1
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Waters CS. Proteins dance to the tune of light. Nat Chem Biol 2024:10.1038/s41589-024-01662-w. [PMID: 38937657 DOI: 10.1038/s41589-024-01662-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Affiliation(s)
- Christopher S Waters
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
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2
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Schreiber SL. Molecular glues and bifunctional compounds: Therapeutic modalities based on induced proximity. Cell Chem Biol 2024; 31:1050-1063. [PMID: 38861986 DOI: 10.1016/j.chembiol.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
This Perspective explores molecular glues and bifunctional compounds-proximity-inducing compounds-and offers a framework to understand and exploit their similarity to hotspots, missense mutations, and posttranslational modifications (PTMs). This view is also shown to be relevant to intramolecular glues, where compounds induce contacts between distinct domains of the same protein. A historical perspective of these compounds is presented that shows the field has come full circle from molecular glues targeting native proteins, to bifunctionals targeting fusion proteins, and back to molecular glues and bifunctionals targeting native proteins. Modern screening methods and data analyses with pre-selected target proteins are shown to yield either cooperative molecular glues or bifunctional compounds that induce proximity, thereby enabling novel functional outcomes.
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Affiliation(s)
- Stuart L Schreiber
- Arena BioWorks, Broad Institute, Harvard University, Cambridge, MA, USA.
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3
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Zhou C, Wagner S, Liang FS. Induced proximity labeling and editing for epigenetic research. Cell Chem Biol 2024; 31:1118-1131. [PMID: 38866004 PMCID: PMC11193966 DOI: 10.1016/j.chembiol.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic regulation plays a pivotal role in various biological and disease processes. Two key lines of investigation have been pursued that aim to unravel endogenous epigenetic events at particular genes (probing) and artificially manipulate the epigenetic landscape (editing). The concept of induced proximity has inspired the development of powerful tools for epigenetic research. Induced proximity strategies involve bringing molecular effectors into spatial proximity with specific genomic regions to achieve the probing or manipulation of local epigenetic environments with increased proximity. In this review, we detail the development of induced proximity methods and applications in shedding light on the intricacies of epigenetic regulation.
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Affiliation(s)
- Chenwei Zhou
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Sarah Wagner
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA.
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4
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Mashita T, Kowada T, Yamamoto H, Hamaguchi S, Sato T, Matsui T, Mizukami S. Quantitative control of subcellular protein localization with a photochromic dimerizer. Nat Chem Biol 2024:10.1038/s41589-024-01654-w. [PMID: 38890432 DOI: 10.1038/s41589-024-01654-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/26/2024] [Indexed: 06/20/2024]
Abstract
Artificial control of intracellular protein dynamics with high precision provides deep insight into complicated biomolecular networks. Optogenetics and caged compound-based chemically induced dimerization (CID) systems are emerging as tools for spatiotemporally regulating intracellular protein dynamics. However, both technologies face several challenges for accurate control such as the duration of activation, deactivation rate and repetition cycles. Herein, we report a photochromic CID system that uses the photoisomerization of a ligand so that both association and dissociation are controlled by light, enabling quick, repetitive and quantitative regulation of the target protein localization upon illumination with violet and green light. We also demonstrate the usability of the photochromic CID system as a potential tool to finely manipulate intracellular protein dynamics during multicolor fluorescence imaging to study diverse cellular processes. We use this system to manipulate PTEN-induced kinase 1 (PINK1)-Parkin-mediated mitophagy, showing that PINK1 recruitment to the mitochondria can promote Parkin recruitment to proceed with mitophagy.
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Affiliation(s)
- Takato Mashita
- Graduate School of Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Kowada
- Graduate School of Science, Tohoku University, Sendai, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hayashi Yamamoto
- Institute for Advanced Medical Sciences, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | | | - Toshizo Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Toshitaka Matsui
- Graduate School of Science, Tohoku University, Sendai, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Shin Mizukami
- Graduate School of Science, Tohoku University, Sendai, Japan.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan.
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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5
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Blake LA, Watkins L, Liu Y, Inoue T, Wu B. A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies. Nat Commun 2024; 15:2720. [PMID: 38548718 PMCID: PMC10979015 DOI: 10.1038/s41467-024-46943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
RNA decay is vital for regulating mRNA abundance and gene expression. Existing technologies lack the spatiotemporal precision or transcript specificity to capture the stochastic and transient decay process. We devise a general strategy to inducibly recruit protein factors to modulate target RNA metabolism. Specifically, we introduce a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNAs within minutes. The fast and synchronous induction enables direct visualization of mRNA decay dynamics in cells. Applying RIDR to endogenous ACTB mRNA reveals rapid formation and dissolution of RNA granules in pre-existing P-bodies. Time-resolved RNA distribution measurements demonstrate rapid RNA decay inside P-bodies, which is further supported by knocking down P-body constituent proteins. Light and oxidative stress modulate P-body behavior, potentially reconciling the contradictory literature about P-body function. This study reveals compartmentalized RNA decay kinetics, establishing RIDR as a pivotal tool for exploring the spatiotemporal RNA metabolism in cells.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Watkins
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Takanari Inoue
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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6
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Zhou C, He H, Chen X. Photoactivatable Nanobody Conjugate Dimerizer Temporally Resolves Tiam1-Rac1 Signaling Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307549. [PMID: 38225743 PMCID: PMC10953561 DOI: 10.1002/advs.202307549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/07/2023] [Indexed: 01/17/2024]
Abstract
The precise spatiotemporal dynamics of protein activities play a crucial role in cell signaling pathways. To control cellular functions in a spatiotemporal manner, a powerful method called photoactivatable chemically induced dimerization (pCID) is used. In this study, photoactivatable nanobody conjugate inducers of dimerization (PANCIDs) is introduced, which combine pCID with nanobody technology. A PANCID consists of a nanobody module that directly binds to an antigenic target, a photocaged small molecule ligand, and a cyclic decaarginine (cR10 *) cell-penetrating peptide (CPP) for efficient nonendocytic intracellular delivery. Therefore, PANCID photodimerizers also benefit from nanobodies, such as their high affinities (in the nm or pm range), specificities, and ability to modulate endogenous proteins. Additionally it is demonstrated that the nanobody moiety can be easily replaced with alternative ones, expanding the potential applications. By using PANCIDs, the dynamics of the Tiam1-Rac1 signaling cascade is investigated and made an interesting finding. It is found that Rac1 and Tiam1 exhibit distinct behaviors in this axis, acting as time-resolved "molecular oscillators" that transit between different functions in the signaling cascade when activated either slowly or rapidly.
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Affiliation(s)
- Chengjian Zhou
- Laboratory of Chemical Biology and Frontier BiotechnologiesThe HIT Center for Life Sciences (HCLS)Harbin Institute of TechnologyHarbin150001P. R. China
- School of Life Science and TechnologyHarbin Institute of TechnologyHarbin150001P. R. China
| | - Huiping He
- Laboratory of Chemical Biology and Frontier BiotechnologiesThe HIT Center for Life Sciences (HCLS)Harbin Institute of TechnologyHarbin150001P. R. China
- School of Life Science and TechnologyHarbin Institute of TechnologyHarbin150001P. R. China
| | - Xi Chen
- Laboratory of Chemical Biology and Frontier BiotechnologiesThe HIT Center for Life Sciences (HCLS)Harbin Institute of TechnologyHarbin150001P. R. China
- School of Life Science and TechnologyHarbin Institute of TechnologyHarbin150001P. R. China
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7
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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8
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Jiang Y, Li R, Ren F, Yang S, Shao A. Coumarin-Conjugated Macromolecular Probe for Sequential Stimuli-Mediated Activation. Bioconjug Chem 2024; 35:72-79. [PMID: 38091529 DOI: 10.1021/acs.bioconjchem.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Protein bioconjugation has emerged as one of the most valuable tools for the development of protein-based biochemical assays. Here, we report a fluorescent macromolecular material, RF16_Halo, in which the coumarin derivative RF16 is specifically conjugated onto HaloTag protein to achieve a dual-stimuli-mediated fluorescence response. RF16 is first obtained by installing a H2O2-sensitive boron cage onto the C7 hydroxy moiety of the coumarin fluorophore with a HaloTag ligand attaching to the pH-labile 1,3-dioxane moiety. Upon stimulation, RF16_Halo exhibits a sequential fluorescence response to H2O2/pH at both liquid and solid interfaces. The fluorescence of the RF16_Halo-based protein film increases linearly toward H2O2 with a higher sensitivity when compared with that of RF16. Subsequently, the H2O2-cleaved RF16_Halo presents a pH-dependent fluorescence decrease under acidic conditions. Such a stimulus-responsive fluorescence "off-on-off" multimode enables RF16_Halo to be applied as a sequential logic circuit. In addition, we evaluate the fluorescence labeling ability of RF16 to intracellular IRE1_Halo protein and demonstrate that RF16 containing the HaloTag ligand could be precisely retained in cells to track IRE1_Halo protein. Hence, we provide a unique structural design strategy to construct a fluorescence dual-responsive macromolecular probe for information encryption and protein tracking in cells.
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Affiliation(s)
- Yu Jiang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Runqi Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Fei Ren
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Shuke Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Andong Shao
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
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9
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Gharios R, Francis RM, DeForest CA. Chemical and Biological Engineering Strategies to Make and Modify Next-Generation Hydrogel Biomaterials. MATTER 2023; 6:4195-4244. [PMID: 38313360 PMCID: PMC10836217 DOI: 10.1016/j.matt.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
There is a growing interest in the development of technologies to probe and direct in vitro cellular function for fundamental organoid and stem cell biology, functional tissue and metabolic engineering, and biotherapeutic formulation. Recapitulating many critical aspects of the native cellular niche, hydrogel biomaterials have proven to be a defining platform technology in this space, catapulting biological investigation from traditional two-dimensional (2D) culture into the 3D world. Seeking to better emulate the dynamic heterogeneity characteristic of all living tissues, global efforts over the last several years have centered around upgrading hydrogel design from relatively simple and static architectures into stimuli-responsive and spatiotemporally evolvable niches. Towards this end, advances from traditionally disparate fields including bioorthogonal click chemistry, chemoenzymatic synthesis, and DNA nanotechnology have been co-opted and integrated to construct 4D-tunable systems that undergo preprogrammed functional changes in response to user-defined inputs. In this Review, we highlight how advances in synthetic, semisynthetic, and bio-based chemistries have played a critical role in the triggered creation and customization of next-generation hydrogel biomaterials. We also chart how these advances stand to energize the translational pipeline of hydrogels from bench to market and close with an outlook on outstanding opportunities and challenges that lay ahead.
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Affiliation(s)
- Ryan Gharios
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Ryan M. Francis
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Cole A. DeForest
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Department of Chemistry, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle WA 98105, USA
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10
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Shafraz O, Davis CMO, Sivasankar S. Light-activated BioID - an optically activated proximity labeling system to study protein-protein interactions. J Cell Sci 2023; 136:jcs261430. [PMID: 37756605 PMCID: PMC10656424 DOI: 10.1242/jcs.261430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Proximity labeling with genetically encoded enzymes is widely used to study protein-protein interactions in cells. However, the accuracy of proximity labeling is limited by a lack of control over the enzymatic labeling process. Here, we present a light-activated proximity labeling technology for mapping protein-protein interactions at the cell membrane with high accuracy and precision. Our technology, called light-activated BioID (LAB), fuses the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1. We demonstrate, in multiple cell lines, that upon illumination with blue light, CRY2 and CIB1 dimerize, reconstitute split-TurboID and initiate biotinylation. Turning off the light leads to the dissociation of CRY2 and CIB1 and halts biotinylation. We benchmark LAB against the widely used TurboID proximity labeling method by measuring the proteome of E-cadherin, an essential cell-cell adhesion protein. We show that LAB can map E-cadherin-binding partners with higher accuracy and significantly fewer false positives than TurboID.
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Affiliation(s)
- Omer Shafraz
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | | | - Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
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11
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Blake LA, Liu Y, Inoue T, Wu B. A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538452. [PMID: 37162943 PMCID: PMC10168379 DOI: 10.1101/2023.04.26.538452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA decay plays a crucial role in regulating mRNA abundance and gene expression. Modulation of RNA degradation is imperative to investigate an RNA's function. However, information regarding where and how RNA decay occurs remains scarce, partially because existing technologies fail to initiate RNA decay with the spatiotemporal precision or transcript specificity required to capture this stochastic and transient process. Here, we devised a general method that employs inducible tethering of regulatory protein factors to target RNAs and modulate their metabolism. Specifically, we established a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNA within minutes. The fast and synchronous induction enabled direct visualization of mRNA decay dynamics in cells with spatiotemporal precision previously unattainable. When applying RIDR to endogenous ACTB mRNA, we observed rapid formation and disappearance of RNA granules, which coincided with pre-existing processing bodies (P-bodies). We measured the time-resolved RNA distribution in P-bodies and cytoplasm after induction, and compared different models of P-body function. We determined that mRNAs rapidly decayed in P-bodies upon induction. Additionally, we validated the functional role of P-bodies by knocking down specific a P-body constituent protein and RNA degradation enzyme. This study determined compartmentalized RNA decay kinetics for the first time. Together, RIDR provides a valuable and generalizable tool to study the spatial and temporal RNA metabolism in cells.
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12
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Jain A, Dokholyan NV, Lee AL. Allosteric inactivation of an engineered optogenetic GTPase. Proc Natl Acad Sci U S A 2023; 120:e2219254120. [PMID: 36972433 PMCID: PMC10083549 DOI: 10.1073/pnas.2219254120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/14/2023] [Indexed: 03/29/2023] Open
Abstract
Optogenetics is a technique for establishing direct spatiotemporal control over molecular function within living cells using light. Light application induces conformational changes within targeted proteins that produce changes in function. One of the applications of optogenetic tools is an allosteric control of proteins via light-sensing domain (LOV2), which allows direct and robust control of protein function. Computational studies supported by cellular imaging demonstrated that application of light allosterically inhibited signaling proteins Vav2, ITSN, and Rac1, but the structural and dynamic basis of such control has yet to be elucidated by experiment. Here, using NMR spectroscopy, we discover principles of action of allosteric control of cell division control protein 42 (CDC42), a small GTPase involved in cell signaling. Both LOV2 and Cdc42 employ flexibility in their function to switch between "dark"/"lit" or active/inactive states, respectively. By conjoining Cdc42 and phototropin1 LOV2 domains into the bi-switchable fusion Cdc42Lov, application of light-or alternatively, mutation in LOV2 to mimic light absorption-allosterically inhibits Cdc42 downstream signaling. The flow and patterning of allosteric transduction in this flexible system are well suited to observation by NMR. Close monitoring of the structural and dynamic properties of dark versus "lit" states of Cdc42Lov revealed lit-induced allosteric perturbations that extend to Cdc42's downstream effector binding site. Chemical shift perturbations for lit mimic, I539E, have distinct regions of sensitivity, and both the domains are coupled together, leading to bidirectional interdomain signaling. Insights gained from this optoallosteric design will increase our ability to control response sensitivity in future designs.
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Affiliation(s)
- Abha Jain
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA17033
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA17033
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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13
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Controlling cellular activities with light. Nat Methods 2023; 20:357-358. [PMID: 36823334 DOI: 10.1038/s41592-022-01745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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14
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Sarkar HS, Mashita T, Kowada T, Hamaguchi S, Sato T, Kasahara K, Matubayasi N, Matsui T, Mizukami S. Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase. ACS Chem Biol 2023; 18:340-346. [PMID: 36662098 DOI: 10.1021/acschembio.2c00749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective inhibitors of Escherichia coli dihydrofolate reductase (eDHFR) are crucial chemical biology tools that have widespread clinical applications. We developed a set of eDHFR-selective photoswitchable inhibitors by derivatizing the structure of our previously reported methotrexate (MTX) azolog, azoMTX. Substitution of the skeletal p-phenylene group of azoMTX with bulky bis-alkylated arylazopyrazole moieties significantly increased its selectivity toward eDHFR over human DHFR. Owing to the physical properties of arylazopyrazoles, the new ligands exhibited nearly complete Z-to-E photoconversion and high thermostability of Z-isomers. In addition, real-time photoreversible control of eDHFR activity was achieved by alternatively switching the illumination light wavelengths.
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Affiliation(s)
- Himadri S Sarkar
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Takato Mashita
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan.,Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Satoshi Hamaguchi
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Toshizo Sato
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3, Machikaneyamacho, Toyonaka 560-8531, Osaka, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3, Machikaneyamacho, Toyonaka 560-8531, Osaka, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan.,Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan.,Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
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15
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Okura T, Tahara M, Otsuki N, Sato M, Takeuchi K, Takeda M. Generation of a photocontrollable recombinant bovine parainfluenza virus type 3. Microbiol Immunol 2023; 67:204-209. [PMID: 36609846 DOI: 10.1111/1348-0421.13052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/29/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Bovine parainfluenza virus type 3 (BPIV3) is a promising vaccine vector against various respiratory virus infections, including the human PIV3, respiratory syncytial virus, and severe acute respiratory syndrome-coronavirus 2 infections. In this study, we combined the Magnet system and reverse genetic approach to generate photocontrollable BPIV3. An optically controllable Magnet gene was inserted into the H2 region of the BPIV3 large protein gene, which encodes an RNA-dependent RNA polymerase. The generated photocontrollable BPIV3 grew in specific regions of the cell sheet only when illuminated with blue light, suggesting that spatiotemporal control can aid in safe clinical applications of BPIV3.
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Affiliation(s)
- Takashi Okura
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriyuki Otsuki
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| | - Kaoru Takeuchi
- Laboratory of Environmental Microbiology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
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16
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
- *Correspondence: Andreas Möglich,
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17
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Wurz AI, Bunner WP, Szatmari EM, Hughes RM. CRY-BARs: Versatile light-gated molecular tools for the remodeling of membrane architectures. J Biol Chem 2022; 298:102388. [PMID: 35987384 PMCID: PMC9530617 DOI: 10.1016/j.jbc.2022.102388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 11/26/2022] Open
Abstract
BAR (Bin, Amphiphysin and Rvs) protein domains are responsible for the generation of membrane curvature and represent a critical mechanical component of cellular functions. Thus, BAR domains have great potential as components of membrane-remodeling tools for cell biologists. In this work, we describe the design and implementation of a family of versatile light-gated I-BAR (inverse-BAR) domain containing tools derived from the fusion of the A. thaliana Cryptochrome 2 photoreceptor and I-BAR protein domains ('CRY-BARs') with applications in the remodeling of membrane architectures and the control of cellular dynamics. By taking advantage of the intrinsic membrane binding propensity of the I-BAR domain, CRY-BARs can be used for spatial and temporal control of cellular processes that require induction of membrane protrusions. Using cell lines and primary neuron cultures, we demonstrate here that the CRY-BAR optogenetic tool evokes membrane dynamics changes associated with cellular activity. Moreover, we provide evidence that ezrin, an actin and PIP2 binding protein, acts as a relay between the plasma membrane and the actin cytoskeleton and therefore is an important mediator of switch function. Overall, we propose that CRY-BARs hold promise as a useful addition to the optogenetic toolkit to study membrane remodeling in live cells.
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Affiliation(s)
- Anna I Wurz
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Wyatt Paul Bunner
- Department of Physical Therapy, East Carolina University, Greenville, North Carolina, United States
| | - Erzsebet M Szatmari
- Department of Physical Therapy, East Carolina University, Greenville, North Carolina, United States
| | - Robert M Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States.
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18
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Yoshii T, Oki C, Tsukiji S. A photoactivatable self-localizing ligand with improved photosensitivity for chemo-optogenetic control of protein localization in living cells. Bioorg Med Chem Lett 2022; 72:128865. [PMID: 35738351 DOI: 10.1016/j.bmcl.2022.128865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/02/2022]
Abstract
Light-mediated control of protein localization in living cells is a powerful approach for manipulating and probing complex biological systems. By incorporating a classical 6-nitroveratryloxycarbonyl (NVOC) caging group into the inner plasma membrane (PM)-localizing trimethoprim ligand, we recently developed a photoactivatable self-localizing ligand (paSL) that can rapidly recruit engineered Escherichia coli dihydrofolate reductase-fusion proteins from the cytoplasm to the PM upon violet (ca. 400 nm)-light illumination. However, because the photosensitivity of the NVOC-caged paSL is low to moderate, photouncaging experiments require high light intensity, which may not be ideal for many cell applications. Herein, we present a new 7-diethylaminocoumarin (DEAC)-caged paSL with improved photosensitivity. DEAC-caged paSL induced efficient protein recruitment upon violet-light irradiation, even at the low intensity under which NVOC-caged paSL does not respond. DEAC-caged paSL was insensitive to excitation light used to image green fluorescent proteins (GFPs), and it was applicable for simultaneous optical stimulation of Gαq signaling and fluorescence imaging of subsequent Ca2+ oscillations using a GFP-based Ca2+ biosensor in living cells.
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Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan; Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.
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19
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Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
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Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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20
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Miura Y, Senoo A, Doura T, Kiyonaka S. Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches. RSC Chem Biol 2022; 3:269-287. [PMID: 35359495 PMCID: PMC8905536 DOI: 10.1039/d1cb00195g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Cell surface receptors transmit extracellular information into cells. Spatiotemporal regulation of receptor signaling is crucial for cellular functions, and dysregulation of signaling causes various diseases. Thus, it is highly desired to control receptor functions with high spatial and/or temporal resolution. Conventionally, genetic engineering or chemical ligands have been used to control receptor functions in cells. As the alternative, chemogenetics has been proposed, in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. The engineered receptor dissects the function of one receptor member among a highly homologous receptor family in a cell-specific manner. Notably, some chemogenetic strategies have been used to reveal the receptor signaling of target cells in living animals. In this review, we summarize the developing chemogenetic methods of transmembrane receptors for cell-specific regulation of receptor signaling. We also discuss the prospects of chemogenetics for clinical applications.
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Affiliation(s)
- Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akinobu Senoo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
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21
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Zhang X, Pan Y, Kang S, Gu L. Combinatorial Approaches for Efficient Design of Photoswitchable Protein-Protein Interactions as In Vivo Actuators. Front Bioeng Biotechnol 2022; 10:844405. [PMID: 35211467 PMCID: PMC8863173 DOI: 10.3389/fbioe.2022.844405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Light switchable two-component protein dimerization systems offer versatile manipulation and dissection of cellular events in living systems. Over the past 20 years, the field has been driven by the discovery of photoreceptor-based interaction systems, the engineering of light-actuatable binder proteins, and the development of photoactivatable compounds as dimerization inducers. This perspective is to categorize mechanisms and design approaches of these dimerization systems, compare their advantages and limitations, and bridge them to emerging applications. Our goal is to identify new opportunities in combinatorial protein design that can address current engineering challenges and expand in vivo applications.
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Affiliation(s)
- Xiao Zhang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Yuxin Pan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Shoukai Kang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
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22
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Shibata K, Nakasone Y, Terazima M. Selective Photoinduced Dimerization and Slow Recovery of a BLUF Domain of EB1. J Phys Chem B 2022; 126:1024-1033. [PMID: 35089048 DOI: 10.1021/acs.jpcb.1c10100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The EAL-BLUF fragment from Magnetococcus marinus BldP1 (EB1) light-dependently hydrolyzes c-di-GMP. Herein, the photoreaction of the BLUF domain of EB1 (eBLUF) is studied. It is found for the first time that a monomeric BLUF domain forms a dimer upon illumination and its dark recovery is very slow. The dimer of light- and dark-state protomers (LD-dimer) is much more stable than that of two light-state protomers (LL-dimer), and the dark recovery of the LD-dimer is approximately 20 times slower than that of the LL-dimer, which is suitable for optogenetic tools. The secondary structure of the L-monomer is different from those of the D-monomer and the LD-dimer. The transient grating measurements reveal that this conformational change occurs simultaneously with dimerization. Although the W91A mutant exhibits a spectral red shift, it forms a heterodimer with the L-monomer of wild-type eBLUF with similar stability to the LD-dimer. This suggests that the conformation of the dimerization site of W91A is similar to that of the dark state (dark-mimic mutant); that is, the light-induced structural changes in the chromophore cavity are not transferred to the other part of the protein. The selective photoinduced dimerization of eBLUF is potentially useful to control interprotein interactions between two different effector domains bound to these proteins.
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Affiliation(s)
- Kosei Shibata
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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23
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Dwijayanti A, Zhang C, Poh CL, Lautier T. Toward Multiplexed Optogenetic Circuits. Front Bioeng Biotechnol 2022; 9:804563. [PMID: 35071213 PMCID: PMC8766309 DOI: 10.3389/fbioe.2021.804563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits. Progressively, more complex systems have been designed in which multiple photoreceptors, each sensing its dedicated wavelength, are combined to simultaneously coordinate cellular responses in a single cell. In this review, we highlight recent works and challenges on multiplexed optogenetic circuits in natural and engineered systems for a dynamic regulation breakthrough in biotechnological applications.
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Affiliation(s)
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Thomas Lautier
- CNRS@CREATE, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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24
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Shen Y, Luchetti A, Fernandes G, Do Heo W, Silva AJ. The emergence of molecular systems neuroscience. Mol Brain 2022; 15:7. [PMID: 34983613 PMCID: PMC8728933 DOI: 10.1186/s13041-021-00885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.
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Affiliation(s)
- Yang Shen
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Alessandro Luchetti
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Giselle Fernandes
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA.
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25
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Yang H, Du S, Ye Z, Wang X, Yan Z, Lian C, Bao C, Zhu L. A system for artificial light signal transduction via molecular translocation in a lipid membrane. Chem Sci 2022; 13:2487-2494. [PMID: 35310493 PMCID: PMC8864706 DOI: 10.1039/d1sc06671d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
Light signal transduction pathways are central components of the mechanisms that regulate plant development, in which photoreceptors receive light and participate in light signal transduction. Chemical systems can be designed...
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Affiliation(s)
- Huiting Yang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Shengjie Du
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Zhicheng Ye
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Xuebin Wang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Zexin Yan
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Chunyan Bao
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology Shanghai 200237 China
| | - Linyong Zhu
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology Shanghai 200237 China
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26
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Dixon RE, Navedo MF, Binder MD, Santana LF. Mechanisms and Physiological Implications of Cooperative Gating of Ion Channels Clusters. Physiol Rev 2021; 102:1159-1210. [PMID: 34927454 DOI: 10.1152/physrev.00022.2021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ion channels play a central role in the regulation of nearly every cellular process. Dating back to the classic 1952 Hodgkin-Huxley model of the generation of the action potential, ion channels have always been thought of as independent agents. A myriad of recent experimental findings exploiting advances in electrophysiology, structural biology, and imaging techniques, however, have posed a serious challenge to this long-held axiom as several classes of ion channels appear to open and close in a coordinated, cooperative manner. Ion channel cooperativity ranges from variable-sized oligomeric cooperative gating in voltage-gated, dihydropyridine-sensitive Cav1.2 and Cav1.3 channels to obligatory dimeric assembly and gating of voltage-gated Nav1.5 channels. Potassium channels, transient receptor potential channels, hyperpolarization cyclic nucleotide-activated channels, ryanodine receptors (RyRs), and inositol trisphosphate receptors (IP3Rs) have also been shown to gate cooperatively. The implications of cooperative gating of these ion channels range from fine tuning excitation-contraction coupling in muscle cells to regulating cardiac function and vascular tone, to modulation of action potential and conduction velocity in neurons and cardiac cells, and to control of pace-making activity in the heart. In this review, we discuss the mechanisms leading to cooperative gating of ion channels, their physiological consequences and how alterations in cooperative gating of ion channels may induce a range of clinically significant pathologies.
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Affiliation(s)
- Rose Ellen Dixon
- Department of Physiology and Membrane Biology, University of California, Davis, CA, United States
| | - Manuel F Navedo
- Department of Pharmacology, University of California, Davis, CA, United States
| | - Marc D Binder
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, United States
| | - L Fernando Santana
- Department of Physiology and Membrane Biology, University of California, Davis, CA, United States
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27
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Zhu C, Kou T, Kadi AA, Li J, Zhang Y. Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets. Org Biomol Chem 2021; 19:9358-9368. [PMID: 34632469 DOI: 10.1039/d1ob01613j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.
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Affiliation(s)
- Chenghong Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Tianzhang Kou
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
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Courtney TM, Hankinson CP, Horst TJ, Deiters A. Targeted protein oxidation using a chromophore-modified rapamycin analog. Chem Sci 2021; 12:13425-13433. [PMID: 34777761 PMCID: PMC8528027 DOI: 10.1039/d1sc04464h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
Chemically induced dimerization of FKBP and FRB using rapamycin and rapamycin analogs has been utilized in a variety of biological applications. Formation of the FKBP-rapamycin-FRB ternary complex is typically used to activate a biological process and this interaction has proven to be essentially irreversible. In many cases, it would be beneficial to also have temporal control over deactivating a biological process once it has been initiated. Thus, we developed the first reactive oxygen species-generating rapamycin analog toward this goal. The BODIPY-rapamycin analog BORap is capable of dimerizing FKBP and FRB to form a ternary complex, and upon irradiation with 530 nm light, generates singlet oxygen to oxidize and inactivate proteins of interest fused to FKBP/FRB.
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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
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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29
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Yoshii T, Oki C, Watahiki R, Nakamura A, Tahara K, Kuwata K, Furuta T, Tsukiji S. Chemo-optogenetic Protein Translocation System Using a Photoactivatable Self-Localizing Ligand. ACS Chem Biol 2021; 16:1557-1565. [PMID: 34339163 DOI: 10.1021/acschembio.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulating subcellular protein localization using light is a powerful approach for controlling signaling processes with high spatiotemporal precision. The most widely used strategy for this is based on light-induced protein heterodimerization. The use of small synthetic molecules that can control the localization of target proteins in response to light without the need for a second protein has several advantages. However, such methods have not been well established. Herein, we present a chemo-optogenetic approach for controlling protein localization using a photoactivatable self-localizing ligand (paSL). We developed a paSL that can recruit tag-fused proteins of interest from the cytoplasm to the plasma membrane within seconds upon light illumination. This paSL-induced protein translocation (paSLIPT) is reversible and enables the spatiotemporal control of signaling processes in living cells, even in a local region. paSLIPT can also be used to implement simultaneous optical stimulation and multiplexed imaging of molecular processes in a single cell, offering an attractive and novel chemo-optogenetic platform for interrogating and engineering dynamic cellular functions.
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Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Watahiki
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Kai Tahara
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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30
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mem-iLID, a fast and economic protein purification method. Biosci Rep 2021; 41:229021. [PMID: 34142112 PMCID: PMC8239496 DOI: 10.1042/bsr20210800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Protein purification is the vital basis to study the function, structure and interaction of proteins. Widely used methods are affinity chromatography-based purifications, which require different chromatography columns and harsh conditions, such as acidic pH and/or adding imidazole or high salt concentration, to elute and collect the purified proteins. Here we established an easy and fast purification method for soluble proteins under mild conditions, based on the light-induced protein dimerization system improved light-induced dimer (iLID), which regulates protein binding and release with light. We utilize the biological membrane, which can be easily separated by centrifugation, as the port to anchor the target proteins. In Xenopus laevis oocyte and Escherichia coli, the blue light-sensitive part of iLID, AsLOV2-SsrA, was targeted to the plasma membrane by different membrane anchors. The other part of iLID, SspB, was fused with the protein of interest (POI) and expressed in the cytosol. The SspB-POI can be captured to the membrane fraction through light-induced binding to AsLOV2-SsrA and then released purely to fresh buffer in the dark after simple centrifugation and washing. This method, named mem-iLID, is very flexible in scale and economic. We demonstrate the quickly obtained yield of two pure and fully functional enzymes: a DNA polymerase and a light-activated adenylyl cyclase. Furthermore, we also designed a new SspB mutant for better dissociation and less interference with the POI, which could potentially facilitate other optogenetic manipulations of protein-protein interaction.
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31
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Bermudez JG, Deiters A, Good MC. Patterning Microtubule Network Organization Reshapes Cell-Like Compartments. ACS Synth Biol 2021; 10:1338-1350. [PMID: 33988978 DOI: 10.1021/acssynbio.0c00575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.
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Affiliation(s)
- Jessica G. Bermudez
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander Deiters
- Chemistry Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew C. Good
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Cell and Developmental Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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32
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Garabedian MV, Good MC. OptoLRP6 Illuminates Wnt Signaling in Early Embryo Development. J Mol Biol 2021; 433:167053. [PMID: 34015280 DOI: 10.1016/j.jmb.2021.167053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Mikael V Garabedian
- Department of Cell and Developmental Biology, University of Pennsylvania, PA 19104, United States
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, PA 19104, United States; Department of Bioengineering, University of Pennsylvania, PA 19104, United States.
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33
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Pearce S, Tucker CL. Dual Systems for Enhancing Control of Protein Activity through Induced Dimerization Approaches. Adv Biol (Weinh) 2021; 5:e2000234. [PMID: 34028215 PMCID: PMC8144547 DOI: 10.1002/adbi.202000234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/29/2020] [Indexed: 12/25/2022]
Abstract
To reveal the underpinnings of complex biological systems, a variety of approaches have been developed that allow switchable control of protein function. One powerful approach for switchable control is the use of inducible dimerization systems, which can be configured to control activity of a target protein upon induced dimerization triggered by chemicals or light. Individually, many inducible dimerization systems suffer from pre-defined dynamic ranges and overwhelming sensitivity to expression level and cellular context. Such systems often require extensive engineering efforts to overcome issues of background leakiness and restricted dynamic range. To address these limitations, recent tool development efforts have explored overlaying dimerizer systems with a second layer of regulation. Albeit more complex, the resulting layered systems have enhanced functionality, such as tighter control that can improve portability of these tools across platforms.
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Affiliation(s)
- Sarah Pearce
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, 80045, Colorado, USA
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, 80045, Colorado, USA
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34
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Chang D, Feng S, Girik V, Riezman H, Winssinger N. Luciferase Controlled Protein Interactions. J Am Chem Soc 2021; 143:3665-3670. [PMID: 33684293 DOI: 10.1021/jacs.0c11016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein trafficking and protein-protein interactions (PPIs) are central to regulatory processes in cells. Induced dimerization systems have been developed to control PPIs and regulate protein trafficking (localization) or interactions. Chemically induced dimerization (CID) has proven to be a robust approach to control protein interactions and localization. The most recent embodiment of this technology relies on CID conjugates that react with a self-labeling protein on one side and a photocaged ligand on the other side to provide spatiotemporal control of the interaction with the protein of interest. Advancing this technology further is limited by the light delivery problem and the phototoxicity of intense irradiation necessary to achieve photouncaging. Herein, we designed a novel chemically induced dimerization system that was triggered by bioluminescence, instead of external light. Protein dimerization showed fast kinetics and was validated by an induced change of localization of a target protein (to and from the nucleus or plasma membrane) upon trigger. The technology was used transiently to activate the phosphatidylinositol 3-kinase (PI3K)/mTOR pathway and measure the impact on lipid synthesis/metabolism, assessed by lipidomics.
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Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Suihan Feng
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Vladimir Girik
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
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35
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Sun H, Jia H, Ramirez‐Diaz DA, Budisa N, Schwille P. Fine-Tuning Protein Self-Organization by Orthogonal Chemo-Optogenetic Tools. Angew Chem Int Ed Engl 2021; 60:4501-4506. [PMID: 33155720 PMCID: PMC7986231 DOI: 10.1002/anie.202008691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/04/2020] [Indexed: 12/18/2022]
Abstract
A universal gain-of-function approach for the spatiotemporal control of protein activity is highly desirable when reconstituting biological modules in vitro. Here we used orthogonal translation with a photocaged amino acid to map and elucidate molecular mechanisms in the self-organization of the prokaryotic filamentous cell-division protein (FtsZ) that is highly relevant for the assembly of the division ring in bacteria. We masked a tyrosine residue of FtsZ by site-specific incorporation of a photocaged tyrosine analogue. While the mutant still shows self-assembly into filaments, dynamic self-organization into ring patterns can no longer be observed. UV-mediated uncaging revealed that tyrosine 222 is essential for the regulation of the protein's GTPase activity, self-organization, and treadmilling dynamics. Thus, the light-mediated assembly of functional protein modules appears to be a promising minimal-regulation strategy for building up molecular complexity towards a minimal cell.
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Affiliation(s)
- Huan Sun
- Technical University of BerlinMüller-Breslau-Str. 1010623BerlinGermany
| | - Haiyang Jia
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | | | - Nediljko Budisa
- Technical University of BerlinMüller-Breslau-Str. 1010623BerlinGermany
- Present address: University of Manitoba44 DysartRdR3T 2N2WinnipegMBCanada
| | - Petra Schwille
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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36
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Nzigou Mombo B, Bijonowski BM, Rasoulinejad S, Mueller M, Wegner SV. Spatiotemporal Control Over Multicellular Migration Using Green Light Reversible Cell-Cell Interactions. Adv Biol (Weinh) 2021; 5:e2000199. [PMID: 34028212 DOI: 10.1002/adbi.202000199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/22/2020] [Indexed: 01/02/2023]
Abstract
The regulation of cell-cell adhesions in space and time plays a crucial role in cell biology, especially in the coordination of multicellular behavior. Therefore, tools that allow for the modulation of cell-cell interactions with high precision are of great interest to a better understanding of their roles and building tissue-like structures. Herein, the green light-responsive protein CarH is expressed at the plasma membrane of cells as an artificial cell adhesion receptor, so that upon addition of its cofactor vitamin B12 specific cell-cell interactions form and lead to cell clustering in a concentration-dependent manner. Upon green light illumination, the CarH based cell-cell interactions disassemble and allow for their reversion with high spatiotemporal control. Moreover, these artificial cell-cell interactions impact cell migration, as observed in a wound-healing assay. When the cells interact with each other in the presence of vitamin B12 in the dark, the cells form on a solid front and migrate collectively; however, under green light illumination, individual cells migrate randomly out of the monolayer. Overall, the possibility of precisely controlling cell-cell interactions and regulating multicellular behavior is a potential pathway to gaining more insight into cell-cell interactions in biological processes.
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Affiliation(s)
- Brice Nzigou Mombo
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, Münster, 48149, Germany
| | - Brent M Bijonowski
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, Münster, 48149, Germany
| | - Samaneh Rasoulinejad
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Marc Mueller
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, Münster, 48149, Germany.,Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
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37
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Sun H, Jia H, Ramirez‐Diaz DA, Budisa N, Schwille P. Fine‐Tuning Protein Self‐Organization by Orthogonal Chemo‐Optogenetic Tools. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Huan Sun
- Technical University of Berlin Müller-Breslau-Str. 10 10623 Berlin Germany
| | - Haiyang Jia
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | | | - Nediljko Budisa
- Technical University of Berlin Müller-Breslau-Str. 10 10623 Berlin Germany
- Present address: University of Manitoba 44 DysartRd R3T 2N2 Winnipeg MB Canada
| | - Petra Schwille
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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38
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Shaaya M, Fauser J, Karginov AV. Optogenetics: The Art of Illuminating Complex Signaling Pathways. Physiology (Bethesda) 2021; 36:52-60. [PMID: 33325819 DOI: 10.1152/physiol.00022.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dissection of cell signaling requires tools that can mimic spatiotemporal dynamics of individual pathways in living cells. Optogenetic methods enable manipulation of signaling processes with precise timing and local control. In this review, we describe recent optogenetic approaches for regulation of cell signaling, highlight their advantages and limitations, and discuss examples of their application.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois.,University of Illinois Cancer Center, The University of Illinois at Chicago, Chicago, Illinois
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39
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Huang Z, Li Z, Zhang X, Kang S, Dong R, Sun L, Fu X, Vaisar D, Watanabe K, Gu L. Creating Red Light-Switchable Protein Dimerization Systems as Genetically Encoded Actuators with High Specificity. ACS Synth Biol 2020; 9:3322-3333. [PMID: 33179507 DOI: 10.1021/acssynbio.0c00397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Protein dimerization systems controlled by red light with increased tissue penetration depth are a highly needed tool for clinical applications such as cell and gene therapies. However, mammalian applications of existing red light-induced dimerization systems are hampered by limitations of their two components: a photosensory protein (or photoreceptor) which often requires a mammalian exogenous chromophore and a naturally occurring photoreceptor binding protein typically having a complex structure and nonideal binding properties. Here, we introduce an efficient, generalizable method (COMBINES-LID) for creating highly specific, reversible light-induced heterodimerization systems independent of any existing binders to a photoreceptor. It involves a two-step binder screen (phage display and yeast two-hybrid) of a combinatorial nanobody library to obtain binders that selectively engage a light-activated form of a photoswitchable protein or domain not the dark form. Proof-of-principle was provided by engineering nanobody-based, red light-induced dimerization (nanoReD) systems comprising a truncated bacterial phytochrome sensory module using a mammalian endogenous chromophore, biliverdin, and light-form specific nanobodies. Selected nanoReD systems were biochemically characterized, exhibiting low dark activity and high induction specificity, and further demonstrated for the reversible control of protein translocation and activation of gene expression in mice. Overall, COMBINES-LID opens new opportunities for creating genetically encoded actuators for the optical manipulation of biological processes.
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Affiliation(s)
- Zhimin Huang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Zengpeng Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography Ministry of Natural Resources, Xiamen 361005, PR China
| | - Xiao Zhang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Shoukai Kang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Runze Dong
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Li Sun
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Xiaonan Fu
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - David Vaisar
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Kurumi Watanabe
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
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40
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Mathony J, Niopek D. Enlightening Allostery: Designing Switchable Proteins by Photoreceptor Fusion. Adv Biol (Weinh) 2020; 5:e2000181. [PMID: 33107225 DOI: 10.1002/adbi.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Indexed: 11/05/2022]
Abstract
Optogenetics harnesses natural photoreceptors to non-invasively control selected processes in cells with previously unmet spatiotemporal precision. Linking the activity of a protein of choice to the conformational state of a photosensor domain through allosteric coupling represents a powerful method for engineering light-responsive proteins. It enables the design of compact and highly potent single-component optogenetic systems with fast on- and off-switching kinetics. However, designing protein-photoreceptor chimeras, in which structural changes of the photoreceptor are effectively propagated to the fused effector protein, is a challenging engineering problem and often relies on trial and error. Here, recent advances in the design and application of optogenetic allosteric switches are reviewed. First, an overview of existing optogenetic tools based on inducible allostery is provided and their utility for cell biology applications is highlighted. Focusing on light-oxygen-voltage domains, a widely applied class of small blue light sensors, the available strategies for engineering light-dependent allostery are presented and their individual advantages and limitations are highlighted. Finally, high-throughput screening technologies based on comprehensive insertion libraries, which could accelerate the creation of stimulus-responsive receptor-protein chimeras for use in optogenetics and beyond, are discussed.
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Affiliation(s)
- Jan Mathony
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany.,BZH graduate school, Heidelberg University, Im Neuheimer Feld 328, Heidelberg, 69120, Germany
| | - Dominik Niopek
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany
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41
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Wittmann T, Dema A, van Haren J. Lights, cytoskeleton, action: Optogenetic control of cell dynamics. Curr Opin Cell Biol 2020; 66:1-10. [PMID: 32371345 PMCID: PMC7577957 DOI: 10.1016/j.ceb.2020.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/29/2023]
Abstract
Cell biology is moving from observing molecules to controlling them in real time, a critical step towards a mechanistic understanding of how cells work. Initially developed from light-gated ion channels to control neuron activity, optogenetics now describes any genetically encoded protein system designed to accomplish specific light-mediated tasks. Recent photosensitive switches use many ingenious designs that bring spatial and temporal control within reach for almost any protein or pathway of interest. This next generation optogenetics includes light-controlled protein-protein interactions and shape-shifting photosensors, which in combination with live microscopy enable acute modulation and analysis of dynamic protein functions in living cells. We provide a brief overview of various types of optogenetic switches. We then discuss how diverse approaches have been used to control cytoskeleton dynamics with light through Rho GTPase signaling, microtubule and actin assembly, mitotic spindle positioning and intracellular transport and highlight advantages and limitations of different experimental strategies.
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Affiliation(s)
- Torsten Wittmann
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Alessandro Dema
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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42
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Lassoued R, Macall DM, Smyth SJ, Phillips PW, Hesseln H. How should we regulate products of new breeding techniques? Opinion of surveyed experts in plant biotechnology. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00460. [PMID: 32617264 PMCID: PMC7322807 DOI: 10.1016/j.btre.2020.e00460] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 01/15/2023]
Abstract
The adoption of genome editing depends among others, on a clear and navigable regulatory framework that renders consistent decisions. Some countries like the United States decided to deregulate specific transgene-free genome edited products that could be created through traditional breeding and are not considered to be plant pests, while others are still challenged to fit emerging technologies in their regulatory system. Here we poll international experts in plant biotechnology on what approach should nations agree upon to accommodate current and future new breeding technologies and derived products. A key finding is product-based models or dual-product/process systems are viewed as potential appropriate frameworks to regulate outcomes of genome editing. As regulation of novel products of biotechnology is expected to impact research and trade, we test the impact of experts' worldviews on these issues. Results show that region influences worldviews of trade but not of agricultural innovation. In contrast, there was no effect of experts' worldviews on how products of novel biotechnologies should be regulated.
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Affiliation(s)
- Rim Lassoued
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Diego Maximiliano Macall
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Stuart J. Smyth
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Peter W.B. Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, SK, S7N 5B8, Canada
| | - Hayley Hesseln
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
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LITESEC-T3SS - Light-controlled protein delivery into eukaryotic cells with high spatial and temporal resolution. Nat Commun 2020; 11:2381. [PMID: 32404906 PMCID: PMC7221075 DOI: 10.1038/s41467-020-16169-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/18/2020] [Indexed: 12/16/2022] Open
Abstract
Many bacteria employ a type III secretion system (T3SS) injectisome to translocate proteins into eukaryotic host cells. Although the T3SS can efficiently export heterologous cargo proteins, a lack of target cell specificity currently limits its application in biotechnology and healthcare. In this study, we exploit the dynamic nature of the T3SS to govern its activity. Using optogenetic interaction switches to control the availability of the dynamic cytosolic T3SS component SctQ, T3SS-dependent effector secretion can be regulated by light. The resulting system, LITESEC-T3SS (Light-induced translocation of effectors through sequestration of endogenous components of the T3SS), allows rapid, specific, and reversible activation or deactivation of the T3SS upon illumination. We demonstrate the light-regulated translocation of heterologous reporter proteins, and induction of apoptosis in cultured eukaryotic cells. LITESEC-T3SS constitutes a new method to control protein secretion and translocation into eukaryotic host cells with unparalleled spatial and temporal resolution.
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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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Klewer L, Wu YW. 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] [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 Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Department of Chemistry, Umeå Centre for Microbial Research, Umeå University, 90187, Umeå, Sweden.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
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