101
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Abstract
In a swift revolution, CRISPR/Cas9 has reshaped the means and ease of interrogating biological questions. Particularly, mutants that result in a nuclease-deactivated Cas9 (dCas9) provide scientists with tools to modulate transcription of genomic loci at will by targeting transcriptional effector domains. To interrogate the temporal order of events during transcriptional regulation, rapidly inducible CRISPR/dCas9 systems provide previously unmet molecular tools. In only a few years of time, numerous light and chemical-inducible switches have been applied to CRISPR/dCas9 to generate dCas9 switches. As these inducible switch systems are able to modulate dCas9 directly at the protein level, they rapidly affect dCas9 stability, activity, or target binding and subsequently rapidly influence downstream transcriptional events. Here we review the current state of such biotechnological CRISPR/dCas9 enhancements. Specifically we provide details on their flaws and strengths and on the differences in molecular design between the switch systems. With this we aim to provide a selection guide for researchers with keen interest in rapid temporal control over transcriptional modulation through the CRISPR/dCas9 system.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Edda G Schulz
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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102
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Guduru SKR, Arya P. Synthesis and biological evaluation of rapamycin-derived, next generation small molecules. MEDCHEMCOMM 2018; 9:27-43. [PMID: 30108899 PMCID: PMC6072512 DOI: 10.1039/c7md00474e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022]
Abstract
Over the years, rapamycin has attracted serious attention due to its remarkable biological properties and as a potent inhibitor of the mammalian target of rapamycin (mTOR) protein through its binding with FKBP-12. Several efficient strategies that utilize synthetic and biosynthetic approaches have been utilized to develop small molecule rapamycin analogs or for synthesizing hybrid compounds containing a partial rapamycin structure to improve pharmacokinetic properties. Herein, we report selected case studies related to the synthesis of rapamycin-derived compounds and hybrid molecules to explore their biological properties.
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Affiliation(s)
- Shiva Krishna Reddy Guduru
- Center for Drug Discovery , Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA . ; ; Tel: +1 713 798 8794
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA
| | - Prabhat Arya
- Chemistry and Chemical Biology , Dr. Reddy's Institute of Life Sciences (DRILS) , University of Hyderabad Campus , Hyderabad 500046 , India
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103
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Hill ZB, Martinko AJ, Nguyen DP, Wells JA. Human antibody-based chemically induced dimerizers for cell therapeutic applications. Nat Chem Biol 2017; 14:112-117. [PMID: 29200207 PMCID: PMC6352901 DOI: 10.1038/nchembio.2529] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/20/2017] [Indexed: 01/27/2023]
Abstract
Chemically induced dimerizers (CIDs) have emerged as one of the most powerful tools to artificially regulate signaling pathways in cells; however, currently available CID systems lack the properties desired for use in regulating cellular therapies. Here, we report the development of human antibody-based chemically induced dimerizers (AbCIDs) from known small-molecule-protein complexes by selecting for synthetic antibodies that recognize the chemical epitope created by the bound small molecule. We demonstrate this concept by generating three antibodies that are highly selective for the BCL-xL/ABT-737 complex over BCL-xL alone. We show the potential of AbCIDs to be applied to regulating human cell therapies by using them to induce CRISPRa-mediated gene expression and to regulate CAR T-cell activation. We believe that the AbCIDs generated in this study will find application in regulating cell therapies, and that the general method of AbCID development may lead to the creation of many new and orthogonal CIDs.
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Affiliation(s)
- Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alexander J Martinko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Duy P Nguyen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
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104
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Fan CH, Huang YS, Huang WE, Lee AA, Ho SY, Kao YL, Wang CL, Lian YL, Ueno T, Andrew Wang TS, Yeh CK, Lin YC. Manipulating Cellular Activities Using an Ultrasound-Chemical Hybrid Tool. ACS Synth Biol 2017; 6:2021-2027. [PMID: 28945972 DOI: 10.1021/acssynbio.7b00162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We developed an ultrasound-chemical hybrid tool to precisely manipulate cellular activities. A focused ultrasound coupled with gas-filled microbubbles was used to rapidly trigger the influx of membrane-impermeable chemical dimerizers into living cells to regulate protein dimerization and location without inducing noticeable toxicity. With this system, we demonstrated the successful modulation of phospholipid metabolism triggered by a short pulse of ultrasound exposure. Our technique offers a powerful and versatile tool for using ultrasound to spatiotemporally manipulate the cellular physiology in living cells.
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Affiliation(s)
| | | | | | | | - Sheng-Yang Ho
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | | | | | | | - Tasuku Ueno
- Graduate
School of Pharmaceutical Sciences, University of Tokyo, Tokyo, 113-8654, Japan
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105
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Zhao J, Stains CI. Identification of a Fragmented Small GTPase Capable of Conditional Effector Binding. RSC Adv 2017; 7:12265-12268. [PMID: 28966788 DOI: 10.1039/c6ra25575b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A fragmented small GTPase capable of conditional effector binding is described. The effector binding function of this split-GTPase can be modulated using a small molecule input, thus allowing for the potential design of cellular signaling pathways.
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Affiliation(s)
- Jia Zhao
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
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106
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Dai X, Chen X, Fang Q, Li J, Bai Z. Inducible CRISPR genome-editing tool: classifications and future trends. Crit Rev Biotechnol 2017; 38:573-586. [DOI: 10.1080/07388551.2017.1378999] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaofeng Dai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiuwu Fang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jia Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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107
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CRISPR-Cas9-based photoactivatable transcription systems to induce neuronal differentiation. Nat Methods 2017; 14:963-966. [PMID: 28892089 DOI: 10.1038/nmeth.4430] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/06/2017] [Indexed: 12/12/2022]
Abstract
Our improved CRISPR-Cas9-based photoactivatable transcription systems, CPTS2.0 and Split-CPTS2.0, enable high blue-light-inducible activation of endogenous target genes in various human cell lines. We achieved reversible activation of target genes with CPTS2.0 and induced neuronal differentiation in induced pluripotent stem cells (iPSCs) by upregulating NEUROD1 with Split-CPTS2.0.
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108
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Janssen AFJ, Tas RP, van Bergeijk P, Oost R, Hoogenraad CC, Kapitein LC. Myosin-V Induces Cargo Immobilization and Clustering at the Axon Initial Segment. Front Cell Neurosci 2017; 11:260. [PMID: 28894417 PMCID: PMC5581344 DOI: 10.3389/fncel.2017.00260] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 08/11/2017] [Indexed: 12/30/2022] Open
Abstract
The selective transport of different cargoes into axons and dendrites underlies the polarized organization of the neuron. Although it has become clear that the combined activity of different motors determines the destination and selectivity of transport, little is known about the mechanistic details of motor cooperation. For example, the exact role of myosin-V in opposing microtubule-based axon entries has remained unclear. Here we use two orthogonal chemically-induced heterodimerization systems to independently recruit different motors to cargoes. We find that recruiting myosin-V to kinesin-propelled cargoes at approximately equal numbers is sufficient to stall motility. Kinesin-driven cargoes entering the axon were arrested in the axon initial segment (AIS) upon myosin-V recruitment and accumulated in distinct actin-rich hotspots. Importantly, unlike proposed previously, myosin-V did not return these cargoes to the cell body, suggesting that additional mechanism are required to establish cargo retrieval from the AIS.
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Affiliation(s)
- Anne F J Janssen
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Roderick P Tas
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Petra van Bergeijk
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Rosalie Oost
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
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109
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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110
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Three-dimensional biomimetic vascular model reveals a RhoA, Rac1, and N-cadherin balance in mural cell-endothelial cell-regulated barrier function. Proc Natl Acad Sci U S A 2017; 114:8758-8763. [PMID: 28765370 DOI: 10.1073/pnas.1618333114] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The integrity of the endothelial barrier between circulating blood and tissue is important for blood vessel function and, ultimately, for organ homeostasis. Here, we developed a vessel-on-a-chip with perfused endothelialized channels lined with human bone marrow stromal cells, which adopt a mural cell-like phenotype that recapitulates barrier function of the vasculature. In this model, barrier function is compromised upon exposure to inflammatory factors such as LPS, thrombin, and TNFα, as has been observed in vivo. Interestingly, we observed a rapid physical withdrawal of mural cells from the endothelium that was accompanied by an inhibition of endogenous Rac1 activity and increase in RhoA activity in the mural cells themselves upon inflammation. Using a system to chemically induce activity in exogenously expressed Rac1 or RhoA within minutes of stimulation, we demonstrated RhoA activation induced loss of mural cell coverage on the endothelium and reduced endothelial barrier function, and this effect was abrogated when Rac1 was simultaneously activated. We further showed that N-cadherin expression in mural cells plays a key role in barrier function, as CRISPR-mediated knockout of N-cadherin in the mural cells led to loss of barrier function, and overexpression of N-cadherin in CHO cells promoted barrier function. In summary, this bicellular model demonstrates the continuous and rapid modulation of adhesive interactions between endothelial and mural cells and its impact on vascular barrier function and highlights an in vitro platform to study the biology of perivascular-endothelial interactions.
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111
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Zeng G, Li H, Wei Y, Xuan W, Zhang R, Breden LE, Wang W, Liang FS. Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity. ACS Synth Biol 2017; 6:921-927. [PMID: 28221778 DOI: 10.1021/acssynbio.6b00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A new synthetic biology engineering strategy integrating chemical reactivity sensing and small molecule induced protein dimerization has been developed to generate artificial Fe2+ signaling circuitry to control tailored cellular events in mammalian cells. The dual function probe ABA-FE18 (Fe2+-sensing and protein dimerization) derived from ABA was developed and used to control gene activation, signal transduction, and cytoskeletal remodeling in response to Fe2+. This technology was utilized to design signal circuitry incorporating "AND" and "OR" biologic gates that enables mammalian cells to translate different combinations of Fe2+ and H2O2 signals into predefined biological outputs.
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Affiliation(s)
- Guihua Zeng
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Huanqiu Li
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
- Department
of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Yongyi Wei
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Weimin Xuan
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Roushu Zhang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Larisa E. Breden
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Wei Wang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Fu-Sen Liang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
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112
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Dejonghe W, Russinova E. Plant Chemical Genetics: From Phenotype-Based Screens to Synthetic Biology. PLANT PHYSIOLOGY 2017; 174:5-20. [PMID: 28275150 PMCID: PMC5411137 DOI: 10.1104/pp.16.01805] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/20/2017] [Indexed: 05/21/2023]
Abstract
The treatment of a biological system with small molecules to specifically perturb cellular functions is commonly referred to as chemical biology. Small molecules are used commercially as drugs, herbicides, and fungicides in different systems, but in recent years they are increasingly exploited as tools for basic research. For instance, chemical genetics involves the discovery of small-molecule effectors of various cellular functions through screens of compound libraries. Whereas the drug discovery field has largely been driven by target-based screening approaches followed by drug optimization, chemical genetics in plant systems tends to be fueled by more general phenotype-based screens, opening the possibility to identify a wide range of small molecules that are not necessarily directly linked to the process of interest. Here, we provide an overview of the current progress in chemical genetics in plants, with a focus on the discoveries regarding small molecules identified in screens designed with a basic biology perspective. We reflect on the possibilities that lie ahead and discuss some of the potential pitfalls that might be encountered upon adopting a given chemical genetics approach.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
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113
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Bao Z, Jain S, Jaroenpuntaruk V, Zhao H. Orthogonal Genetic Regulation in Human Cells Using Chemically Induced CRISPR/Cas9 Activators. ACS Synth Biol 2017; 6:686-693. [PMID: 28054767 DOI: 10.1021/acssynbio.6b00313] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The concerted action of multiple genes in a time-dependent manner controls complex cellular phenotypes, yet the temporal regulation of gene expressions is restricted on a single-gene level, which limits our ability to control higher-order gene networks and understand the consequences of multiplex genetic perturbations. Here we developed a system for temporal regulation of multiple genes. This system combines the simplicity of CRISPR/Cas9 activators for orthogonal targeting of multiple genes and the orthogonality of chemically induced dimerizing (CID) proteins for temporal control of CRISPR/Cas9 activator function. In human cells, these transcription activators exerted simultaneous activation of multiple genes and orthogonal regulation of different genes in a ligand-dependent manner with minimal background. We envision that our system will enable the perturbation of higher-order gene networks with high temporal resolution and accelerate our understanding of gene-gene interactions in a complex biological setting.
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Affiliation(s)
- Zehua Bao
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Surbhi Jain
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Valerie Jaroenpuntaruk
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Departments of Chemical and Biomolecular Engineering, Chemistry, and Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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114
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Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods 2016; 13:1043-1049. [PMID: 27776111 DOI: 10.1038/nmeth.4042] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022]
Abstract
The ability to dynamically manipulate the transcriptome is important for studying how gene networks direct cellular functions and how network perturbations cause disease. Nuclease-dead CRISPR-dCas9 transcriptional regulators, while offering an approach for controlling individual gene expression, remain incapable of dynamically coordinating complex transcriptional events. Here, we describe a flexible dCas9-based platform for chemical-inducible complex gene regulation. From a screen of chemical- and light-inducible dimerization systems, we identified two potent chemical inducers that mediate efficient gene activation and repression in mammalian cells. We combined these inducers with orthogonal dCas9 regulators to independently control expression of different genes within the same cell. Using this platform, we further devised AND, OR, NAND, and NOR dCas9 logic operators and a diametric regulator that activates gene expression with one inducer and represses with another. This work provides a robust CRISPR-dCas9-based platform for enacting complex transcription programs that is suitable for large-scale transcriptome engineering.
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Affiliation(s)
- Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Cancer Biology Program, Stanford University, Stanford, California, USA
| | - Xin Xiong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
| | - Spencer Wong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Emeric J Charles
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA.,ChEM-H, Stanford University, Stanford, California, USA
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115
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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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116
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Abstract
The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.
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Affiliation(s)
- Eli Zamir
- a Department of Systemic Cell Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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117
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Niu J, Ben Johny M, Dick IE, Inoue T. Following Optogenetic Dimerizers and Quantitative Prospects. Biophys J 2016; 111:1132-1140. [PMID: 27542508 DOI: 10.1016/j.bpj.2016.07.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 01/06/2023] Open
Abstract
Optogenetics describes the use of genetically encoded photosensitive proteins to direct intended biological processes with light in recombinant and native systems. While most of these light-responsive proteins were originally discovered in photosynthetic organisms, the past few decades have been punctuated by experiments that not only commandeer but also engineer and enhance these natural tools to explore a wide variety of physiological questions. In addition, the ability to tune dynamic range and kinetic rates of optogenetic actuators is a challenging question that is heavily explored with computational methods devised to facilitate optimization of these systems. Here, we explain the basic mechanisms of a few popular photodimerizing optogenetic systems, discuss applications, compare optogenetic tools against more traditional chemical methods, and propose a simple quantitative understanding of how actuators exert their influence on targeted processes.
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Affiliation(s)
- Jacqueline Niu
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland.
| | - Manu Ben Johny
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Ivy E Dick
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Takanari Inoue
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; The Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, Maryland; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan.
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118
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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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119
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Wilmington SR, Matouschek A. An Inducible System for Rapid Degradation of Specific Cellular Proteins Using Proteasome Adaptors. PLoS One 2016; 11:e0152679. [PMID: 27043013 PMCID: PMC4820223 DOI: 10.1371/journal.pone.0152679] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/17/2016] [Indexed: 11/25/2022] Open
Abstract
A common way to study protein function is to deplete the protein of interest from cells and observe the response. Traditional methods involve disrupting gene expression but these techniques are only effective against newly synthesized proteins and leave previously existing and stable proteins untouched. Here, we introduce a technique that induces the rapid degradation of specific proteins in mammalian cells by shuttling the proteins to the proteasome for degradation in a ubiquitin-independent manner. We present two implementations of the system in human culture cells that can be used individually to control protein concentration. Our study presents a simple, robust, and flexible technology platform for manipulating intracellular protein levels.
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Affiliation(s)
- Shameika R. Wilmington
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Andreas Matouschek
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States of America
- * E-mail:
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120
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Hughes JH, Kumar S. Synthetic mechanobiology: engineering cellular force generation and signaling. Curr Opin Biotechnol 2016; 40:82-89. [PMID: 27023733 DOI: 10.1016/j.copbio.2016.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 10/24/2022]
Abstract
Mechanobiology seeks to understand and control mechanical and related biophysical communication between cells and their surroundings. While experimental efforts in this field have traditionally emphasized manipulation of the extracellular force environment, a new suite of approaches has recently emerged in which cell phenotype and signaling are controlled by directly engineering the cell itself. One route is to control cell behavior by modulating gene expression using conditional promoters. Alternatively, protein activity can be actuated directly using synthetic protein ligands, chemically induced protein dimerization, optogenetic strategies, or functionalized magnetic nanoparticles. Proof-of-principle studies are already demonstrating the translational potential of these approaches, and future technological development will permit increasingly precise control over cell mechanobiology and improve our understanding of the underlying signaling events.
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Affiliation(s)
- Jasmine Hannah Hughes
- Department of Bioengineering, University of California, Berkeley, United States; UC Berkeley - UCSF Graduate Program in Bioengineering, United States
| | - Sanjay Kumar
- Department of Bioengineering, University of California, Berkeley, United States.
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121
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Kim AK, DeRose R, Ueno T, Lin B, Komatsu T, Nakamura H, Inoue T. Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology. Sci Signal 2016; 9:re1. [DOI: 10.1126/scisignal.aac4779] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Allen K. Kim
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert DeRose
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Benjamin Lin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
| | - 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, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Nakamura
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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122
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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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123
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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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124
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van Bergeijk P, Hoogenraad CC, Kapitein LC. Right Time, Right Place: Probing the Functions of Organelle Positioning. Trends Cell Biol 2015; 26:121-134. [PMID: 26541125 DOI: 10.1016/j.tcb.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
The proper spatial arrangement of organelles underlies many cellular processes including signaling, polarization, and growth. Despite the importance of local positioning, the precise connection between subcellular localization and organelle function is often not fully understood. To address this, recent studies have developed and employed different strategies to directly manipulate organelle distributions, such as the use of (light-sensitive) heterodimerization to control the interaction between selected organelles and specific motor proteins, adaptor molecules, or anchoring factors. We review here the importance of subcellular localization as well as tools to control local organelle positioning. Because these approaches allow spatiotemporal control of organelle distribution, they will be invaluable tools to unravel local functioning and the mechanisms that control positioning.
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Affiliation(s)
- Petra van Bergeijk
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.
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125
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Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. Science 2015; 350:aab4077. [PMID: 26405231 PMCID: PMC4721629 DOI: 10.1126/science.aab4077] [Citation(s) in RCA: 510] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022]
Abstract
There is growing interest in using engineered cells as therapeutic agents. For example, synthetic chimeric antigen receptors (CARs) can redirect T cells to recognize and eliminate tumor cells expressing specific antigens. Despite promising clinical results, these engineered T cells can exhibit excessive activity that is difficult to control and can cause severe toxicity. We designed "ON-switch" CARs that enable small-molecule control over T cell therapeutic functions while still retaining antigen specificity. In these split receptors, antigen-binding and intracellular signaling components assemble only in the presence of a heterodimerizing small molecule. This titratable pharmacologic regulation could allow physicians to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity. This work illustrates the potential of combining cellular engineering with orthogonal chemical tools to yield safer therapeutic cells that tightly integrate cell-autonomous recognition and user control.
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Affiliation(s)
- Chia-Yung Wu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Kole T Roybal
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Elias M Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - James Onuffer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA.
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA. Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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126
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Zeng G, Zhang R, Xuan W, Wang W, Liang FS. Constructing de novo H2O2 signaling via induced protein proximity. ACS Chem Biol 2015; 10:1404-10. [PMID: 25775006 PMCID: PMC4849873 DOI: 10.1021/acschembio.5b00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new chemical strategy has been developed to generate de novo signaling pathways that link a signaling molecule, H2O2, to different downstream cellular events in mammalian cells. This approach combines the reactivity-based H2O2 sensing with the chemically induced protein proximity technology. By chemically modifying abscisic acid with an H2O2-sensitive boronate ester probe, novel H2O2 signaling pathways can be engineered to induce transcription, protein translocation and membrane ruffle formation upon exogenous or endogenous H2O2 stimulation. This strategy has also been successfully applied to gibberellic acid, which provides the potential to build signaling networks based on orthogonal cell stimuli.
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Affiliation(s)
- Guihua Zeng
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Roushu Zhang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Weimin Xuan
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Wei Wang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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127
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Chemical biology strategies for posttranslational control of protein function. ACTA ACUST UNITED AC 2015; 21:1238-52. [PMID: 25237866 DOI: 10.1016/j.chembiol.2014.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023]
Abstract
A common strategy to understand a biological system is to selectively perturb it and observe its response. Although technologies now exist to manipulate cellular systems at the genetic and transcript level, the direct manipulation of functions at the protein level can offer significant advantages in precision, speed, and reversibility. Combining the specificity of genetic manipulation and the spatiotemporal resolution of light- and small molecule-based approaches now allows exquisite control over biological systems to subtly perturb a system of interest in vitro and in vivo. Conditional perturbation mechanisms may be broadly characterized by change in intracellular localization, intramolecular activation, or degradation of a protein-of-interest. Here we review recent advances in technologies for conditional regulation of protein function and suggest further areas of potential development.
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128
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MacKay JL, Kumar S. Simultaneous and independent tuning of RhoA and Rac1 activity with orthogonally inducible promoters. Integr Biol (Camb) 2015; 6:885-94. [PMID: 25044255 DOI: 10.1039/c4ib00099d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The GTPases RhoA and Rac1 are key regulators of cell spreading, adhesion, and migration, and they exert distinct effects on the actin cytoskeleton. While RhoA classically stimulates stress fiber assembly and contraction, Rac1 promotes branched actin polymerization and membrane protrusion. These competing influences are reinforced by antagonistic crosstalk between RhoA and Rac1, which has complicated efforts to identify the specific mechanisms by which each GTPase regulates cell behavior. We therefore wondered whether RhoA and Rac1 are intrinsically coupled or whether they can be manipulated independently. To address this question, we placed constitutively active (CA) RhoA under a doxycycline-inducible promoter and CA Rac1 under an orthogonal cumate-inducible promoter, and we stably introduced both constructs into glioblastoma cells. We found that doxycycline addition increased RhoA activity without altering Rac1, and similarly cumate addition increased Rac1 activity without altering RhoA. Furthermore, co-expression of both mutants enabled high activation of RhoA and Rac1 simultaneously. When cells were cultured on collagen hydrogels, RhoA activation prevented cell spreading and motility, whereas Rac1 activation stimulated migration and dynamic cell protrusions. Interestingly, high activation of both GTPases induced a third phenotype, in which cells migrated at intermediate speeds similar to control cells but also aggregated into large, contractile clusters. In addition, we demonstrate dynamic and reversible switching between high RhoA and high Rac1 phenotypes. Overall, this approach represents a unique way to access different combinations of RhoA and Rac1 activity levels in a single cell and may serve as a valuable tool for multiplexed dissection and control of mechanobiological signals.
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Affiliation(s)
- Joanna L MacKay
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, California 94720, USA
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129
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Wright CW, Guo ZF, Liang FS. Light control of cellular processes by using photocaged abscisic acid. Chembiochem 2015; 16:254-61. [PMID: 25530501 PMCID: PMC4849874 DOI: 10.1002/cbic.201402576] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Indexed: 11/08/2022]
Abstract
Abscisic acid (ABA) was chemically modified with a photocaging group to promote photo-induced protein dimerization. This photocontrolled chemically induced dimerization (CID) method based on caged ABA enables dose-dependent light regulation of cellular processes, including transcription, protein translocation, signal transduction, and cytoskeletal remodeling, without the need to perform extensive protein engineering. Caged ABA can be easily modified to respond to different wavelengths of light. Consequently, this strategy should be applicable to the design of light-regulated protein dimerization systems and potentially be used orthogonally with other light-controlled CID systems.
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Affiliation(s)
- Catherine W Wright
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131 (USA)
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130
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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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131
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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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132
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van Bergeijk P, Adrian M, Hoogenraad CC, Kapitein LC. Optogenetic control of organelle transport and positioning. Nature 2015; 518:111-114. [PMID: 25561173 DOI: 10.1038/nature14128] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 12/01/2014] [Indexed: 01/20/2023]
Abstract
Proper positioning of organelles by cytoskeleton-based motor proteins underlies cellular events such as signalling, polarization and growth. For many organelles, however, the precise connection between position and function has remained unclear, because strategies to control intracellular organelle positioning with spatiotemporal precision are lacking. Here we establish optical control of intracellular transport by using light-sensitive heterodimerization to recruit specific cytoskeletal motor proteins (kinesin, dynein or myosin) to selected cargoes. We demonstrate that the motility of peroxisomes, recycling endosomes and mitochondria can be locally and repeatedly induced or stopped, allowing rapid organelle repositioning. We applied this approach in primary rat hippocampal neurons to test how local positioning of recycling endosomes contributes to axon outgrowth and found that dynein-driven removal of endosomes from axonal growth cones reversibly suppressed axon growth, whereas kinesin-driven endosome enrichment enhanced growth. Our strategy for optogenetic control of organelle positioning will be widely applicable to explore site-specific organelle functions in different model systems.
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Affiliation(s)
- Petra van Bergeijk
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Max Adrian
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
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133
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ogunleye LO, Ghosh I. Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 2014; 136:17078-86. [PMID: 25409264 DOI: 10.1021/ja5080745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
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Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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134
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Adjobo-Hermans MJW. Fast reversibility of dimeriser system enables quantification of signal molecule turnover. Chembiochem 2014; 15:2037-9. [PMID: 25145328 DOI: 10.1002/cbic.201402294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/10/2022]
Abstract
The design of a brake: Chemical induced dimerisation systems have revolutionised signal transduction research by allowing fast activation of specific proteins. A recent report describes the design of tools that enable the rapid switching off of the induced signal, thereby enabling quantification of signal molecule turnover.
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Affiliation(s)
- Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen (The Netherlands).
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135
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Razavi S, Su S, Inoue T. Cellular signaling circuits interfaced with synthetic, post-translational, negating Boolean logic devices. ACS Synth Biol 2014; 3:676-85. [PMID: 25000210 PMCID: PMC4169742 DOI: 10.1021/sb500222z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 12/11/2022]
Abstract
A negating functionality is fundamental to information processing of logic circuits within cells and computers. Aiming to adapt unutilized electronic concepts to the interrogation of signaling circuits in cells, we first took a bottom-up strategy whereby we created protein-based devices that perform negating Boolean logic operations such as NOT, NOR, NAND, and N-IMPLY. These devices function in living cells within a minute by precisely commanding the localization of an activator molecule among three subcellular spaces. We networked these synthetic gates to an endogenous signaling circuit and devised a physiological output. In search of logic functions in signal transduction, we next took a top-down approach and computationally screened 108 signaling pathways to identify commonalities and differences between these biological pathways and electronic circuits. This combination of synthetic and systems approaches will guide us in developing foundations for deconstruction of intricate cell signaling, as well as construction of biomolecular computers.
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Affiliation(s)
- Shiva Razavi
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Steven Su
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Takanari Inoue
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
- Japan
Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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136
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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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137
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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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138
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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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139
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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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140
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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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141
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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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142
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Inoue T. [Unraveling molecular mechanism of cell migration using novel perturbation tools]. YAKUGAKU ZASSHI 2014; 134:647-54. [PMID: 24790048 DOI: 10.1248/yakushi.14-00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Complexity in signaling networks is often derived from co-opting particular sets of molecules for multiple operations. Understanding how cells achieve such sophisticated processing using a finite set of molecules within a confined space - what we call the "signaling paradox"- is critical to cell biology and bioengineering as well as the emerging field of synthetic biology. We have recently developed a series of chemical-molecular tools that allow for inducible, quick-onset and specific perturbation of various signaling molecules. The present technique has been employed to unravel several important, previously unresolved questions regarding the regulatory mechanisms of potassium ion channels, the membrane targeting mechanisms of small GTPases and positive feedback machinery in neutrophil migration. Using this novel technique in conjunction with conventional fluorescence imaging and biochemical analysis, we are currently further dissecting intricate signaling networks in living cells. Ultimately, we will generate completely orthogonal machinery in cells to achieve existing, as well as novel, cellular functions. Our synthetic, multidisciplinary approach will elucidate the signaling paradox in cells created by nature.
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Affiliation(s)
- Takanari Inoue
- Johns Hopkins University, School of Medicine, Department of Cell Biology
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143
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Sample V, Mehta S, Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J Cell Sci 2014; 127:1151-60. [PMID: 24634506 PMCID: PMC3953811 DOI: 10.1242/jcs.099994] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/22/2013] [Indexed: 01/05/2023] Open
Abstract
In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction.
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Affiliation(s)
- Vedangi Sample
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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144
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Mancini RJ, Tom JK, Esser-Kahn AP. Covalently Coupled Immunostimulant Heterodimers. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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145
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Mancini RJ, Tom JK, Esser-Kahn AP. Covalently coupled immunostimulant heterodimers. Angew Chem Int Ed Engl 2013; 53:189-92. [PMID: 24259411 DOI: 10.1002/anie.201306551] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/16/2013] [Indexed: 02/02/2023]
Abstract
We report increased stimulation of dendritic cells via heterodimers of immunostimulants formed at a discrete molecular distance. Many vaccines present spatially organized agonists to immune cell receptors. These receptors cluster suggesting that signaling is increased by spatial organization and receptor proximity, but this has not been directly tested for multiple, unique receptors. In this study we probe the spatial aspect of immune cell activation using heterodimers of two covalently attached immunostimulants.
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Affiliation(s)
- Rock J Mancini
- Department of Chemistry, University of California, Irvine, 3038A Frederick Reines Hall, Irvine, CA 92697-2025 (USA)
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146
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Erhart D, Zimmermann M, Jacques O, Wittwer MB, Ernst B, Constable E, Zvelebil M, Beaufils F, Wymann MP. Chemical development of intracellular protein heterodimerizers. ACTA ACUST UNITED AC 2013; 20:549-57. [PMID: 23601644 DOI: 10.1016/j.chembiol.2013.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/13/2013] [Accepted: 03/20/2013] [Indexed: 12/19/2022]
Abstract
Cell activation initiated by receptor ligands or oncogenes triggers complex and convoluted intracellular signaling. Techniques initiating signals at defined starting points and cellular locations are attractive to elucidate the output of selected pathways. Here, we present the development and validation of a protein heterodimerization system based on small molecules cross-linking fusion proteins derived from HaloTags and SNAP-tags. Chemical dimerizers of HaloTag and SNAP-tag (HaXS) show excellent selectivity and have been optimized for intracellular reactivity. HaXS force protein-protein interactions and can translocate proteins to various cellular compartments. Due to the covalent nature of the HaloTag-HaXS-SNAP-tag complex, intracellular dimerization can be easily monitored. First applications include protein targeting to cytoskeleton, to the plasma membrane, to lysosomes, the initiation of the PI3K/mTOR pathway, and multiplexed protein complex formation in combination with the rapamycin dimerization system.
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Affiliation(s)
- Dominik Erhart
- Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
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147
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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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148
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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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149
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Hobert EM, Doerner AE, Walker AS, Schepartz A. Effective molarity redux: Proximity as a guiding force in chemistry and biology. Isr J Chem 2013; 53:567-576. [PMID: 25418998 PMCID: PMC4238305 DOI: 10.1002/ijch.201300063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The cell interior is a complex and demanding environment. An incredible variety of molecules jockey to identify the correct position-the specific interactions that promote biology that are hidden among countless unproductive options. Ensuring that the business of the cell is successful requires sophisticated mechanisms to impose temporal and spatial specificity-both on transient interactions and their eventual outcomes. Two strategies employed to regulate macromolecular interactions in a cellular context are co-localization and compartmentalization. Macromolecular interactions can be promoted and specified by localizing the partners within the same subcellular compartment, or by holding them in proximity through covalent or non-covalent interactions with proteins, lipids, or DNA- themes that are familiar to any biologist. The net result of these strategies is an increase in effective molarity: the local concentration of a reactive molecule near its reaction partners. We will focus on this general mechanism, employed by Nature and adapted in the lab, which allows delicate control in complex environments: the power of proximity to accelerate, guide, or otherwise influence the reactivity of signaling proteins and the information that they encode.
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150
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Moe-Behrens GH. The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 2013; 7:e201304003. [PMID: 24688733 PMCID: PMC3962179 DOI: 10.5936/csbj.201304003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 01/21/2023] Open
Abstract
Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
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