591 PMCID: PMC4901268 DOI: 10.1038/srep27766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/24/2016] [Indexed: 01/11/2023] Open
Abstract
When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true- from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Förster resonance energy transfer (FRET)- based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality.
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Affiliation(s)
- Tonni Grube Andersen
- Center for Dynamic Molecular Interactions (DynaMo), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Sebastian J. Nintemann
- Center for Dynamic Molecular Interactions (DynaMo), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Barbara A. Halkier
- Center for Dynamic Molecular Interactions (DynaMo), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Alexander Schulz
- Center for Dynamic Molecular Interactions (DynaMo), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Meike Burow
- Center for Dynamic Molecular Interactions (DynaMo), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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111
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Probing Mitosis by Manipulating the Interactions of Mitotic Regulator Proteins Using Rapamycin-Inducible Dimerization. Methods Mol Biol 2016; 1413:325-31. [PMID: 27193858 DOI: 10.1007/978-1-4939-3542-0_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Inducible dimerization is a general approach to experimentally manipulate protein-protein interactions with temporal control. This chapter describes the use of rapamycin-inducible dimerization to manipulate mitotic regulatory proteins, for example to control kinetochore localization. A significant feature of this method relative to previously described protocols is the depletion of endogenous FKBP12 protein, which markedly improves dimerization efficiency.
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112
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Guglielmi G, Barry JD, Huber W, De Renzis S. An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis. Dev Cell 2016; 35:646-660. [PMID: 26777292 PMCID: PMC4683098 DOI: 10.1016/j.devcel.2015.10.020] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 09/05/2015] [Accepted: 10/22/2015] [Indexed: 11/09/2022]
Abstract
Morphogenesis of multicellular organisms is driven by localized cell shape changes. How, and to what extent, changes in behavior in single cells or groups of cells influence neighboring cells and large-scale tissue remodeling remains an open question. Indeed, our understanding of multicellular dynamics is limited by the lack of methods allowing the modulation of cell behavior with high spatiotemporal precision. Here, we developed an optogenetic approach to achieve local modulation of cell contractility and used it to control morphogenetic movements during Drosophila embryogenesis. We show that local inhibition of apical constriction is sufficient to cause a global arrest of mesoderm invagination. By varying the spatial pattern of inhibition during invagination, we further demonstrate that coordinated contractile behavior responds to local tissue geometrical constraints. Together, these results show the efficacy of this optogenetic approach to dissect the interplay between cell-cell interaction, force transmission, and tissue geometry during complex morphogenetic processes. Optogenetics provides a powerful approach to control tissue morphogenesis Two-photon illumination allows precise patterns of optogenetic activation Local modulation of cell contractility reveals mechanisms of tissue invagination Tissue geometry constrains the cell contractile behavior driving invagination
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Affiliation(s)
| | - Joseph D Barry
- EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wolfgang Huber
- EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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113
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Zaytsev AV, Segura-Peña D, Godzi M, Calderon A, Ballister ER, Stamatov R, Mayo AM, Peterson L, Black BE, Ataullakhanov FI, Lampson MA, Grishchuk EL. Bistability of a coupled Aurora B kinase-phosphatase system in cell division. eLife 2016; 5:e10644. [PMID: 26765564 PMCID: PMC4798973 DOI: 10.7554/elife.10644] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/13/2016] [Indexed: 01/08/2023] Open
Abstract
Aurora B kinase, a key regulator of cell division, localizes to specific cellular locations, but the regulatory mechanisms responsible for phosphorylation of substrates located remotely from kinase enrichment sites are unclear. Here, we provide evidence that this activity at a distance depends on both sites of high kinase concentration and the bistability of a coupled kinase-phosphatase system. We reconstitute this bistable behavior and hysteresis using purified components to reveal co-existence of distinct high and low Aurora B activity states, sustained by a two-component kinase autoactivation mechanism. Furthermore, we demonstrate these non-linear regimes in live cells using a FRET-based phosphorylation sensor, and provide a mechanistic theoretical model for spatial regulation of Aurora B phosphorylation. We propose that bistability of an Aurora B-phosphatase system underlies formation of spatial phosphorylation patterns, which are generated and spread from sites of kinase autoactivation, thereby regulating cell division.
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Affiliation(s)
- Anatoly V Zaytsev
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Dario Segura-Peña
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Maxim Godzi
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Abram Calderon
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Edward R Ballister
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Rumen Stamatov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Alyssa M Mayo
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Laura Peterson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Fazly I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Federal Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Department of Physics, Moscow State University, Moscow, Russia
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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114
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Xu B, Zhou X, Stains CI. An improved miniprotein host for fluorogenic supramolecular assembly on the surface of living cells. RSC Adv 2016. [DOI: 10.1039/c6ra01215a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new host–guest pair produces a significant increase in the brightness of supramolecular complexes on the surface of living cells.
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Affiliation(s)
- Bi Xu
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Xinqi Zhou
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Cliff I. Stains
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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115
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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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116
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Xu B, Zhou X, Stains CI. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair. J Am Chem Soc 2015; 137:14252-5. [DOI: 10.1021/jacs.5b09494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bi Xu
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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117
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Chemically induced dimerization: reversible and spatiotemporal control of protein function in cells. Curr Opin Chem Biol 2015; 28:194-201. [DOI: 10.1016/j.cbpa.2015.09.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/21/2015] [Accepted: 09/07/2015] [Indexed: 12/21/2022]
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118
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Abstract
Chromosome segregation during cell division depends on interactions of kinetochores with dynamic microtubules (MTs). In many eukaryotes, each kinetochore binds multiple MTs, but the collective behavior of these coupled MTs is not well understood. We present a minimal model for collective kinetochore-MT dynamics, based on in vitro measurements of individual MTs and their dependence on force and kinetochore phosphorylation by Aurora B kinase. For a system of multiple MTs connected to the same kinetochore, the force-velocity relation has a bistable regime with two possible steady-state velocities: rapid shortening or slow growth. Bistability, combined with the difference between the growing and shrinking speeds, leads to center-of-mass and breathing oscillations in bioriented sister kinetochore pairs. Kinetochore phosphorylation shifts the bistable region to higher tensions, so that only the rapidly shortening state is stable at low tension. Thus, phosphorylation leads to error correction for kinetochores that are not under tension. We challenged the model with new experiments, using chemically induced dimerization to enhance Aurora B activity at metaphase kinetochores. The model suggests that the experimentally observed disordering of the metaphase plate occurs because phosphorylation increases kinetochore speeds by biasing MTs to shrink. Our minimal model qualitatively captures certain characteristic features of kinetochore dynamics, illustrates how biochemical signals such as phosphorylation may regulate the dynamics, and provides a theoretical framework for understanding other factors that control the dynamics in vivo.
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119
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Terai T, Kohno M, Boncompain G, Sugiyama S, Saito N, Fujikake R, Ueno T, Komatsu T, Hanaoka K, Okabe T, Urano Y, Perez F, Nagano T. Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport. J Am Chem Soc 2015; 137:10464-7. [DOI: 10.1021/jacs.5b05672] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | - Shigeru Sugiyama
- Graduate
School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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120
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Goodchild RE, Buchwalter AL, Naismith TV, Holbrook K, Billion K, Dauer WT, Liang CC, Dear ML, Hanson PI. Access of torsinA to the inner nuclear membrane is activity dependent and regulated in the endoplasmic reticulum. J Cell Sci 2015; 128:2854-65. [PMID: 26092934 DOI: 10.1242/jcs.167452] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 06/12/2015] [Indexed: 11/20/2022] Open
Abstract
TorsinA (also known as torsin-1A) is a membrane-embedded AAA+ ATPase that has an important role in the nuclear envelope lumen. However, most torsinA is localized in the peripheral endoplasmic reticulum (ER) lumen where it has a slow mobility that is incompatible with free equilibration between ER subdomains. We now find that nuclear-envelope-localized torsinA is present on the inner nuclear membrane (INM) and ask how torsinA reaches this subdomain. The ER system contains two transmembrane proteins, LAP1 and LULL1 (also known as TOR1AIP1 and TOR1AIP2, respectively), that reversibly co-assemble with and activate torsinA. Whereas LAP1 localizes on the INM, we show that LULL1 is in the peripheral ER and does not enter the INM. Paradoxically, interaction between torsinA and LULL1 in the ER targets torsinA to the INM. Native gel electrophoresis reveals torsinA oligomeric complexes that are destabilized by LULL1. Mutations in torsinA or LULL1 that inhibit ATPase activity reduce the access of torsinA to the INM. Furthermore, although LULL1 binds torsinA in the ER lumen, its effect on torsinA localization requires cytosolic-domain-mediated oligomerization. These data suggest that LULL1 oligomerizes to engage and transiently disassemble torsinA oligomers, and is thereby positioned to transduce cytoplasmic signals to the INM through torsinA.
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Affiliation(s)
- Rose E Goodchild
- VIB Centre for the Biology of Disease and KU Leuven, Department of Human Genetics, Campus Gasthuisberg, Leuven 3000, Belgium
| | - Abigail L Buchwalter
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Teresa V Naismith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Kristen Holbrook
- Department of Biochemistry, Cell and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Karolien Billion
- VIB Centre for the Biology of Disease and KU Leuven, Department of Human Genetics, Campus Gasthuisberg, Leuven 3000, Belgium
| | - William T Dauer
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chun-Chi Liang
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mary Lynn Dear
- Department of Biochemistry, Cell and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Phyllis I Hanson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63130, USA
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121
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A single-cell model of PIP3 dynamics using chemical dimerization. Bioorg Med Chem 2015; 23:2868-76. [DOI: 10.1016/j.bmc.2015.04.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 11/22/2022]
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122
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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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123
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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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124
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Brown KA, Zou Y, Shirvanyants D, Zhang J, Samanta S, Mantravadi PK, Dokholyan NV, Deiters A. Light-cleavable rapamycin dimer as an optical trigger for protein dimerization. Chem Commun (Camb) 2015; 51:5702-5. [DOI: 10.1039/c4cc09442e] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein heterodimerization of FKBP12 and FRB can be optically controlled with a photocleavable rapamycin dimer.
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Affiliation(s)
- Kalyn A. Brown
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
| | - Yan Zou
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - David Shirvanyants
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Jie Zhang
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Subhas Samanta
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| | | | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Alexander Deiters
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
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125
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Alao JP, Michlikova S, Dinér P, Grøtli M, Sunnerhagen P. Selective inhibition of RET mediated cell proliferation in vitro by the kinase inhibitor SPP86. BMC Cancer 2014; 14:853. [PMID: 25409876 PMCID: PMC4252022 DOI: 10.1186/1471-2407-14-853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The RET tyrosine kinase receptor has emerged as a target in thyroid and endocrine resistant breast cancer. We previously reported the synthesis of kinase inhibitors with potent activity against RET. Herein, we have further investigated the effect of the lead compound SPP86 on RET mediated signaling and proliferation. Based on these observations, we hypothesized that SPP86 may be useful for studying the cellular activity of RET. METHODS We compared the effects of SPP86 on RET-induced signaling and proliferation in thyroid cancer cell lines expressing RET-PTC1 (TPC1), or the activating mutations BRAFV600E (8505C) and RASG13R (C643). The effect of SPP86 on RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK pathway signaling and cell proliferation in MCF7 breast cancer cells was also investigated. RESULTS SPP86 inhibited MAPK signaling and proliferation in RET/PTC1 expressing TPC1 but not 8505C or C643 cells. In TPC1 cells, the inhibition of RET phosphorylation required co-exposure to SPP86 and the focal adhesion kinase (FAK) inhibitor PF573228. In MCF7 cells, SPP86 inhibited RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK signaling and estrogen receptorα (ERα) phosphorylation, and inhibited proliferation to a similar degree as tamoxifen. Interestingly, SPP86 and PF573228 inhibited RET/PTC1 and GDNF- RET induced activation of Akt and MAPK signaling to a similar degree. CONCLUSION SPP86 selectively inhibits RET downstream signaling in RET/PTC1 but not BRAFV600E or RASG13R expressing cells, indicating that downstream kinases were not affected. SPP86 also inhibited RET signaling in MCF7 breast cancer cells. Additionally, RET- FAK crosstalk may play a key role in facilitating PTC1/RET and GDNF- RET induced activation of Akt and MAPK signaling in TPC1 and MCF7 cells.
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Affiliation(s)
- John P Alao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden.
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126
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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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127
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How chemistry supports cell biology: the chemical toolbox at your service. Trends Cell Biol 2014; 24:751-60. [PMID: 25108565 DOI: 10.1016/j.tcb.2014.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/10/2014] [Accepted: 07/10/2014] [Indexed: 01/07/2023]
Abstract
Chemical biology is a young and rapidly developing scientific field. In this field, chemistry is inspired by biology to create various tools to monitor and modulate biochemical and cell biological processes. Chemical contributions such as small-molecule inhibitors and activity-based probes (ABPs) can provide new and unique insights into previously unexplored cellular processes. This review provides an overview of recent breakthroughs in chemical biology that are likely to have a significant impact on cell biology. We also discuss the application of several chemical tools in cell biology research.
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128
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Liu P, Calderon A, Konstantinidis G, Hou J, Voss S, Chen X, Li F, Banerjee S, Hoffmann JE, Theiss C, Dehmelt L, Wu YW. A Bioorthogonal Small-Molecule-Switch System for Controlling Protein Function in Live Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403463] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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129
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Liu P, Calderon A, Konstantinidis G, Hou J, Voss S, Chen X, Li F, Banerjee S, Hoffmann JE, Theiss C, Dehmelt L, Wu YW. A bioorthogonal small-molecule-switch system for controlling protein function in live cells. Angew Chem Int Ed Engl 2014; 53:10049-55. [PMID: 25065762 DOI: 10.1002/anie.201403463] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/23/2014] [Indexed: 12/13/2022]
Abstract
Chemically induced dimerization (CID) has proven to be a powerful tool for modulating protein interactions. However, the traditional dimerizer rapamycin has limitations in certain in vivo applications because of its slow reversibility and its affinity for endogenous proteins. Described herein is a bioorthogonal system for rapidly reversible CID. A novel dimerizer with synthetic ligand of FKBP' (SLF') linked to trimethoprim (TMP). The SLF' moiety binds to the F36V mutant of FK506-binding protein (FKBP) and the TMP moiety binds to E. coli dihydrofolate reductase (eDHFR). SLF'-TMP-induced heterodimerization of FKBP(F36V) and eDHFR with a dissociation constant of 0.12 μM. Addition of TMP alone was sufficient to rapidly disrupt this heterodimerization. Two examples are presented to demonstrate that this system is an invaluable tool, which can be widely used to rapidly and reversibly control protein function in vivo.
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Affiliation(s)
- Peng Liu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund (Germany) http://www.cgc.mpg.de/index.php/research-groups/rg-dr-yaowen-wu/research; Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund (Germany)
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130
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Onuma H, Komatsu T, Arita M, Hanaoka K, Ueno T, Terai T, Nagano T, Inoue T. Rapidly rendering cells phagocytic through a cell surface display technique and concurrent Rac activation. Sci Signal 2014; 7:rs4. [PMID: 25028719 DOI: 10.1126/scisignal.2005123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell surfaces represent a platform through which extracellular signals that determine diverse cellular processes, including migration, division, adhesion, and phagocytosis, are transduced. Techniques to rapidly reconfigure the surface properties of living cells should thus offer the ability to harness these cellular functions. Although the molecular mechanism of phagocytosis is well characterized, the minimal molecular players that are sufficient to activate this elaborate process remain elusive. We developed and implemented a technique to present a molecule of interest at the cell surface in an inducible manner on a time scale of minutes. We simultaneously induced the cell surface display of the C2 domain of milk fat globule epidermal growth factor factor 8 (MFG-E8) and activated the intracellular small guanosine triphosphatase Rac, which stimulates actin polymerization at the cell periphery. The C2 domain binds to phosphatidylserine, a lipid exposed on the surface of apoptotic cells. By integrating the stimulation of these two processes, we converted HeLa cells into a phagocytic cell line that bound to and engulfed apoptotic human Jurkat cells. Inducing either the cell surface display of the C2 domain or activating Rac alone was not sufficient to stimulate phagocytosis, which suggests that attachment to the target cell and actin reorganization together constitute the minimal molecular events that are needed to induce phagocytosis. This cell surface display technique might be useful as part of a targeted, cell-based therapy in which unwanted cells with characteristic surface molecules could be rapidly consumed by engineered cells.
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Affiliation(s)
- Hiroki Onuma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan. Precursory Research for Embryonic Science and Technology Investigator, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.
| | - Makoto Arita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tetsuo Nagano
- Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takanari Inoue
- Precursory Research for Embryonic Science and Technology Investigator, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan. Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 North Wolfe Street, Baltimore, MD 21205, USA. Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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131
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Rutkowska A, Plass T, Hoffmann JE, Yushchenko DA, Feng S, Schultz C. T-CrAsH: A Heterologous Chemical Crosslinker. Chembiochem 2014; 15:1765-8. [DOI: 10.1002/cbic.201402189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 01/12/2023]
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132
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Ballister ER, Riegman M, Lampson MA. Recruitment of Mad1 to metaphase kinetochores is sufficient to reactivate the mitotic checkpoint. ACTA ACUST UNITED AC 2014; 204:901-8. [PMID: 24637323 PMCID: PMC3998811 DOI: 10.1083/jcb.201311113] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Mad1 recruitment to metaphase kinetochores reactivates the mitotic checkpoint, which requires the C terminus of Mad1 in addition to its Mad2-binding domain. The mitotic checkpoint monitors kinetochore–microtubule attachment and prevents anaphase until all kinetochores are stably attached. Checkpoint regulation hinges on the dynamic localization of checkpoint proteins to kinetochores. Unattached, checkpoint-active kinetochores accumulate multiple checkpoint proteins, which are depleted from kinetochores upon stable attachment, allowing checkpoint silencing. Because multiple proteins are recruited simultaneously to unattached kinetochores, it is not known what changes at kinetochores are essential for anaphase promoting complex/cyclosome (APC/C) inhibition. Using chemically induced dimerization to manipulate protein localization with temporal control, we show that recruiting the checkpoint protein Mad1 to metaphase kinetochores is sufficient to reactivate the checkpoint without a concomitant increase in kinetochore levels of Mps1 or BubR1. Furthermore, Mad2 binding is necessary but not sufficient for Mad1 to activate the checkpoint; a conserved C-terminal motif is also required. The results of our checkpoint reactivation assay suggest that Mad1, in addition to converting Mad2 to its active conformation, scaffolds formation of a higher-order mitotic checkpoint complex at kinetochores.
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Affiliation(s)
- Edward R Ballister
- Department of Biology and 2 Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104
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133
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Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angew Chem Int Ed Engl 2014; 53:6720-3. [PMID: 24841150 DOI: 10.1002/anie.201402294] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 01/11/2023]
Abstract
Chemical dimerizers are powerful tools for non-invasive manipulation of enzyme activities in intact cells. Here we introduce the first rapidly reversible small-molecule-based dimerization system and demonstrate a sufficiently fast switch-off to determine kinetics of lipid metabolizing enzymes in living cells. We applied this new method to induce and stop phosphatidylinositol 3-kinase (PI3K) activity, allowing us to quantitatively measure the turnover of phosphatidylinositol 3,4,5-trisphosphate (PIP3) and its downstream effectors by confocal fluorescence microscopy as well as standard biochemical methods.
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Affiliation(s)
- Suihan Feng
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
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134
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Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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135
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Reversi A, Loeser E, Subramanian D, Schultz C, De Renzis S. Plasma membrane phosphoinositide balance regulates cell shape during Drosophila embryo morphogenesis. ACTA ACUST UNITED AC 2014; 205:395-408. [PMID: 24798734 PMCID: PMC4018783 DOI: 10.1083/jcb.201309079] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ratio of different phosphoinositide species coordinates actomyosin contractility and plasma membrane expansion during tissue morphogenesis, thus ensuring proper cell shape. Remodeling of cell shape during morphogenesis is driven by the coordinated expansion and contraction of specific plasma membrane domains. Loss of this coordination results in abnormal cell shape and embryonic lethality. Here, we show that plasma membrane lipid composition plays a key role in coordinating plasma membrane contraction during expansion. We found that an increase in PI(4,5)P2 levels caused premature actomyosin contraction, resulting in the formation of shortened cells. Conversely, acute depletion of PI(4,5)P2 blocked plasma membrane expansion and led to premature actomyosin disassembly. PI(4,5)P2-mediated contractility is counteracted by PI(3,4,5)P3 and the zygotic gene bottleneck, which acts by limiting myosin recruitment during plasma membrane expansion. Collectively, these data support a model in which the ratio of PI(4,5)P2/PI(3,4,5)P3 coordinates actomyosin contractility and plasma membrane expansion during tissue morphogenesis, thus ensuring proper cell shape.
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Affiliation(s)
- Alessandra Reversi
- European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany
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136
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Chang CL, Hsieh TS, Yang TT, Rothberg KG, Azizoglu DB, Volk E, Liao JC, Liou J. Feedback regulation of receptor-induced Ca2+ signaling mediated by E-Syt1 and Nir2 at endoplasmic reticulum-plasma membrane junctions. Cell Rep 2013; 5:813-25. [PMID: 24183667 DOI: 10.1016/j.celrep.2013.09.038] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/06/2013] [Accepted: 09/25/2013] [Indexed: 11/18/2022] Open
Abstract
Endoplasmic reticulum (ER)-plasma membrane (PM) junctions are highly conserved subcellular structures. Despite their importance in Ca(2+) signaling and lipid trafficking, the molecular mechanisms underlying the regulation and functions of ER-PM junctions remain unclear. By developing a genetically encoded marker that selectively monitors ER-PM junctions, we found that the connection between ER and PM was dynamically regulated by Ca(2+) signaling. Elevation of cytosolic Ca(2+) triggered translocation of E-Syt1 to ER-PM junctions to enhance ER-to-PM connection. This subsequently facilitated the recruitment of Nir2, a phosphatidylinositol transfer protein (PITP), to ER-PM junctions following receptor stimulation. Nir2 promoted the replenishment of PM phosphatidylinositol 4,5-bisphosphate (PIP2) after receptor-induced hydrolysis via its PITP activity. Disruption of the enhanced ER-to-PM connection resulted in reduced PM PIP2 replenishment and defective Ca(2+) signaling. Altogether, our results suggest a feedback mechanism that replenishes PM PIP2 during receptor-induced Ca(2+) signaling via the Ca(2+) effector E-Syt1 and the PITP Nir2 at ER-PM junctions.
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Affiliation(s)
- Chi-Lun Chang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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137
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Ishida M, Watanabe H, Takigawa K, Kurishita Y, Oki C, Nakamura A, Hamachi I, Tsukiji S. Synthetic Self-Localizing Ligands That Control the Spatial Location of Proteins in Living Cells. J Am Chem Soc 2013; 135:12684-9. [DOI: 10.1021/ja4046907] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Yasutaka Kurishita
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | | | | | - Itaru Hamachi
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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138
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Voss S, Wu YW. Tandem Orthogonal Chemically Induced Dimerization. Chembiochem 2013; 14:1525-7. [DOI: 10.1002/cbic.201300446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Indexed: 12/19/2022]
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139
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Lin YC, Phua SC, Lin B, Inoue T. Visualizing molecular diffusion through passive permeability barriers in cells: conventional and novel approaches. Curr Opin Chem Biol 2013; 17:663-71. [PMID: 23731778 DOI: 10.1016/j.cbpa.2013.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/23/2013] [Indexed: 12/19/2022]
Abstract
Diffusion barriers are universal solutions for cells to achieve distinct organizations, compositions, and activities within a limited space. The influence of diffusion barriers on the spatiotemporal dynamics of signaling molecules often determines cellular physiology and functions. Over the years, the passive permeability barriers in various subcellular locales have been characterized using elaborate analytical techniques. In this review, we will summarize the current state of knowledge on the various passive permeability barriers present in mammalian cells. We will conclude with a description of several conventional techniques and one new approach based on chemically inducible diffusion trap (CIDT) for probing permeable barriers.
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Affiliation(s)
- Yu-Chun Lin
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, United States.
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140
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Lin YC, Nihongaki Y, Liu TY, Razavi S, Sato M, Inoue T. Rapidly reversible manipulation of molecular activity with dual chemical dimerizers. Angew Chem Int Ed Engl 2013; 52:6450-4. [PMID: 23649661 DOI: 10.1002/anie.201301219] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Yu-Chun Lin
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA.
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141
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Lin YC, Nihongaki Y, Liu TY, Razavi S, Sato M, Inoue T. Rapidly Reversible Manipulation of Molecular Activity with Dual Chemical Dimerizers. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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142
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Abstract
One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.
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Affiliation(s)
- Takafumi Miyamoto
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
| | - Shiva Razavi
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205
| | - Robert DeRose
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
- PRESTO Investigator, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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143
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Dang DT, Nguyen HD, Merkx M, Brunsveld L. Supramolecular Control of Enzyme Activity through Cucurbit[8]uril-Mediated Dimerization. Angew Chem Int Ed Engl 2013; 52:2915-9. [DOI: 10.1002/anie.201208239] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/02/2013] [Indexed: 12/13/2022]
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144
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Dang DT, Nguyen HD, Merkx M, Brunsveld L. Supramolecular Control of Enzyme Activity through Cucurbit[8]uril-Mediated Dimerization. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208239] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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145
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DeRose R, Miyamoto T, Inoue T. Manipulating signaling at will: chemically-inducible dimerization (CID) techniques resolve problems in cell biology. Pflugers Arch 2013; 465:409-17. [PMID: 23299847 DOI: 10.1007/s00424-012-1208-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022]
Abstract
Chemically-inducible dimerization (CID) is a powerful tool that has proved useful in solving numerous problems in cell biology and related fields. In this review, we focus on case studies where CID was able to provide insight into otherwise refractory problems. Of particular interest are the cases of lipid second messengers and small GTPases, where the "signaling paradox" (how a small pool of signaling molecules can generate a large range of responses) can be at least partly explained through results gleaned from CID experiments. We also discuss several recent technical advances that provide improved specificity in CID action, novel CID substrates that allow simultaneous orthogonal manipulation of multiple systems in one cell, and several applications that move beyond the traditional CID technique of moving a protein of interest to a specific spatiotemporal location.
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Affiliation(s)
- Robert DeRose
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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146
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Abstract
Chemically induced dimerization is an important tool in chemical biology for the analysis of protein function in cells. Here we report the use of the natural product fusicoccin (FC) to induce dimerization of 14-3-3-fused target proteins with proteins tagged to the C terminus (CT) of the H(+)-ATPase PMA2. To prevent nonproductive or detrimental interactions of the 14-3-3 proteins and CT fusions with endogenous cell proteins, their interaction surface was engineered to facilitate FC-induced dimerization exclusively between the introduced protein constructs. Live-cell imaging documented the reversible FC-induced translocation of 14-3-3 and CT to different cell compartments depending on localization sequences fused to their dimerization partner protein. The functionality of this system was demonstrated by the FC-induced importation of the NF-κB-CT into the nucleus. In HeLa cells, FC-mediated dimerization of the NF-κB-CT with a constitutively nuclear-localized 14-3-3 protein led to an NF-κB-specific cellular response by inducing IL-8 secretion.
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