51
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Zhao W, Wang Y, Liang FS. Chemical and Light Inducible Epigenome Editing. Int J Mol Sci 2020; 21:ijms21030998. [PMID: 32028669 PMCID: PMC7037166 DOI: 10.3390/ijms21030998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.
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52
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Parag-Sharma K, O’Banion CP, Henry EC, Musicant AM, Cleveland JL, Lawrence DS, Amelio AL. Engineered BRET-Based Biologic Light Sources Enable Spatiotemporal Control over Diverse Optogenetic Systems. ACS Synth Biol 2020; 9:1-9. [PMID: 31834783 PMCID: PMC7875091 DOI: 10.1021/acssynbio.9b00277] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-inducible optogenetic systems offer precise spatiotemporal control over a myriad of biologic processes. Unfortunately, current systems are inherently limited by their dependence on external light sources for their activation. Further, the utility of laser/LED-based illumination strategies are often constrained by the need for invasive surgical procedures to deliver such devices and local heat production, photobleaching and phototoxicity that compromises cell and tissue viability. To overcome these limitations, we developed a novel BRET-activated optogenetics (BEACON) system that employs biologic light to control optogenetic tools. BEACON is driven by self-illuminating bioluminescent-fluorescent proteins that generate "spectrally tuned" biologic light via bioluminescence resonance energy transfer (BRET). Notably, BEACON robustly activates a variety of commonly used optogenetic systems in a spatially restricted fashion, and at physiologically relevant time scales, to levels that are achieved by conventional laser/LED light sources.
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Affiliation(s)
- Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology and Physiology, Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Colin P. O’Banion
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, United States
| | - Erin C. Henry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Adele M. Musicant
- Graduate Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John L. Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - David S. Lawrence
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Molecular Therapeutics Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Antonio L. Amelio
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Cancer Cell Biology Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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53
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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54
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Wang Y, Barnett SFH, Le S, Guo Z, Zhong X, Kanchanawong P, Yan J. Label-free Single-Molecule Quantification of Rapamycin-induced FKBP-FRB Dimerization for Direct Control of Cellular Mechanotransduction. NANO LETTERS 2019; 19:7514-7525. [PMID: 31466449 DOI: 10.1021/acs.nanolett.9b03364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemically induced dimerization (CID) has been applied to study numerous biological processes and has important pharmacological applications. However, the complex multistep interactions under various physical constraints involved in CID impose a great challenge for the quantification of the interactions. Furthermore, the mechanical stability of the ternary complexes has not been characterized; hence, their potential application in mechanotransduction studies remains unclear. Here, we report a single-molecule detector that can accurately quantify almost all key interactions involved in CID and the mechanical stability of the ternary complex, in a label-free manner. Its application is demonstrated using rapamycin-induced heterodimerization of FRB and FKBP as an example. We revealed the sufficient mechanical stability of the FKBP/rapamycin/FRB ternary complex and demonstrated its utility in the precise switching of talin-mediated force transmission in integrin-based cell adhesions.
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Affiliation(s)
- Yinan Wang
- Department of Physics , National University of Singapore , Singapore 117546
| | - Samuel F H Barnett
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Shimin Le
- Department of Physics , National University of Singapore , Singapore 117546
| | - Zhenhuan Guo
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Xueying Zhong
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Pakorn Kanchanawong
- Mechanobiology Institute , National University of Singapore , Singapore 117411
- Department of Biomedical Engineering , National University of Singapore , Singapore 117583
| | - Jie Yan
- Department of Physics , National University of Singapore , Singapore 117546
- Mechanobiology Institute , National University of Singapore , Singapore 117411
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55
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Kostrz D, Wayment-Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR, Gosse C. A modular DNA scaffold to study protein-protein interactions at single-molecule resolution. NATURE NANOTECHNOLOGY 2019; 14:988-993. [PMID: 31548690 DOI: 10.1038/s41565-019-0542-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The residence time of a drug on its target has been suggested as a more pertinent metric of therapeutic efficacy than the traditionally used affinity constant. Here, we introduce junctured-DNA tweezers as a generic platform that enables real-time observation, at the single-molecule level, of biomolecular interactions. This tool corresponds to a double-strand DNA scaffold that can be nanomanipulated and on which proteins of interest can be engrafted thanks to widely used genetic tagging strategies. Thus, junctured-DNA tweezers allow a straightforward and robust access to single-molecule force spectroscopy in drug discovery, and more generally in biophysics. Proof-of-principle experiments are provided for the rapamycin-mediated association between FKBP12 and FRB, a system relevant in both medicine and chemical biology. Individual interactions were monitored under a range of applied forces and temperatures, yielding after analysis the characteristic features of the energy profile along the dissociation landscape.
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Affiliation(s)
- Dorota Kostrz
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France
| | | | - Jing L Wang
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France
| | - Maryne Follenfant
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France.
- Programme Equipe Labellisée, Ligue Nationale Contre le Cancer, Paris, France.
| | - Charlie Gosse
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France.
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56
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Klewer L, Wu Y. Light-Induced Dimerization Approaches to Control Cellular Processes. Chemistry 2019; 25:12452-12463. [PMID: 31304989 PMCID: PMC6790656 DOI: 10.1002/chem.201900562] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/13/2019] [Indexed: 12/20/2022]
Abstract
Light-inducible approaches provide a means to control biological systems with spatial and temporal resolution that is unmatched by traditional genetic perturbations. Recent developments of optogenetic and chemo-optogenetic systems for induced proximity in cells facilitate rapid and reversible manipulation of highly dynamic cellular processes and have become valuable tools in diverse biological applications. New expansions of the toolbox facilitate control of signal transduction, genome editing, "painting" patterns of active molecules onto cellular membranes, and light-induced cell cycle control. A combination of light- and chemically induced dimerization approaches have also seen interesting progress. Herein, an overview of optogenetic systems and emerging chemo-optogenetic systems is provided, and recent applications in tackling complex biological problems are discussed.
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Affiliation(s)
- Laura Klewer
- Max Planck Institute of Molecular PhysiologyOtto-Hahn-Str. 1144227DortmundGermany
| | - Yao‐Wen Wu
- Department of ChemistryUmeå Centre for Microbial ResearchUmeå University90187UmeåSweden
- Max Planck Institute of Molecular PhysiologyOtto-Hahn-Str. 1144227DortmundGermany
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57
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Chojnowski A, Werner H, Cook M, Sobota RM, Burke B, Stewart CL. Protein-Protein Interaction Mapping by 2C-BioID. ACTA ACUST UNITED AC 2019; 84:e96. [PMID: 31483108 DOI: 10.1002/cpcb.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions (PPIs) add an essential layer of complexity to the information encoded by the genome. Modulation of such interactions is a key feature of most, if not all, cellular activities and allows cells to respond rapidly to both internal and external signals and stimuli. In this respect, the development of the BioID assay to interrogate PPIs within a cellular context represents an important adjunct to the range of tools currently at researchers' disposal. To address some of its current limitations, we devised 2C-BioID, in which biotin ligase and the protein of interest remain as separate entities until induced to associate. This is accomplished using the well-established FKBP-FRB dimerization system (based on the rapamycin-induced binding of FK506 binding protein and FKBP12-rapamycin binding domain.). The design of 2C-BioID ensures that biotin ligase association with the protein of interest occurs only after addition of the rapamycin analogue AP21967. As such, 2C-BioID alleviates potential targeting issues and improves the ability to exclude false positives, thereby refining the specificity of BioID-generated interactomes. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Alexandre Chojnowski
- Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hendrikje Werner
- Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Matthew Cook
- Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular & Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brian Burke
- Nuclear Dynamics and Architecture, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Colin L Stewart
- Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technical University, Singapore, Singapore
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58
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Courtney TM, Horst TJ, Hankinson CP, Deiters A. Synthesis and application of light-switchable arylazopyrazole rapamycin analogs. Org Biomol Chem 2019; 17:8348-8353. [PMID: 31469140 DOI: 10.1039/c9ob01719d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Rapamycin-induced dimerization of FKBP and FRB has been utilized as a tool for co-localizing two proteins of interest in numerous applications. Due to the tight binding interaction of rapamycin with FKBP and FRB, the ternary complex formation is essentially irreversible. Since biological processes occur in a highly dynamic fashion with cycles of protein association and dissociation to generate a cellular response, it is useful to have chemical tools that function in a similar manner. We have developed arylazopyrazole-modified rapamycin analogs which undergo a configurational change upon light exposure and we observed enhanced ternary complex formation for the cis-isomer over the trans-isomer for one of the analogs.
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Affiliation(s)
- Taylor M Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Trevor J Horst
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Chasity P Hankinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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59
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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60
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Cunningham-Bryant D, Dieter EM, Foight GW, Rose JC, Loutey DE, Maly DJ. A Chemically Disrupted Proximity System for Controlling Dynamic Cellular Processes. J Am Chem Soc 2019; 141:3352-3355. [PMID: 30735038 DOI: 10.1021/jacs.8b12382] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chemical methods that allow the spatial proximity of proteins to be temporally modulated are powerful tools for studying biology and engineering synthetic cellular behaviors. Here, we describe a new chemically controlled method for rapidly disrupting the interaction between two basally colocalized protein binding partners. Our chemically disrupted proximity (CDP) system is based on the interaction between the hepatitis C virus protease (HCVp) NS3a and a genetically encoded peptide inhibitor. Using clinically approved antiviral inhibitors as chemical disrupters of the NS3a/peptide interaction, we demonstrate that our CDP system can be used to confer temporal control over diverse intracellular processes. This NS3a-based CDP system represents a new modality for engineering chemical control over intracellular protein function that is complementary to currently available techniques.
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61
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Vasjari L, Bresan S, Biskup C, Pai G, Rubio I. Ras signals principally via Erk in G1 but cooperates with PI3K/Akt for Cyclin D induction and S-phase entry. Cell Cycle 2019; 18:204-225. [PMID: 30560710 DOI: 10.1080/15384101.2018.1560205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous studies exploring oncogenic Ras or manipulating physiological Ras signalling have established an irrefutable role for Ras as driver of cell cycle progression. Despite this wealth of information the precise signalling timeline and effectors engaged by Ras, particularly during G1, remain obscure as approaches for Ras inhibition are slow-acting and ill-suited for charting discrete Ras signalling episodes along the cell cycle. We have developed an approach based on the inducible recruitment of a Ras-GAP that enforces endogenous Ras inhibition within minutes. Applying this strategy to inhibit Ras stepwise in synchronous cell populations revealed that Ras signaling was required well into G1 for Cyclin D induction, pocket protein phosphorylation and S-phase entry, irrespective of whether cells emerged from quiescence or G2/M. Unexpectedly, Erk, and not PI3K/Akt or Ral was activated by Ras at mid-G1, albeit PI3K/Akt signalling was a necessary companion of Ras/Erk for sustaining cyclin-D levels and G1/S transition. Our findings chart mitogenic signaling by endogenous Ras during G1 and identify limited effector engagement restricted to Raf/MEK/Erk as a cogent distinction from oncogenic Ras signalling.
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Affiliation(s)
- Ledia Vasjari
- a Institute of Molecular Cell Biology, Center for Molecular Biomedicine , Jena University Hospital , Jena , Germany
| | - Stephanie Bresan
- a Institute of Molecular Cell Biology, Center for Molecular Biomedicine , Jena University Hospital , Jena , Germany
| | - Christoph Biskup
- b Biomolecular Photonics Group , Jena University Hospital , Jena , Germany
| | - Govind Pai
- a Institute of Molecular Cell Biology, Center for Molecular Biomedicine , Jena University Hospital , Jena , Germany
| | - Ignacio Rubio
- a Institute of Molecular Cell Biology, Center for Molecular Biomedicine , Jena University Hospital , Jena , Germany
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62
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Mediated nuclear import and export of TAZ and the underlying molecular requirements. Nat Commun 2018; 9:4966. [PMID: 30470756 PMCID: PMC6251892 DOI: 10.1038/s41467-018-07450-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 10/26/2018] [Indexed: 12/14/2022] Open
Abstract
Nucleocytoplasmic distribution of Yap/TAZ is regulated by the Hippo pathway and the cytoskeleton. While interactions with cytosolic and nuclear “retention factors” (14–3–3 and TEAD) are known to control their localization, fundamental aspects of Yap/TAZ shuttling remain undefined. It is unclear if translocation occurs only by passive diffusion or via mediated transport, and neither the potential nuclear localization and efflux signals (NLS, NES) nor their putative regulation have been identified. Here we show that TAZ cycling is a mediated process and identify the underlying NLS and NES. The C-terminal NLS, representing a new class of import motifs, is necessary and sufficient for efficient nuclear uptake via a RAN-independent mechanism. RhoA activity directly stimulates this import. The NES lies within the TEAD-binding domain and can be masked by TEAD, thereby preventing efflux. Thus, we describe a RhoA-regulated NLS, a TEAD-regulated NES and propose an improved model of nucleocytoplasmic TAZ shuttling beyond "retention". The transcriptional co-factors Yap and TAZ are regulated by Hippo signalling and mechanical forces via their nucleocytoplasmic shuttling. Here the authors identify a RhoA-regulated C-terminal nuclear localization signal and a TEAD-regulated N-terminal nuclear export signal of TAZ in an epithelial cell line.
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63
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Carro L. Protein-protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics. Beilstein J Org Chem 2018; 14:2881-2896. [PMID: 30546472 PMCID: PMC6278769 DOI: 10.3762/bjoc.14.267] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial infections; however, the growing antibiotic resistance of microorganisms is compromising the efficacy of the currently available pharmacotherapies. Even though antimicrobial resistance is not a new problem, antibiotic development has failed to match the growth of resistant pathogens and hence, it is highly critical to discover new anti-infective drugs with novel mechanisms of action which will help reducing the burden of multidrug-resistant microorganisms. Protein-protein interactions (PPIs) are involved in a myriad of vital cellular processes and have become an attractive target to treat diseases. Therefore, targeting PPI networks in bacteria may offer a new and unconventional point of intervention to develop novel anti-infective drugs which can combat the ever-increasing rate of multidrug-resistant bacteria. This review describes the progress achieved towards the discovery of molecules that disrupt PPI systems in bacteria for which inhibitors have been identified and whose targets could represent an alternative lead discovery strategy to obtain new anti-infective molecules.
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Affiliation(s)
- Laura Carro
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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64
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2C-BioID: An Advanced Two Component BioID System for Precision Mapping of Protein Interactomes. iScience 2018; 10:40-52. [PMID: 30500481 PMCID: PMC6263017 DOI: 10.1016/j.isci.2018.11.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/26/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
The modulation of protein-protein interactions (PPIs) is an essential regulatory activity defining diverse cell functions in development and disease. BioID is an unbiased proximity-dependent biotinylation method making use of a biotin-protein ligase fused to a protein of interest and has become an important tool for mapping of PPIs within cellular contexts. We devised an advanced method, 2C-BioID, in which the biotin-protein ligase is kept separate from the protein of interest, until the two are induced to associate by the addition of a dimerizing agent. As proof of principle, we compared the interactomes of lamina-associated polypeptide 2β (LAP2β) with those of lamins A and C, using 2C- and conventional BioID. 2C-BioID greatly enhanced data robustness by facilitating the in silico elimination of non-specific interactors as well as overcoming the problems associated with aberrant protein localization. 2C-BioID therefore significantly strengthens the specificity and reliability of BioID-based interactome analysis, by the more stringent exclusion of false-positives and more efficient intracellular targeting.
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65
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Jester BW, Tinberg CE, Rich MS, Baker D, Fields S. Engineered Biosensors from Dimeric Ligand-Binding Domains. ACS Synth Biol 2018; 7:2457-2467. [PMID: 30204430 DOI: 10.1021/acssynbio.8b00242] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biosensors are important components of many synthetic biology and metabolic engineering applications. Here, we report a second generation of Saccharomyces cerevisiae digoxigenin and progesterone biosensors based on destabilized dimeric ligand-binding domains that undergo ligand-induced stabilization. The biosensors, comprising one ligand-binding domain monomer fused to a DNA-binding domain and another fused to a transcriptional activation domain, activate reporter gene expression in response to steroid binding and receptor dimerization. The introduction of a destabilizing mutation to the dimer interface increased biosensor dynamic range by an order of magnitude. Computational redesign of the dimer interface and functional selections were used to create heterodimeric pairs with further improved dynamic range. A heterodimeric biosensor built from the digoxigenin and progesterone ligand-binding domains functioned as a synthetic "AND"-gate, with 20-fold stronger response to the two ligands in combination than to either one alone. We also identified mutations that increase the sensitivity or selectivity of the biosensors to chemically similar ligands. These dimerizing biosensors provide additional flexibility for the construction of logic gates and other applications.
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Affiliation(s)
- Benjamin W. Jester
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Christine E. Tinberg
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Matthew S. Rich
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Department of Medicine, University of Washington, Seattle, Washington 98195, United States
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66
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Aonbangkhen C, Zhang H, Wu DZ, Lampson MA, Chenoweth DM. Reversible Control of Protein Localization in Living Cells Using a Photocaged-Photocleavable Chemical Dimerizer. J Am Chem Soc 2018; 140:11926-11930. [PMID: 30196699 PMCID: PMC6499933 DOI: 10.1021/jacs.8b07753] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many dynamic biological processes are regulated by protein-protein interactions and protein localization. Experimental techniques to probe such processes with temporal and spatial precision include photoactivatable proteins and chemically induced dimerization (CID) of proteins. CID has been used to study several cellular events, especially cell signaling networks, which are often reversible. However, chemical dimerizers that can be both rapidly activated and deactivated with high spatiotemporal resolution are currently limited. Herein, we present a novel chemical inducer of protein dimerization that can be rapidly turned on and off using single pulses of light at two orthogonal wavelengths. We demonstrate the utility of this molecule by controlling peroxisome transport and mitotic checkpoint signaling in living cells. Our system highlights and enhances the spatiotemporal control offered by CID. This tool addresses biological questions on subcellular levels by controlling protein-protein interactions.
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67
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USP45 and Spindly are part of the same complex implicated in cell migration. Sci Rep 2018; 8:14375. [PMID: 30258100 PMCID: PMC6158257 DOI: 10.1038/s41598-018-32685-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Ubiquitylation is a protein modification implicated in several cellular processes. This process is reversible by the action of deubiquinating enzymes (DUBs). USP45 is a ubiquitin specific protease about which little is known, aside from roles in DNA damage repair and differentiation of the vertebrate retina. Here, by using mass spectrometry we have identified Spindly as a new target of USP45. Our data show that Spindly and USP45 are part of the same complex and that their interaction specifically depends on the catalytic activity of USP45. In addition, we describe the type of ubiquitin chains associated with the complex that can be cleaved by USP45, with a preferential activity on K48 ubiquitin chain type and potentially K6. Here, we also show that Spindly is mono-ubiquitylated and this can be specifically removed by USP45 in its active form but not by the catalytic inactive form. Lastly, we identified a new role for USP45 in cell migration, similar to that which was recently described for Spindly.
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68
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Chen X, Venkatachalapathy M, Dehmelt L, Wu YW. Multidirectional Activity Control of Cellular Processes by a Versatile Chemo-optogenetic Approach. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Emil-Figge-Straße 50 44227 Dortmund Germany
| | - Leif Dehmelt
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Emil-Figge-Straße 50 44227 Dortmund Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
- Department of Chemistry; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
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69
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Chen X, Venkatachalapathy M, Dehmelt L, Wu YW. Multidirectional Activity Control of Cellular Processes by a Versatile Chemo-optogenetic Approach. Angew Chem Int Ed Engl 2018; 57:11993-11997. [PMID: 30048030 PMCID: PMC6175152 DOI: 10.1002/anie.201806976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Indexed: 12/23/2022]
Abstract
The spatiotemporal dynamics of proteins or organelles plays a vital role in controlling diverse cellular processes. However, acute control of activity at distinct locations within a cell is challenging. A versatile multidirectional activity control (MAC) approach is presented, which employs a photoactivatable system that may be dimerized upon chemical inducement. The system comprises second‐generation SLF*‐TMP (S*T) and photocaged NvocTMP‐Cl dimerizers; where, SLF*‐TMP features a synthetic ligand of the FKBP(F36V) binding protein, Nvoc is a caging group, and TMP is the antibiotic trimethoprim. Two MAC strategies are demonstrated to spatiotemporally control cellular signaling and intracellular cargo transport. The novel platform enables tunable, reversible, and rapid control of activity at multiple compartments in living cells.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Muthukumaran Venkatachalapathy
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Emil-Figge-Straße 50, 44227, Dortmund, Germany
| | - Leif Dehmelt
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Emil-Figge-Straße 50, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Department of Chemistry, Umeå Centre for Microbial Research, Umeå University, 90187, Umeå, Sweden
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70
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Hung CW, Martínez-Márquez JY, Javed FT, Duncan MC. A simple and inexpensive quantitative technique for determining chemical sensitivity in Saccharomyces cerevisiae. Sci Rep 2018; 8:11919. [PMID: 30093662 PMCID: PMC6085351 DOI: 10.1038/s41598-018-30305-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/27/2018] [Indexed: 12/18/2022] Open
Abstract
Chemical sensitivity, growth inhibition in response to a chemical, is a powerful phenotype that can reveal insight into diverse cellular processes. Chemical sensitivity assays are used in nearly every model system, however the yeast Saccharomyces cerevisiae provides a particularly powerful platform for discovery and mechanistic insight from chemical sensitivity assays. Here we describe a simple and inexpensive approach to determine chemical sensitivity quantitatively in yeast in the form of half maximal inhibitory concentration (IC50) using common laboratory equipment. We demonstrate the utility of this method using chemicals commonly used to monitor changes in membrane traffic. When compared to traditional agar-based plating methods, this method is more sensitive and can detect defects not apparent using other protocols. Additionally, this method reduces the experimental protocol from five days to 18 hours for the toxic amino acid canavanine. Furthermore, this method provides reliable results using lower amounts of chemicals. Finally, this method is easily adapted to additional chemicals as demonstrated with an engineered system that activates the spindle assembly checkpoint in response to rapamycin with differing efficiencies. This approach provides researchers with a cost-effective method to perform chemical genetic profiling without specialized equipment.
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Affiliation(s)
- Chao-Wei Hung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
- Department of Medicine, University of California, San Diego, California, USA.
| | | | - Fatima T Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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71
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Zhao W, Nguyen H, Zeng G, Gao D, Yan H, Liang FS. A chemically induced proximity system engineered from the plant auxin signaling pathway. Chem Sci 2018; 9:5822-5827. [PMID: 30079194 PMCID: PMC6050582 DOI: 10.1039/c8sc02353k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/09/2018] [Indexed: 12/16/2022] Open
Abstract
Methods based on chemically induced proximity (CIP) serve as powerful tools to control cellular processes in a temporally specific manner. To expand the repertoire of CIP systems available for studies of cellular processes, we engineered the plant auxin signaling pathway to create a new indole-3-acetic acid (IAA) based CIP method. Auxin-induced protein degradation that occurs in the natural pathway was eliminated in the system. The new IAA based method is both readily inducible and reversible, and used to control the production of therapeutic proteins that induced the apoptosis of cancer cells. The approach is also orthogonal to existing CIP systems and used to construct a biological Boolean logic gate controlling gene expression system. We believe that the new CIP method will be applicable to the artificial control and dissection of complex cellular functions.
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Affiliation(s)
- Weiye Zhao
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Huong Nguyen
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Guihua Zeng
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Dan Gao
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Hao Yan
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
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72
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van Unen J, Botman D, Yin T, Wu YI, Hink MA, Gadella TWJ, Postma M, Goedhart J. The C-terminus of the oncoprotein TGAT is necessary for plasma membrane association and efficient RhoA-mediated signaling. BMC Cell Biol 2018; 19:6. [PMID: 29879899 PMCID: PMC5992656 DOI: 10.1186/s12860-018-0155-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/28/2018] [Indexed: 02/08/2023] Open
Abstract
Background Rho guanine exchange factors (RhoGEFs) control cellular processes such as migration, adhesion and proliferation. Alternative splicing of the RhoGEF Trio produces TGAT. The RhoGEF TGAT is an oncoprotein with constitutive RhoGEF activity. We investigated whether the subcellular location of TGAT is critical for its RhoGEF activity. Methods Since plasma membrane associated RhoGEFs are particularly effective at activating RhoA, plasma membrane localization of TGAT was examined. To this end, we developed a highly sensitive image analysis method to quantitatively measure plasma membrane association. The method requires a cytoplasmic marker and a plasma membrane marker, which are co-imaged with the tagged protein of interest. Linear unmixing is performed to determine the plasma membrane and cytoplasmic component in the fluorescence signal of protein of interest. Results The analysis revealed that wild-type TGAT is partially co-localized with the plasma membrane. Strikingly, cysteine TGAT-mutants lacking one or more putative palmitoylation sites in the C-tail, still showed membrane association. In contrast, a truncated variant, lacking the last 15 amino acids, TGATΔ15, lost membrane association. We show that membrane localization of TGAT was responsible for high RhoGEF activity by using a RhoA FRET-sensor and by determining F-actin levels. Mutants of TGAT that still maintained membrane association showed similar activity as wild-type TGAT. In contrast, the activity was abrogated for the cytoplasmic TGATΔ15 variant. Synthetic recruitment of TGATΔ15 to membranes confirmed that TGAT effectively activates RhoA at the plasma membrane. Conclusion Together, these results show that membrane association of TGAT is critical for its activity. Electronic supplementary material The online version of this article (10.1186/s12860-018-0155-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J van Unen
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands
| | - D Botman
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands
| | - T Yin
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06032-6406, USA
| | - Y I Wu
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06032-6406, USA
| | - M A Hink
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands
| | - T W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands
| | - M Postma
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands.
| | - J Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL, -1090, GE, Amsterdam, The Netherlands.
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73
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Chen X, Wu YW. Tunable and Photoswitchable Chemically Induced Dimerization for Chemo-optogenetic Control of Protein and Organelle Positioning. Angew Chem Int Ed Engl 2018; 57:6796-6799. [PMID: 29637703 PMCID: PMC6032859 DOI: 10.1002/anie.201800140] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/18/2018] [Indexed: 11/10/2022]
Abstract
The spatiotemporal dynamics of proteins and organelles play an important role in controlling diverse cellular processes. Optogenetic tools using photosensitive proteins and chemically induced dimerization (CID), which allow control of protein dimerization, have been used to elucidate the dynamics of biological systems and to dissect the complicated biological regulatory networks. However, the inherent limitations of current optogenetic and CID systems remain a significant challenge for the fine‐tuning of cellular activity at precise times and locations. Herein, we present a novel chemo‐optogenetic approach, photoswitchable chemically induced dimerization (psCID), for controlling cellular function by using blue light in a rapid and reversible manner. Moreover, psCID is tunable; that is, the dimerization and dedimerization degrees can be fine‐tuned by applying different doses of illumination. Using this approach, we control the localization of proteins and positioning of organelles in live cells with high spatial (μm) and temporal (ms) precision.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Department of Chemistry, Umeå University, 90187, Umeå, Sweden
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74
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Chen X, Wu YW. Tunable and Photoswitchable Chemically Induced Dimerization for Chemo-optogenetic Control of Protein and Organelle Positioning. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
- Department of Chemistry; Umeå University; 90187 Umeå Sweden
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Str. 11 44227 Dortmund Germany
- Department of Chemistry; Umeå University; 90187 Umeå Sweden
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75
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Hong SR, Wang CL, Huang YS, Chang YC, Chang YC, Pusapati GV, Lin CY, Hsu N, Cheng HC, Chiang YC, Huang WE, Shaner NC, Rohatgi R, Inoue T, Lin YC. Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling. Nat Commun 2018; 9:1732. [PMID: 29712905 PMCID: PMC5928066 DOI: 10.1038/s41467-018-03952-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 03/22/2018] [Indexed: 12/22/2022] Open
Abstract
Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells and are suggested to be involved in a wide range of cellular activities. However, the complexity and dynamic distribution of tubulin PTMs within cells have hindered the understanding of their physiological roles in specific subcellular compartments. Here, we develop a method to rapidly deplete tubulin glutamylation inside the primary cilia, a microtubule-based sensory organelle protruding on the cell surface, by targeting an engineered deglutamylase to the cilia in minutes. This rapid deglutamylation quickly leads to altered ciliary functions such as kinesin-2-mediated anterograde intraflagellar transport and Hedgehog signaling, along with no apparent crosstalk to other PTMs such as acetylation and detyrosination. Our study offers a feasible approach to spatiotemporally manipulate tubulin PTMs in living cells. Future expansion of the repertoire of actuators that regulate PTMs may facilitate a comprehensive understanding of how diverse tubulin PTMs encode ciliary as well as cellular functions. Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells, therefore assessing the physiological roles in specific subcellular compartments has been challenging. Here the authors develop a method to rapidly deplete tubulin glutamylation inside the primary cilia by targeting an engineered deglutamylase to the axoneme.
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Affiliation(s)
- Shi-Rong Hong
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Cuei-Ling Wang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yao-Shen Huang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chen Chang
- Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ya-Chu Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ganesh V Pusapati
- Departments of Medicine and Biochemistry, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Chun-Yu Lin
- Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ning Hsu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hsiao-Chi Cheng
- Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yueh-Chen Chiang
- Interdisciplinary Program of Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-En Huang
- Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Nathan C Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, 92121, CA, USA
| | - Rajat Rohatgi
- Departments of Medicine and Biochemistry, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, 21205, MD, USA.
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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76
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Zielich J, Mangal S, Zanin E, Lambie E. Establishment of a CRISPR/Cas9-based strategy for inducible protein dimerization. MICROPUBLICATION BIOLOGY 2018; 2018. [PMID: 32550367 PMCID: PMC7252319 DOI: 10.17912/w2208r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey Zielich
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Sriyash Mangal
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Esther Zanin
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Eric Lambie
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
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77
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Mangal S, Zielich J, Lambie E, Zanin E. Rapamycin-induced protein dimerization as a tool for C. elegans research. MICROPUBLICATION BIOLOGY 2018; 2018. [PMID: 32550365 PMCID: PMC7252237 DOI: 10.17912/w2bh3h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Sriyash Mangal
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Jeffrey Zielich
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Eric Lambie
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Esther Zanin
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
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78
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Benedetti L, Barentine AES, Messa M, Wheeler H, Bewersdorf J, De Camilli P. Light-activated protein interaction with high spatial subcellular confinement. Proc Natl Acad Sci U S A 2018; 115:E2238-E2245. [PMID: 29463750 PMCID: PMC5877946 DOI: 10.1073/pnas.1713845115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other component (the prey) is fused to the protein of interest. Upon illumination, binding of the prey to the bait results in its subcellular redistribution. Here, we compared and quantified the extent of light-dependent dimer occurrence in small, subcellular volumes controlled by three such tools: Cry2/CIB1, iLID, and Magnets. We show that both the location of the photoreceptor protein(s) in the dimer pair and its (their) switch-off kinetics determine the subcellular volume where dimer formation occurs and the amount of protein recruited in the illuminated volume. Efficient spatial confinement of dimer to the area of illumination is achieved when the photosensitive component of the dimerization pair is tethered to the membrane of intracellular compartments and when on and off kinetics are extremely fast, as achieved with iLID or Magnets. Magnets and the iLID variants with the fastest switch-off kinetics induce and maintain protein dimerization in the smallest volume, although this comes at the expense of the total amount of dimer. These findings highlight the distinct features of different optical dimerization systems and will be useful guides in the choice of tools for specific applications.
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Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
| | - Mirko Messa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Heather Wheeler
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510;
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
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79
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- 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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80
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Zana M, Péterfi Z, Kovács HA, Tóth ZE, Enyedi B, Morel F, Paclet MH, Donkó Á, Morand S, Leto TL, Geiszt M. Interaction between p22 phox and Nox4 in the endoplasmic reticulum suggests a unique mechanism of NADPH oxidase complex formation. Free Radic Biol Med 2018; 116:41-49. [PMID: 29278739 DOI: 10.1016/j.freeradbiomed.2017.12.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/06/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022]
Abstract
The p22phox protein is an essential component of the phagocytic- and inner ear NADPH oxidases but its relationship to other Nox proteins is less clear. We have studied the role of p22phox in the TGF-β1-stimulated H2O2 production of primary human and murine fibroblasts. TGF-β1 induced H2O2 release of the examined cells, and the response was dependent on the expression of both Nox4 and p22phox. Interestingly, the p22phox protein was present in the absence of any detectable Nox/Duox expression, and the p22phox level was unaffected by TGF-β1. On the other hand, Nox4 expression was dependent on the presence of p22phox, establishing an asymmetrical relationship between the two proteins. Nox4 and p22phox proteins localized to the endoplasmic reticulum and their distribution was unaffected by TGF-β1. We used a chemically induced protein dimerization method to study the orientation of p22phox and Nox4 in the endoplasmic reticulum membrane. This technique is based on the rapamycin-mediated heterodimerization of the mammalian FRB domain with the FK506 binding protein. The results of these experiments suggest that the enzyme complex produces H2O2 into the lumen of the endoplasmic reticulum, indicating that Nox4 contributes to the development of the oxidative milieu within this organelle.
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Affiliation(s)
- Melinda Zana
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; "Momentum" Peroxidase Enzyme Research Group of the Semmelweis University and the Hungarian Academy of Sciences, Budapest, Hungary
| | - Zalán Péterfi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Hajnal A Kovács
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; "Momentum" Peroxidase Enzyme Research Group of the Semmelweis University and the Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsuzsanna E Tóth
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Balázs Enyedi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Françoise Morel
- GREPI AGIM FRE CNRS 3405, Joseph Fourier University Grenoble France, EFS Rhône-Alpes, France
| | - Marie-Hélène Paclet
- GREPI AGIM FRE CNRS 3405, Joseph Fourier University Grenoble France, EFS Rhône-Alpes, France
| | - Ágnes Donkó
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; "Momentum" Peroxidase Enzyme Research Group of the Semmelweis University and the Hungarian Academy of Sciences, Budapest, Hungary
| | | | - Thomas L Leto
- Laboratory of Host Defenses, NIAID, NIH, United States
| | - Miklós Geiszt
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; "Momentum" Peroxidase Enzyme Research Group of the Semmelweis University and the Hungarian Academy of Sciences, Budapest, Hungary.
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81
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- 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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82
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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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83
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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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84
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Abstract
Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.
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Affiliation(s)
- Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - André Nadler
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstraße 108, 01307 Dresden, Germany
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85
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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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86
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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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87
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Bonner JM, Boulianne GL. Diverse structures, functions and uses of FK506 binding proteins. Cell Signal 2017; 38:97-105. [DOI: 10.1016/j.cellsig.2017.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023]
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88
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Liebick M, Henze S, Vogt V, Oppermann M. Functional consequences of chemically-induced β-arrestin binding to chemokine receptors CXCR4 and CCR5 in the absence of ligand stimulation. Cell Signal 2017; 38:201-211. [PMID: 28733085 DOI: 10.1016/j.cellsig.2017.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/26/2017] [Accepted: 07/15/2017] [Indexed: 01/14/2023]
Abstract
Chemokine receptor signaling is a tightly regulated process which was for a long time exclusively attributed to heterotrimeric G proteins. β-Arrestins constitute a separable signaling arm from classical heterotrimeric G proteins, in addition to their well-established roles in receptor desensitization and endocytosis. In order to clearly dissect β-arrestin- from G protein-dependent effects we forced the recruitment of β-arrestin to CXCR4 and CCR5 independently of agonist-promoted receptor activation through chemically-induced dimerization. Targeting β-arrestins to receptors at the plasma membrane prior to chemokine stimulation attenuated G protein-mediated calcium release. Association of β-arrestins to the receptors was sufficient to induce their internalization in the absence of ligand and this effect could be further enhanced by translocation of a constitutively active β-arrestin 1 variant. CXCR4 and CCR5 were targeted to different intracellular compartments upon chemical-induced dimerization with β-arrestins and reproduced the intracellular distribution of receptors after activation with their respective ligands. Our data further provide evidence for direct β-arrestin-mediated signaling via MAP kinases ERK 1/2. These results provide clear evidence that CXCR4- or CCR5-β-arrestin complexes induce receptor endocytosis and signaling in the absence of G protein coupling and ligand-induced conformational changes of the receptor.
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Affiliation(s)
- Marcel Liebick
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany.
| | - Sarah Henze
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Viola Vogt
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Martin Oppermann
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
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89
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Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
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90
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Identification of postsynaptic phosphatidylinositol-4,5-bisphosphate (PIP 2) roles for synaptic plasticity using chemically induced dimerization. Sci Rep 2017; 7:3351. [PMID: 28611378 PMCID: PMC5469801 DOI: 10.1038/s41598-017-03520-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 05/02/2017] [Indexed: 11/16/2022] Open
Abstract
Phosphatidylinositol-4,5-bisphosphate (PIP2), one of the key phospholipids, directly interacts with several membrane and cytosolic proteins at neuronal plasma membranes, leading to changes in neuronal properties including the feature and surface expression of ionotropic receptors. Although PIP2 is also concentrated at the dendritic spines, little is known about the direct physiological functions of PIP2 at postsynaptic as opposed to presynaptic sites. Most previous studies used genetic and pharmacological methods to modulate enzymes that alter PIP2 levels, making it difficult to delineate time- or region-specific roles of PIP2. We used chemically-induced dimerization to translocate inositol polyphosphate 5-phosphatase (Inp54p) to plasma membranes in the presence of rapamycin. Upon redistribution of Inp54p, long-term depression (LTD) induced by low-frequency stimulation was blocked in the mouse hippocampal CA3-CA1 pathway, but the catalytically-dead mutant did not affect LTD induction. Collectively, PIP2 is critically required for induction of LTD whereas translocation of Inp54p to plasma membranes has no effect on the intrinsic properties of the neurons, basal synaptic transmission, long-term potentiation or expression of LTD.
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91
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Chang CL, Chen YJ, Liou J. ER-plasma membrane junctions: Why and how do we study them? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1494-1506. [PMID: 28554772 DOI: 10.1016/j.bbamcr.2017.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/09/2017] [Accepted: 05/17/2017] [Indexed: 12/17/2022]
Abstract
Endoplasmic reticulum (ER)-plasma membrane (PM) junctions are membrane microdomains important for communication between the ER and the PM. ER-PM junctions were first reported in muscle cells in 1957, but mostly ignored in non-excitable cells due to their scarcity and lack of functional significance. In 2005, the discovery of stromal interaction molecule 1 (STIM1) mediating a universal Ca2+ feedback mechanism at ER-PM junctions in mammalian cells led to a resurgence of research interests toward ER-PM junctions. In the past decade, several major advancements have been made in this emerging topic in cell biology, including the generation of tools for labeling ER-PM junctions and the unraveling of mechanisms underlying regulation and functions of ER-PM junctions. This review summarizes early studies, recently developed tools, and current advances in the characterization and understanding of ER-PM junctions. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.
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Affiliation(s)
- Chi-Lun Chang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Ju Chen
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jen Liou
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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92
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Verboogen DRJ, González Mancha N, Ter Beest M, van den Bogaart G. Fluorescence Lifetime Imaging Microscopy reveals rerouting of SNARE trafficking driving dendritic cell activation. eLife 2017; 6. [PMID: 28524818 PMCID: PMC5473687 DOI: 10.7554/elife.23525] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/18/2017] [Indexed: 11/13/2022] Open
Abstract
SNARE proteins play a crucial role in intracellular trafficking by catalyzing membrane fusion, but assigning SNAREs to specific intracellular transport routes is challenging with current techniques. We developed a novel Förster resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM)-based technique allowing visualization of real-time local interactions of fluorescently tagged SNARE proteins in live cells. We used FRET-FLIM to delineate the trafficking steps underlying the release of the inflammatory cytokine interleukin-6 (IL-6) from human blood-derived dendritic cells. We found that activation of dendritic cells by bacterial lipopolysaccharide leads to increased FRET of fluorescently labeled syntaxin 4 with VAMP3 specifically at the plasma membrane, indicating increased SNARE complex formation, whereas FRET with other tested SNAREs was unaltered. Our results revealed that SNARE complexing is a key regulatory step for cytokine production by immune cells and prove the applicability of FRET-FLIM for visualizing SNARE complexes in live cells with subcellular spatial resolution.
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Affiliation(s)
- Daniëlle Rianne José Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Natalia González Mancha
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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93
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Goedhart J, van Unen J. Molecular perturbation strategies to examine spatiotemporal features of Rho GEF and Rho GTPase activity in living cells. Small GTPases 2017; 10:178-186. [PMID: 28521592 PMCID: PMC6548299 DOI: 10.1080/21541248.2017.1302551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Much of our current knowledge of Rho GTPase networks and the regulation by Rho guanine exchange factors (Rho GEFs) and Rho GTPase activating proteins (Rho GAPs) is based on population-based techniques. Over the last decades, technologies that enable single cell analysis with high spatial and temporal resolution have revealed that Rho GTPase activity in cells is regulated on second timescales and at submicrometer length scales. Therefore, perturbation methods with matching spatial and temporal resolution are crucial to further our understanding of Rho GTPase signaling. Here, we give a brief overview of the components of Rho GTPase signaling networks and review a range of existing perturbation strategies that target a specific component of the Rho GTPase signaling module. The advantages and limitations of each perturbation method are discussed. Several recommendations are formulated to guide future studies aimed at addressing spatiotemporal aspects of Rho GEF and Rho GTPase signaling.
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Affiliation(s)
- Joachim Goedhart
- a Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam , The Netherlands
| | - Jakobus van Unen
- a Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam , The Netherlands
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94
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Kashima D, Kawade R, Nagamune T, Kawahara M. A Chemically Inducible Helper Module for Detecting Protein–Protein Interactions with Tunable Sensitivity Based on KIPPIS. Anal Chem 2017; 89:4824-4830. [DOI: 10.1021/acs.analchem.6b04063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Daiki Kashima
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Raiji Kawade
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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95
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: Switch-like, Light-Controlled Perturbations inside Living Cells. Angew Chem Int Ed Engl 2017; 56:5916-5920. [DOI: 10.1002/anie.201611432] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Dominic Kamps
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Simone Weigel
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Orlich
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Ruben Garrecht
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
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96
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: schaltbare, lichtgesteuerte Manipulation in lebenden Zellen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Muthukumaran Venkatachalapathy
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Dominic Kamps
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Simone Weigel
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Ravi Kumar
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Orlich
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Ruben Garrecht
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Hirtz
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Leif Dehmelt
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
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97
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Czapiński J, Kiełbus M, Kałafut J, Kos M, Stepulak A, Rivero-Müller A. How to Train a Cell-Cutting-Edge Molecular Tools. Front Chem 2017; 5:12. [PMID: 28344971 PMCID: PMC5344921 DOI: 10.3389/fchem.2017.00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.
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Affiliation(s)
- Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of WarsawWarsaw, Poland
| | - Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi UniversityTurku, Finland
- Department of Biosciences, Åbo Akademi UniversityTurku, Finland
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98
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Mondal P, Khamo JS, Krishnamurthy VV, Cai Q, Zhang K. Drive the Car(go)s-New Modalities to Control Cargo Trafficking in Live Cells. Front Mol Neurosci 2017; 10:4. [PMID: 28163671 PMCID: PMC5247435 DOI: 10.3389/fnmol.2017.00004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/05/2017] [Indexed: 11/13/2022] Open
Abstract
Synaptic transmission is a fundamental molecular process underlying learning and memory. Successful synaptic transmission involves coupled interaction between electrical signals (action potentials) and chemical signals (neurotransmitters). Defective synaptic transmission has been reported in a variety of neurological disorders such as Autism and Alzheimer’s disease. A large variety of macromolecules and organelles are enriched near functional synapses. Although a portion of macromolecules can be produced locally at the synapse, a large number of synaptic components especially the membrane-bound receptors and peptide neurotransmitters require active transport machinery to reach their sites of action. This spatial relocation is mediated by energy-consuming, motor protein-driven cargo trafficking. Properly regulated cargo trafficking is of fundamental importance to neuronal functions, including synaptic transmission. In this review, we discuss the molecular machinery of cargo trafficking with emphasis on new experimental strategies that enable direct modulation of cargo trafficking in live cells. These strategies promise to provide insights into a quantitative understanding of cargo trafficking, which could lead to new intervention strategies for the treatment of neurological diseases.
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Affiliation(s)
- Payel Mondal
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - John S Khamo
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | | | - Qi Cai
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbana, IL, USA; Neuroscience Program, University of Illinois at Urbana-ChampaignUrbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
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99
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Abstract
An optimal tool to unravel the role of a specific player within a cellular network or process requires its spatiotemporally resolved perturbation. Chemically induced dimerization (CID) by the rapamycin system has proven useful to induce protein dimerization or translocation with high spatiotemporal precision. Recently, we and others have added reversibility of the dimerization event as a novel feature to CID approaches. Among those, our reversible chemical dimerizer (rCD1) shows the fastest release kinetics observed, comparable to optogenetic methods. Induction and termination of enzyme activities, including phosphatidylinositol 3-kinase (PI3K) and 5-phosphatase (5Ptase), therefore allowed us to monitor the relaxation of the downstream effectors within living cells by imaging and traditional biochemical methods. Because switching off the rCD1-induced enzyme activity is sufficiently fast, it is possible to estimate kinetic parameters for enzyme activity and metabolism. Fast reversible CIDs are therefore unique tools for performing semiquantitative biochemistry in intact cells. In this chapter, we discuss advantages and constraints for the design of reversible CID applications. We provide detailed protocols for rCD1 synthesis, CID component expression in and delivery to mammalian cells and the determination of enzyme kinetics inside intact cells by a specially designed image acquisition and data analysis method.
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Affiliation(s)
- M Schifferer
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - S Feng
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - F Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - C Schultz
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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100
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Ruch TR, Bryant DM, Mostov KE, Engel JN. Par3 integrates Tiam1 and phosphatidylinositol 3-kinase signaling to change apical membrane identity. Mol Biol Cell 2016; 28:252-260. [PMID: 27881661 PMCID: PMC5231894 DOI: 10.1091/mbc.e16-07-0541] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 01/31/2023] Open
Abstract
Pathogens can alter epithelial polarity by recruiting polarity proteins to the apical membrane, but how a change in protein localization is linked to polarity disruption is not clear. In this study, we used chemically induced dimerization to rapidly relocalize proteins from the cytosol to the apical surface. We demonstrate that forced apical localization of Par3, which is normally restricted to tight junctions, is sufficient to alter apical membrane identity through its interactions with phosphatidylinositol 3-kinase (PI3K) and the Rac1 guanine nucleotide exchange factor Tiam1. We further show that PI3K activity is required upstream of Rac1, and that simultaneously targeting PI3K and Tiam1 to the apical membrane has a synergistic effect on membrane remodeling. Thus, Par3 coordinates the action of PI3K and Tiam1 to define membrane identity, revealing a signaling mechanism that can be exploited by human mucosal pathogens.
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Affiliation(s)
- Travis R Ruch
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143
| | - David M Bryant
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Cancer Research UK Beatson Institute, University of Glasgow, Glasgow G61 1BD, United Kingdom.,Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Keith E Mostov
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Joanne N Engel
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143
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