1
|
Fu W, Hu X, Yuan Q, Xu Z, Cheng J, Li Z, Shao X. Design, synthesis and bioassay of the emerging photo-responsive fungicides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
2
|
Hilgers F, Hogenkamp F, Klaus O, Kruse L, Loeschcke A, Bier C, Binder D, Jaeger KE, Pietruszka J, Drepper T. Light-mediated control of gene expression in the anoxygenic phototrophic bacterium Rhodobacter capsulatus using photocaged inducers. Front Bioeng Biotechnol 2022; 10:902059. [PMID: 36246361 PMCID: PMC9561348 DOI: 10.3389/fbioe.2022.902059] [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: 03/22/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Photocaged inducer molecules, especially photocaged isopropyl-β-d-1-thiogalactopyranoside (cIPTG), are well-established optochemical tools for light-regulated gene expression and have been intensively applied in Escherichia coli and other bacteria including Corynebacterium glutamicum, Pseudomonas putida or Bacillus subtilis. In this study, we aimed to implement a light-mediated on-switch for target gene expression in the facultative anoxygenic phototroph Rhodobacter capsulatus by using different cIPTG variants under both phototrophic and non-phototrophic cultivation conditions. We could demonstrate that especially 6-nitropiperonyl-(NP)-cIPTG can be applied for light-mediated induction of target gene expression in this facultative phototrophic bacterium. Furthermore, we successfully applied the optochemical approach to induce the intrinsic carotenoid biosynthesis to showcase engineering of a cellular function. Photocaged IPTG thus represents a light-responsive tool, which offers various promising properties suitable for future applications in biology and biotechnology including automated multi-factorial control of cellular functions as well as optimization of production processes.
Collapse
Affiliation(s)
- Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Oliver Klaus
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Luzie Kruse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Jörg Pietruszka, ; Thomas Drepper,
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Jörg Pietruszka, ; Thomas Drepper,
| |
Collapse
|
3
|
Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
Collapse
Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
| |
Collapse
|
4
|
Hogenkamp F, Hilgers F, Bitzenhofer NL, Ophoven V, Haase M, Bier C, Binder D, Jaeger KE, Drepper T, Pietruszka J. Optochemical Control of Bacterial Gene Expression: Novel Photocaged Compounds for Different Promoter Systems. Chembiochem 2021; 23:e202100467. [PMID: 34750949 PMCID: PMC9299732 DOI: 10.1002/cbic.202100467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Indexed: 12/05/2022]
Abstract
Photocaged compounds are applied for implementing precise, optochemical control of gene expression in bacteria. To broaden the scope of UV‐light‐responsive inducer molecules, six photocaged carbohydrates were synthesized and photochemically characterized, with the absorption exhibiting a red‐shift. Their differing linkage through ether, carbonate, and carbamate bonds revealed that carbonate and carbamate bonds are convenient. Subsequently, those compounds were successfully applied in vivo for controlling gene expression in E. coli via blue light illumination. Furthermore, benzoate‐based expression systems were subjected to light control by establishing a novel photocaged salicylic acid derivative. Besides its synthesis and in vitro characterization, we demonstrate the challenging choice of a suitable promoter system for light‐controlled gene expression in E. coli. We illustrate various bottlenecks during both photocaged inducer synthesis and in vivo application and possibilities to overcome them. These findings pave the way towards novel caged inducer‐dependent systems for wavelength‐selective gene expression.
Collapse
Affiliation(s)
- Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Vera Ophoven
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Mona Haase
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Dennis Binder
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC).,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC)
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich Stetternicher Forst, 52426, Jülich, Germany.,Bioeconomy Science Center (BioSC).,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| |
Collapse
|
5
|
Burmeister A, Akhtar Q, Hollmann L, Tenhaef N, Hilgers F, Hogenkamp F, Sokolowsky S, Marienhagen J, Noack S, Kohlheyer D, Grünberger A. (Optochemical) Control of Synthetic Microbial Coculture Interactions on a Microcolony Level. ACS Synth Biol 2021; 10:1308-1319. [PMID: 34075749 DOI: 10.1021/acssynbio.0c00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic microbial cocultures carry enormous potential for applied biotechnology and are increasingly the subject of fundamental research. So far, most cocultures have been designed and characterized based on bulk cultivations without considering the potentially highly heterogeneous and diverse single-cell behavior. However, an in-depth understanding of cocultures including their interacting single cells is indispensable for the development of novel cultivation approaches and control of cocultures. We present the development, validation, and experimental characterization of an optochemically controllable bacterial coculture on a microcolony level consisting of two Corynebacterium glutamicum strains. Our coculture combines an l-lysine auxotrophic strain together with a l-lysine-producing variant carrying the genetically IPTG-mediated induction of l-lysine production. We implemented two control approaches utilizing IPTG as inducer molecule. First, unmodified IPTG was supplemented to the culture enabling a medium-based control of the production of l-lysine, which serves as the main interacting component. Second, optochemical control was successfully performed by utilizing photocaged IPTG activated by appropriate illumination. Both control strategies were validated studying cellular growth on a microcolony level. The novel microfluidic single-cell cultivation strategies applied in this work can serve as a blueprint to validate cellular control strategies of synthetic mono- and cocultures with single-cell resolution at defined environmental conditions.
Collapse
Affiliation(s)
- Alina Burmeister
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, 33615 Bielefeld, Germany
| | - Qiratt Akhtar
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lina Hollmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Sascha Sokolowsky
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Aachener Verfahrenstechnik (AVT-MSB), RWTH Aachen University, 52074 Aachen, Germany
| | | |
Collapse
|
6
|
Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
Collapse
Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| |
Collapse
|
7
|
Hogenkamp F, Hilgers F, Knapp A, Klaus O, Bier C, Binder D, Jaeger KE, Drepper T, Pietruszka J. Effect of Photocaged Isopropyl β-d-1-thiogalactopyranoside Solubility on the Light Responsiveness of LacI-controlled Expression Systems in Different Bacteria. Chembiochem 2020; 22:539-547. [PMID: 32914927 PMCID: PMC7894499 DOI: 10.1002/cbic.202000377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/31/2020] [Indexed: 01/02/2023]
Abstract
Photolabile protecting groups play a significant role in controlling biological functions and cellular processes in living cells and tissues, as light offers high spatiotemporal control, is non‐invasive as well as easily tuneable. In the recent past, photo‐responsive inducer molecules such as 6‐nitropiperonyl‐caged IPTG (NP‐cIPTG) have been used as optochemical tools for Lac repressor‐controlled microbial expression systems. To further expand the applicability of the versatile optochemical on‐switch, we have investigated whether the modulation of cIPTG water solubility can improve the light responsiveness of appropriate expression systems in bacteria. To this end, we developed two new cIPTG derivatives with different hydrophobicity and demonstrated both an easy applicability for the light‐mediated control of gene expression and a simple transferability of this optochemical toolbox to the biotechnologically relevant bacteria Pseudomonas putida and Bacillus subtilis. Notably, the more water‐soluble cIPTG derivative proved to be particularly suitable for light‐mediated gene expression in these alternative expression hosts.
Collapse
Affiliation(s)
- Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Oliver Klaus
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| |
Collapse
|
8
|
de Geus MAR, Groenewold GJM, Maurits E, Araman C, van Kasteren SI. Synthetic methodology towards allylic trans-cyclooctene-ethers enables modification of carbohydrates: bioorthogonal manipulation of the lac repressor. Chem Sci 2020; 11:10175-10179. [PMID: 34094281 PMCID: PMC8162276 DOI: 10.1039/d0sc03216f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
The inverse electron-demand Diels-Alder (IEDDA) pyridazine elimination is one of the key bioorthogonal bond-breaking reactions. In this reaction trans-cyclooctene (TCO) serves as a tetrazine responsive caging moiety for amines, carboxylic acids and alcohols. One issue to date has been the lack of synthetic methods towards TCO ethers from functionalized (aliphatic) alcohols, thereby restricting bioorthogonal utilization. Two novel reagents were developed to enable controlled formation of cis-cyclooctene (CCO) ethers, followed by optimized photochemical isomerization to obtain TCO ethers. The method was exemplified by the controlled bioorthogonal activation of the lac operon system in E. coli using a TCO-ether-modified carbohydrate inducer.
Collapse
Affiliation(s)
- Mark A R de Geus
- Leiden Institute of Chemistry, The Institute for Chemical Immunology, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - G J Mirjam Groenewold
- Leiden Institute of Chemistry, The Institute for Chemical Immunology, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Elmer Maurits
- Leiden Institute of Chemistry, The Institute for Chemical Immunology, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Can Araman
- Leiden Institute of Chemistry, The Institute for Chemical Immunology, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sander I van Kasteren
- Leiden Institute of Chemistry, The Institute for Chemical Immunology, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
9
|
Hamouri F, Zhang W, Aujard I, Le Saux T, Ducos B, Vriz S, Jullien L, Bensimon D. Optical control of protein activity and gene expression by photoactivation of caged cyclofen. Methods Enzymol 2019; 624:1-23. [PMID: 31370925 DOI: 10.1016/bs.mie.2019.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of light to control the expression of genes and the activity of proteins is a rapidly expanding field. While many of these approaches use a fusion between a light activatable protein and the protein of interest to control the activity of the latter, it is also possible to control the activity of a protein by uncaging a specific ligand. In that context, controlling the activation of a protein fused to the modified estrogen receptor (ERT) by uncaging its ligand cyclofen-OH has emerged as a generic and versatile method to control the activation of proteins quantitatively, quickly and locally in a live organism. Here, we present the experimental details behind this approach.
Collapse
Affiliation(s)
- Fatima Hamouri
- Laboratoire de Physique de l'ENS, CNRS-UMR8023, PSL Research University, Paris, France; Institut de Biologie de l'ENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France
| | - Weiting Zhang
- Laboratoire de Physique de l'ENS, CNRS-UMR8023, PSL Research University, Paris, France; Institut de Biologie de l'ENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France
| | - Isabelle Aujard
- PASTEUR, Département de Chimie de l'ENS, CNRS, PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Thomas Le Saux
- PASTEUR, Département de Chimie de l'ENS, CNRS, PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique de l'ENS, CNRS-UMR8023, PSL Research University, Paris, France; Institut de Biologie de l'ENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, Paris, France; Department of Life Sciences, Paris-Diderot University, Sorbonne-Paris-Cité, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie de l'ENS, CNRS, PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - David Bensimon
- Laboratoire de Physique de l'ENS, CNRS-UMR8023, PSL Research University, Paris, France; Institut de Biologie de l'ENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France; Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, United States.
| |
Collapse
|
10
|
Hansen MJ, Hille JI, Szymanski W, Driessen AJ, Feringa BL. Easily Accessible, Highly Potent, Photocontrolled Modulators of Bacterial Communication. Chem 2019. [DOI: 10.1016/j.chempr.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
11
|
Collins SL, Saha J, Bouchez LC, Hammond EM, Conway SJ. Hypoxia-Activated, Small-Molecule-Induced Gene Expression. ACS Chem Biol 2018; 13:3354-3360. [PMID: 30451487 DOI: 10.1021/acschembio.8b00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hypoxia, a condition of reduced oxygen, occurs in a wide variety of biological contexts, including solid tumors and bacterial biofilms, which are relevant to human health. Consequently, the development of chemical tools to study hypoxia is vital. Here we report a hypoxia-activated, small-molecule-mediated gene expression system using a bioreductive prodrug of the inducer isopropyl 1-thio-β-d-galactopyranoside. As a proof-of-concept we have placed the production of a green fluorescent protein under the control of hypoxia. Our system has the potential to be extended to regulate the production of any given protein of choice.
Collapse
Affiliation(s)
- Sarah L Collins
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
- Cancer Research U.K./MRC Oxford Institute for Radiation Oncology, Department of Oncology , University of Oxford , Old Road Campus Research Building , Oxford OX3 7DQ , U.K
| | - Jaideep Saha
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| | - Laure C Bouchez
- Chemical Biology and Therapeutics , Novartis Institutes for BioMedical Research , Fabrikstrasse 22 , 4054 Basel , Switzerland
| | - Ester M Hammond
- Cancer Research U.K./MRC Oxford Institute for Radiation Oncology, Department of Oncology , University of Oxford , Old Road Campus Research Building , Oxford OX3 7DQ , U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| |
Collapse
|
12
|
Wang H, Li W, Zeng K, Wu Y, Zhang Y, Xu T, Chen Y. Photocatalysis Enables Visible‐Light Uncaging of Bioactive Molecules in Live Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haoyan Wang
- State Key Laboratory of Bioorganic and Natural Products ChemistryCentre of Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Wei‐Guang Li
- Centre for Brain Science and Department of Anatomy and PhysiologyShanghai Jiao Tong University School of Medicine 280 South Chongqing Road Shanghai 200025 China
| | - Kaixing Zeng
- State Key Laboratory of Bioorganic and Natural Products ChemistryCentre of Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and TechnologyShanghaiTech University 100 Haike Road Shanghai 201210 China
| | - Yan‐Jiao Wu
- Centre for Brain Science and Department of Anatomy and PhysiologyShanghai Jiao Tong University School of Medicine 280 South Chongqing Road Shanghai 200025 China
| | - Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products ChemistryCentre of Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Tian‐Le Xu
- Centre for Brain Science and Department of Anatomy and PhysiologyShanghai Jiao Tong University School of Medicine 280 South Chongqing Road Shanghai 200025 China
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products ChemistryCentre of Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and TechnologyShanghaiTech University 100 Haike Road Shanghai 201210 China
| |
Collapse
|
13
|
Wang H, Li WG, Zeng K, Wu YJ, Zhang Y, Xu TL, Chen Y. Photocatalysis Enables Visible-Light Uncaging of Bioactive Molecules in Live Cells. Angew Chem Int Ed Engl 2018; 58:561-565. [PMID: 30418695 DOI: 10.1002/anie.201811261] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/31/2018] [Indexed: 12/17/2022]
Abstract
The photo-manipulation of bioactive molecules provides unique advantages due to the high temporal and spatial precision of light. The first visible-light uncaging reaction by photocatalytic deboronative hydroxylation in live cells is now demonstrated. Using Fluorescein and Rhodamine derivatives as photocatalysts and ascorbates as reductants, transient hydrogen peroxides were generated from molecular oxygen to uncage phenol, alcohol, and amine functional groups on bioactive molecules in bacteria and mammalian cells, including neurons. This effective visible-light uncaging reaction enabled the light-inducible protein expression, the photo-manipulation of membrane potentials, and the subcellular-specific photo-release of small molecules.
Collapse
Affiliation(s)
- Haoyan Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wei-Guang Li
- Centre for Brain Science and Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Kaixing Zeng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,School of Physical Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Yan-Jiao Wu
- Centre for Brain Science and Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Tian-Le Xu
- Centre for Brain Science and Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,School of Physical Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| |
Collapse
|
14
|
Sankaran S, Zhao S, Muth C, Paez J, del Campo A. Toward Light-Regulated Living Biomaterials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800383. [PMID: 30128245 PMCID: PMC6097140 DOI: 10.1002/advs.201800383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/09/2018] [Indexed: 05/12/2023]
Abstract
Living materials are an emergent material class, infused with the productive, adaptive, and regenerative properties of living organisms. Property regulation in living materials requires encoding responsive units in the living components to allow external manipulation of their function. Here, an optoregulated Escherichia coli (E. coli)-based living biomaterial that can be externally addressed using light to interact with mammalian cells is demonstrated. This is achieved by using a photoactivatable inducer of gene expression and bacterial surface display technology to present an integrin-specific miniprotein on the outer membrane of an endotoxin-free E. coli strain. Hydrogel surfaces functionalized with the bacteria can expose cell adhesive molecules upon in situ light-activation, and trigger cell adhesion. Surface immobilized bacteria are able to deliver a fluorescent protein to the mammalian cells with which they are interacting, indicating the potential of such a bacterial material to deliver molecules to cells in a targeted manner.
Collapse
Affiliation(s)
| | - Shifang Zhao
- INM – Leibniz Institute for New MaterialsCampus D2 266123SaarbrückenGermany
- Chemistry DepartmentSaarland University66123SaarbrückenGermany
| | - Christina Muth
- INM – Leibniz Institute for New MaterialsCampus D2 266123SaarbrückenGermany
| | - Julieta Paez
- INM – Leibniz Institute for New MaterialsCampus D2 266123SaarbrückenGermany
| | - Aránzazu del Campo
- INM – Leibniz Institute for New MaterialsCampus D2 266123SaarbrückenGermany
- Chemistry DepartmentSaarland University66123SaarbrückenGermany
| |
Collapse
|
15
|
Hughes RM. A compendium of chemical and genetic approaches to light-regulated gene transcription. Crit Rev Biochem Mol Biol 2018; 53:453-474. [PMID: 30040498 DOI: 10.1080/10409238.2018.1487382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
On-cue regulation of gene transcription is an invaluable tool for the study of biological processes and the development and integration of next-generation therapeutics. Ideal reagents for the precise regulation of gene transcription should be nontoxic to the host system, highly tunable, and provide a high level of spatial and temporal control. Light, when coupled with protein or small molecule-linked photoresponsive elements, presents an attractive means of meeting the demands of an ideal system for regulating gene transcription. In this review, we cover recent developments in the burgeoning field of light-regulated gene transcription, covering both genetically encoded and small-molecule based strategies for optical regulation of transcription during the period 2012 till present.
Collapse
Affiliation(s)
- Robert M Hughes
- a Department of Chemistry , East Carolina University , Greenville , NC , USA
| |
Collapse
|
16
|
Pérez-García F, Wendisch VF. Transport and metabolic engineering of the cell factory Corynebacterium glutamicum. FEMS Microbiol Lett 2018; 365:5047308. [DOI: 10.1093/femsle/fny166] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/28/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Fernando Pérez-García
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstr. 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstr. 25, 33615, Bielefeld, Germany
| |
Collapse
|
17
|
Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A. Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Cabrera R, Filevich O, García-Acosta B, Athilingam J, Bender KJ, Poskanzer KE, Etchenique R. A Visible-Light-Sensitive Caged Serotonin. ACS Chem Neurosci 2017; 8:1036-1042. [PMID: 28460173 DOI: 10.1021/acschemneuro.7b00083] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Serotonin, or 5-hydroxytryptamine (5HT), is an important neurotransmitter in the nervous system of both vertebrates and invertebrates. Deficits in 5HT signaling are responsible for many disabling psychiatric conditions, and its molecular machinery is the target of many pharmaceuticals. We present a new 5HT phototrigger, the compound [Ru(bpy)2(PMe3)(5HT)]2+, where PMe3 is trimethylphosphine. As with other ruthenium-bipyridyl based caged compounds, [Ru(bpy)2(PMe3)(5HT)]2+ presents activity in the visible region of the spectrum. We characterize and discuss the photochemical properties of the caged compound, and demonstrate its use by modulating the excitability of mouse prefrontal principal neurons.
Collapse
Affiliation(s)
- Ricardo Cabrera
- Departamento de
Química Inorgánica,
Analítica y Química Física, INQUIMAE, Facultad
de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Ciudad Universitaria Pabellón 2, AR1428EHA Buenos Aires, Argentina
- Ciclo
Básico Común, Universidad de Buenos Aires, 1053 Buenos Aires, Argentina
| | - Oscar Filevich
- Laboratorio de Neurobiología
Molecular, BIOMED, Pontificia Universidad Católica Argentina,
CONICET, C1107AFB Buenos Aires, Argentina
| | - Beatriz García-Acosta
- Departamento de
Química Inorgánica,
Analítica y Química Física, INQUIMAE, Facultad
de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Ciudad Universitaria Pabellón 2, AR1428EHA Buenos Aires, Argentina
| | - Jegath Athilingam
- Kavli
Institute for Fundamental Neuroscience, UCSF Weill Institute for Neuroscience, San Francisco, California, United States
- Department
of Neurology, University of California, San Francisco, San Francisco, California 94143, United States
| | - Kevin J. Bender
- Kavli
Institute for Fundamental Neuroscience, UCSF Weill Institute for Neuroscience, San Francisco, California, United States
- Department
of Neurology, University of California, San Francisco, San Francisco, California 94143, United States
| | - Kira E. Poskanzer
- Kavli
Institute for Fundamental Neuroscience, UCSF Weill Institute for Neuroscience, San Francisco, California, United States
- Department
of Biochemistry and Biophysics, University of California, San Francisco, San
Francisco, California 94143, United States
| | - Roberto Etchenique
- Departamento de
Química Inorgánica,
Analítica y Química Física, INQUIMAE, Facultad
de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Ciudad Universitaria Pabellón 2, AR1428EHA Buenos Aires, Argentina
| |
Collapse
|
19
|
Light-controlled gene expression in yeast using photocaged Cu 2. J Biotechnol 2017; 258:117-125. [PMID: 28455204 DOI: 10.1016/j.jbiotec.2017.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/21/2022]
Abstract
The manipulation of cellular function, such as the regulation of gene expression, is of great interest to many biotechnological applications and often achieved by the addition of small effector molecules. By combining effector molecules with photolabile protecting groups that mask their biological activity until they are activated by light, precise, yet minimally invasive, photocontrol is enabled. However, applications of this trendsetting technology are limited by the small number of established caged compound-based expression systems. Supported by computational chemistry, we used the versatile photolabile chelator DMNP-EDTA, long-established in neurobiology for photolytic Ca2+ release, to control Cu2+ release upon specific UV-A irradiation. This permits light-mediated control over the widely used Cu2+-inducible pCUP1 promoter from S. cerevisiae and thus constitutes the first example of a caged metal ion to regulate recombinant gene expression. We screened our novel DMNP-EDTA-Cu system for best induction time and expression level of eYFP with a high-throughput online monitoring system equipped with an LED array for individual illumination of every single well. Thereby, we realized a minimally invasive, easy-to-control, parallel and automated optical expression regulation via caged Cu2+ allowing temporal and quantitative control as a beneficial alternative to conventional induction via pipetting CuCl2 as effector molecule.
Collapse
|
20
|
Wang P. Developing photolabile protecting groups based on the excited state meta effect. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.11.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
21
|
Kusen PM, Wandrey G, Probst C, Grünberger A, Holz M, Meyer zu Berstenhorst S, Kohlheyer D, Büchs J, Pietruszka J. Optogenetic Regulation of Tunable Gene Expression in Yeast Using Photo-Labile Caged Methionine. ACS Chem Biol 2016; 11:2915-2922. [PMID: 27570879 DOI: 10.1021/acschembio.6b00462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Light-mediated gene expression enables the noninvasive regulation of cellular functions. Apart from their classical application of regulating single cells with high spatiotemporal resolution, we highlight the potential of light-mediated gene expression for biotechnological issues. Here, we demonstrate the first light-mediated gene regulation in Saccharomyces cerevisiae using the repressible pMET17 promoter and the photolabile NVOC methionine that releases methionine upon irradiation with UVA light. In this system, the expression can be repressed upon irradiation and is reactivated due to consumption of methionine. The photolytic release allows precise control over the methionine concentration and therefore over the repression duration. Using this light regulation mechanism, we were able to apply an in-house constructed 48-well cultivation system which allows parallelized and automated irradiation programs as well as online detection of fluorescence and growth. This system enables screening of multiple combinations of several repression/derepression intervals to realize complex expression programs (e.g., a stepwise increase of temporally constant expression levels, linear expression rates with variable slopes, and accurate control over the expression induction, although we used a repressible promoter.) Thus, we were able to control all general parameters of a gene expression experiment precisely, namely start, pause, and stop at desired time points, as well as the ongoing expression rate. Furthermore, we gained detailed insights into single-cell expression dynamics with spatiotemporal resolution by applying microfluidics cultivation technology combined with fluorescence time-lapse microscopy.
Collapse
Affiliation(s)
- Peter M. Kusen
- Institute
for Bioorganic Chemistry, Heinrich Heine University Düsseldorf at the Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Georg Wandrey
- AVT
− Biochemical Engineering, RWTH Aachen University, Worringer
Weg 1, 52074 Aachen, Germany
| | - Christopher Probst
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426 Jülich, Germany
| | - Alexander Grünberger
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426 Jülich, Germany
| | - Martina Holz
- Institute
for Bioorganic Chemistry, Heinrich Heine University Düsseldorf at the Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Sonja Meyer zu Berstenhorst
- Institute
for Bioorganic Chemistry, Heinrich Heine University Düsseldorf at the Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Dietrich Kohlheyer
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426 Jülich, Germany
| | - Jochen Büchs
- AVT
− Biochemical Engineering, RWTH Aachen University, Worringer
Weg 1, 52074 Aachen, Germany
| | - Jörg Pietruszka
- Institute
for Bioorganic Chemistry, Heinrich Heine University Düsseldorf at the Forschungszentrum Jülich, 52426 Jülich, Germany
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52426 Jülich, Germany
| |
Collapse
|
22
|
Padilla MS, Farley CA, Chatkewitz LE, Young DD. Synthesis and incorporation of a caged tyrosine amino acid possessing a bioorthogonal handle. Tetrahedron Lett 2016; 57:4709-4712. [PMID: 28533567 PMCID: PMC5438197 DOI: 10.1016/j.tetlet.2016.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy-ortho-nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary.
Collapse
Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christopher A Farley
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Lindsay E Chatkewitz
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| |
Collapse
|
23
|
Ding X, Devalankar DA, Wang P. Structurally Simple Benzylidene-Type Photolabile Diol Protecting Groups. Org Lett 2016; 18:5396-5399. [DOI: 10.1021/acs.orglett.6b02777] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiong Ding
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Dattatray A. Devalankar
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Pengfei Wang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| |
Collapse
|
24
|
Light-Controlled Cell Factories: Employing Photocaged Isopropyl-β-d-Thiogalactopyranoside for Light-Mediated Optimization of lac Promoter-Based Gene Expression and (+)-Valencene Biosynthesis in Corynebacterium glutamicum. Appl Environ Microbiol 2016; 82:6141-6149. [PMID: 27520809 DOI: 10.1128/aem.01457-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/28/2016] [Indexed: 11/20/2022] Open
Abstract
Precise control of microbial gene expression resulting in a defined, fast, and homogeneous response is of utmost importance for synthetic bio(techno)logical applications. However, even broadly applied biotechnological workhorses, such as Corynebacterium glutamicum, for which induction of recombinant gene expression commonly relies on the addition of appropriate inducer molecules, perform moderately in this respect. Light offers an alternative to accurately control gene expression, as it allows for simple triggering in a noninvasive fashion with unprecedented spatiotemporal resolution. Thus, optogenetic switches are promising tools to improve the controllability of existing gene expression systems. In this regard, photocaged inducers, whose activities are initially inhibited by light-removable protection groups, represent one of the most valuable photoswitches for microbial gene expression. Here, we report on the evaluation of photocaged isopropyl-β-d-thiogalactopyranoside (IPTG) as a light-responsive control element for the frequently applied tac-based expression module in C. glutamicum In contrast to conventional IPTG, the photocaged inducer mediates a tightly controlled, strong, and homogeneous expression response upon short exposure to UV-A light. To further demonstrate the unique potential of photocaged IPTG for the optimization of production processes in C. glutamicum, the optogenetic switch was finally used to improve biosynthesis of the growth-inhibiting sesquiterpene (+)-valencene, a flavoring agent and aroma compound precursor in food industry. The variation in light intensity as well as the time point of light induction proved crucial for efficient production of this toxic compound. IMPORTANCE Optogenetic tools are light-responsive modules that allow for a simple triggering of cellular functions with unprecedented spatiotemporal resolution and in a noninvasive fashion. Specifically, light-controlled gene expression exhibits an enormous potential for various synthetic bio(techno)logical purposes. Before our study, poor inducibility, together with phenotypic heterogeneity, was reported for the IPTG-mediated induction of lac-based gene expression in Corynebacterium glutamicum By applying photocaged IPTG as a synthetic inducer, however, these drawbacks could be almost completely abolished. Especially for increasing numbers of parallelized expression cultures, noninvasive and spatiotemporal light induction qualifies for a precise, homogeneous, and thus higher-order control to fully automatize or optimize future biotechnological applications.
Collapse
|
25
|
Wandrey G, Bier C, Binder D, Hoffmann K, Jaeger KE, Pietruszka J, Drepper T, Büchs J. Light-induced gene expression with photocaged IPTG for induction profiling in a high-throughput screening system. Microb Cell Fact 2016; 15:63. [PMID: 27107964 PMCID: PMC4842301 DOI: 10.1186/s12934-016-0461-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inducible expression systems are frequently used for the production of heterologous proteins. Achieving maximum product concentrations requires induction profiling, namely the optimization of induction time and inducer concentration. However, the respective experiments can be very laborious and time-consuming. In this work, a new approach for induction profiling is presented where induction in a microtiter plate based cultivation system (BioLector) is achieved by light using photocaged isopropyl β-D-1-thiogalactopyranoside (cIPTG). RESULTS A flavin mononucleotide-based fluorescent reporter protein (FbFP) was expressed using a T7-RNA-polymerase dependent E. coli expression system which required IPTG as inducer. High power UV-A irradiation was directed into a microtiter plate by light-emitting diodes placed above each well of a 48-well plate. Upon UV irradiation, IPTG is released (uncaged) and induces product formation. IPTG uncaging, formation of the fluorescent reporter protein and biomass growth were monitored simultaneously in up to four 48-well microtiter plates in parallel with an in-house constructed BioLector screening system. The amount of released IPTG can be gradually and individually controlled for each well by duration of UV-A exposure, irradiance and concentration of photocaged IPTG added at the start of the cultivation. A comparison of experiments with either optical or conventional IPTG induction shows that product formation and growth are equivalent. Detailed induction profiles revealed that for the strain and conditions used maximum product formation is reached for very early induction times and with just 6-8 s of UV-A irradiation or 60-80 µM IPTG. CONCLUSIONS Optical induction and online monitoring were successfully combined in a high-throughput screening system and the effect of optical induction with photocaged IPTG was shown to be equivalent to conventional induction with IPTG. In contrast to conventional induction, optical induction is less costly to parallelize, easy to automate, non-invasive and without risk of contamination. Therefore, light-induced gene expression with photocaged IPTG is a highly advantageous method for the efficient optimization of heterologous protein production and has the potential to replace conventional induction with IPTG.
Collapse
Affiliation(s)
- Georg Wandrey
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Kyra Hoffmann
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany.,Institut für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany.,Institut für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany.
| |
Collapse
|
26
|
Wang X, Feng M, Xiao L, Tong A, Xiang Y. Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme. ACS Chem Biol 2016; 11:444-51. [PMID: 26669486 DOI: 10.1021/acschembio.5b00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.
Collapse
Affiliation(s)
- Xiaoyan Wang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Mengli Feng
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| |
Collapse
|
27
|
Binder D, Bier C, Grünberger A, Drobietz D, Hage-Hülsmann J, Wandrey G, Büchs J, Kohlheyer D, Loeschcke A, Wiechert W, Jaeger KE, Pietruszka J, Drepper T. Photocaged Arabinose: A Novel Optogenetic Switch for Rapid and Gradual Control of Microbial Gene Expression. Chembiochem 2016; 17:296-9. [DOI: 10.1002/cbic.201500609] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Dennis Binder
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Dagmar Drobietz
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Georg Wandrey
- AVT-Biochemical Engineering; RWTH Aachen University; Worringer Weg 1 52074 Aachen Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering; RWTH Aachen University; Worringer Weg 1 52074 Aachen Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| |
Collapse
|
28
|
Brown KA, Zou Y, Shirvanyants D, Zhang J, Samanta S, Mantravadi PK, Dokholyan NV, Deiters A. Light-cleavable rapamycin dimer as an optical trigger for protein dimerization. Chem Commun (Camb) 2015; 51:5702-5. [DOI: 10.1039/c4cc09442e] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein heterodimerization of FKBP12 and FRB can be optically controlled with a photocleavable rapamycin dimer.
Collapse
Affiliation(s)
- Kalyn A. Brown
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
| | - Yan Zou
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - David Shirvanyants
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Jie Zhang
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Subhas Samanta
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| | | | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Alexander Deiters
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
| |
Collapse
|
29
|
Binder D, Grünberger A, Loeschcke A, Probst C, Bier C, Pietruszka J, Wiechert W, Kohlheyer D, Jaeger KE, Drepper T. Light-responsive control of bacterial gene expression: precise triggering of thelacpromoter activity using photocaged IPTG. Integr Biol (Camb) 2014; 6:755-65. [DOI: 10.1039/c4ib00027g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An optogenetic tool was established allowing for precise, gradual and homogeneous light-triggering oflac-based gene expression in a non-invasive fashion.
Collapse
|
30
|
Basu S, Sachidanandan C. Zebrafish: a multifaceted tool for chemical biologists. Chem Rev 2013; 113:7952-80. [PMID: 23819893 DOI: 10.1021/cr4000013] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sandeep Basu
- Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology (CSIR-IGIB) , South Campus, New Delhi 110025, India
| | | |
Collapse
|
31
|
Lee JM, Lee J, Kim T, Lee SK. Switchable gene expression in Escherichia coli using a miniaturized photobioreactor. PLoS One 2013; 8:e52382. [PMID: 23349683 PMCID: PMC3547951 DOI: 10.1371/journal.pone.0052382] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/12/2012] [Indexed: 12/22/2022] Open
Abstract
We present a light-switchable gene expression system for both inducible and switchable control of gene expression at a single cell level in Escherichia coli using a previously constructed light-sensing system. The λ cI repressor gene with an LVA degradation tag was expressed under the control of the ompC promoter on the chromosome. The green fluorescent protein (GFP) gene fused to a λ repressor-repressible promoter was used as a reporter. This light-switchable system allows rapid and reversible induction or repression of expression of the target gene at any desired time. This system also ensures homogenous expression across the entire cell population. We also report the design of a miniaturized photobioreactor to be used in combination with the light-switchable gene expression system. The miniaturized photobioreactor helps to reduce unintended induction of the light receptor due to environmental disturbances and allows precise control over the duration of induction. This system would be a good tool for switchable, homogenous, strong, and highly regulatable expression of target genes over a wide range of induction times. Hence, it could be applied to study gene function, optimize metabolic pathways, and control biological systems both spatially and temporally.
Collapse
Affiliation(s)
- Jae Myung Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Junhyeong Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Taesung Kim
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Mechanical and Advanced Materials Engineering, UNIST, Ulsan, Republic of Korea
- * E-mail: (SKL); (TK)
| | - Sung Kuk Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Urban and Environmental Engineering, UNIST, Ulsan, Republic of Korea
- * E-mail: (SKL); (TK)
| |
Collapse
|
32
|
Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1229] [Impact Index Per Article: 111.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Wang Y, Wu L, Wang P, Lv C, Yang Z, Tang X. Manipulation of gene expression in zebrafish using caged circular morpholino oligomers. Nucleic Acids Res 2012; 40:11155-62. [PMID: 23002141 PMCID: PMC3505977 DOI: 10.1093/nar/gks840] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Morpholino oligomers (MOs) have been widely used to knock down specific genes in zebrafish, but their constitutive activities limit their experimental applications for studying a gene with multiple functions or within a gene network. We report herein a new design and synthesis of caged circular MOs (caged cMOs) with two ends linked by a photocleavable moiety. These caged cMOs were successfully used to photomodulate β-catenin-2 and no tail expression in zebrafish embryos.
Collapse
Affiliation(s)
- Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing 100191, China
| | | | | | | | | | | |
Collapse
|
34
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 734] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
Collapse
Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | | | | | | | | |
Collapse
|
35
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| |
Collapse
|
36
|
Gardner L, Deiters A. Light-controlled synthetic gene circuits. Curr Opin Chem Biol 2012; 16:292-9. [PMID: 22633822 DOI: 10.1016/j.cbpa.2012.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 04/10/2012] [Accepted: 04/15/2012] [Indexed: 01/09/2023]
Abstract
Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.
Collapse
Affiliation(s)
- Laura Gardner
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, United States
| | | |
Collapse
|
37
|
Abate-Pella D, Zeliadt NA, Ochocki JD, Warmka JK, Dore TM, Blank DA, Wattenberg EV, Distefano MD. Photochemical modulation of Ras-mediated signal transduction using caged farnesyltransferase inhibitors: activation by one- and two-photon excitation. Chembiochem 2012; 13:1009-16. [PMID: 22492666 PMCID: PMC3436068 DOI: 10.1002/cbic.201200063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Indexed: 01/04/2023]
Abstract
The creation of caged molecules involves the attachment of protecting groups to biologically active compounds such as ligands, substrates and drugs that can be removed under specific conditions. Photoremovable caging groups are the most common due to their ability to be removed with high spatial and temporal resolution. Here, the synthesis and photochemistry of a caged inhibitor of protein farnesyltransferase is described. The inhibitor, FTI, was caged by alkylation of a critical thiol group with a bromohydroxycoumarin (Bhc) moiety. While Bhc is well established as a protecting group for carboxylates and phosphates, it has not been extensively used to cage sulfhydryl groups. The resulting caged molecule, Bhc-FTI, can be photolyzed with UV light to release the inhibitor that prevents Ras farnesylation, Ras membrane localization and downstream signaling. Finally, it is shown that Bhc-FTI can be uncaged by two-photon excitation to produce FTI at levels sufficient to inhibit Ras localization and alter cell morphology. Given the widespread involvement of Ras proteins in signal transduction pathways, this caged inhibitor should be useful in a plethora of studies.
Collapse
Affiliation(s)
- Daniel Abate-Pella
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Nicholette A. Zeliadt
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Joshua D. Ochocki
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Janel K. Warmka
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Timothy M. Dore
- Department of Chemistry, University of Georgia, Athens, GA 30602 (USA)
| | - David A. Blank
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Elizabeth V. Wattenberg
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Mark D. Distefano
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| |
Collapse
|
38
|
Yang H, Zhou L, Wang P. Development of hydrophilic photolabile hydroxyl protecting groups. Photochem Photobiol Sci 2012; 11:514-7. [DOI: 10.1039/c1pp05281k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Gardner L, Zou Y, Mara A, Cropp TA, Deiters A. Photochemical control of bacterial signal processing using a light-activated erythromycin. MOLECULAR BIOSYSTEMS 2011; 7:2554-7. [PMID: 21785768 DOI: 10.1039/c1mb05166k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial cells control resistance to the macrolide antibiotic erythromycin using the MphR(A) repressor protein. Erythromycin binds to MphR(A), causing release of the PmphR promoter, activating expression of the 2'-phosphotransferase Mph(A). We engineered the MphR(A)/promoter system to, in conjunction with a light-activatable derivative of erythromycin, enable photochemical activation of gene expression in E. coli. We applied this photochemical gene switch to the construction of a light-triggered logic gate, a light-controlled band-pass filter, as well as spatial and temporal control of gene expression.
Collapse
Affiliation(s)
- Laura Gardner
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | |
Collapse
|
40
|
Zhou L, Yang H, Wang P. Development of Trityl-Based Photolabile Hydroxyl Protecting Groups. J Org Chem 2011; 76:5873-81. [DOI: 10.1021/jo200692c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lei Zhou
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| | - Haishen Yang
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| | - Pengfei Wang
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| |
Collapse
|
41
|
Yang H, Zhang X, Zhou L, Wang P. Development of a Photolabile Carbonyl-Protecting Group Toolbox. J Org Chem 2011; 76:2040-8. [DOI: 10.1021/jo102429g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Haishen Yang
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| | - Xin Zhang
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| | - Lei Zhou
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| | - Pengfei Wang
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United States
| |
Collapse
|
42
|
Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J, Jaeger KE. Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 2011; 90:23-40. [PMID: 21336931 DOI: 10.1007/s00253-011-3141-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 01/10/2023]
Abstract
Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.
Collapse
Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.
| | | | | | | | | |
Collapse
|
43
|
Karginov AV, Zou Y, Shirvanyants D, Kota P, Dokholyan NV, Young DD, Hahn KM, Deiters A. Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc 2010; 133:420-3. [PMID: 21162531 DOI: 10.1021/ja109630v] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We developed a new system for light-induced protein dimerization in living cells using a photocaged analogue of rapamycin together with an engineered rapamycin binding domain. Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo.
Collapse
Affiliation(s)
- Andrei V Karginov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Yuan L, Lin W, Cao Z, Long L, Song J. Photocontrollable Analyte‐Responsive Fluorescent Probes: A Photocaged Copper‐Responsive Fluorescence Turn‐On Probe. Chemistry 2010; 17:689-96. [DOI: 10.1002/chem.201001923] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082 (P. R. China), Fax: (+86) 731‐888‐21464
| | - Weiying Lin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082 (P. R. China), Fax: (+86) 731‐888‐21464
| | - Zengmei Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082 (P. R. China), Fax: (+86) 731‐888‐21464
| | - Lingliang Long
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082 (P. R. China), Fax: (+86) 731‐888‐21464
| | - Jizeng Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082 (P. R. China), Fax: (+86) 731‐888‐21464
| |
Collapse
|
45
|
Riggsbee CW, Deiters A. Recent advances in the photochemical control of protein function. Trends Biotechnol 2010; 28:468-75. [PMID: 20667607 DOI: 10.1016/j.tibtech.2010.06.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/21/2010] [Accepted: 06/01/2010] [Indexed: 12/20/2022]
Abstract
Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.
Collapse
Affiliation(s)
- Chad W Riggsbee
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
| | | |
Collapse
|
46
|
Chou C, Young DD, Deiters A. Photocaged t7 RNA polymerase for the light activation of transcription and gene function in pro- and eukaryotic cells. Chembiochem 2010; 11:972-7. [PMID: 20301166 DOI: 10.1002/cbic.201000041] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A light-activatable bacteriophage T7 RNA polymerase (T7RNAP) has been generated through the site-specific introduction of a photocaged tyrosine residue at the crucial position Tyr639 within the active site of the enzyme. The photocaged tyrosine disrupts polymerase activity by blocking the incoming nucleotide from reaching the active site of the enzyme. However, a brief irradiation with nonphototoxic UV light of 365 nm removes the ortho-nitrobenzyl caging group from Tyr639 and restores the RNA polymerase activity of T7RNAP. The complete orthogonality of T7RNAP to all endogenous RNA polymerases in pro- and eukaryotic systems allowed for the photochemical activation of gene expression in bacterial and mammalian cells. Specifically, E. coli cells were engineered to produce photocaged T7RNAP in the presence of a GFP reporter gene under the control of a T7 promoter. UV irradiation of these cells led to the spatiotemporal activation of GFP expression. In an analogous fashion, caged T7RNAP was transfected into human embryonic kidney (HEK293T) cells. Irradiation with UV light led to the activation of T7RNAP, thereby inducing RNA polymerization and expression of a luciferase reporter gene in tissue culture. The ability to achieve spatiotemporal regulation of orthogonal RNA synthesis enables the precise dissection and manipulation of a wide range of cellular events, including gene function.
Collapse
Affiliation(s)
- Chungjung Chou
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | | |
Collapse
|
47
|
Sauers DJ, Temburni MK, Biggins JB, Ceo LM, Galileo DS, Koh JT. Light-activated gene expression directs segregation of co-cultured cells in vitro. ACS Chem Biol 2010; 5:313-20. [PMID: 20050613 DOI: 10.1021/cb9002305] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-directed gene patterning methods have been described as a means to regulate gene expression in a spatially and temporally controlled manner. Several methods have been reported that use photocaged forms of small molecule effectors to control ligand-dependent transcription factors. Whereas these methods offer many advantages including high specificity and transient light-sensitivity, the free diffusion of the uncaged effector can limit both the magnitude and resolution of localized gene induction. Methods to date have been limited by the small fraction of irradiated cells that have expression levels significantly above uninduced background and have not been shown to affect a defined biological response. The tetracycline-dependent transactivator/transrepressor system, RetroTET-ART, combined with a photocaged form of doxycycline (NvOC-Dox) can be used to form photolithographic patterns of induced expression wherein up to 85% of the patterned cells show expression levels above uninduced regions. The efficiency and inducibility of the RetroTET-ART system allows one to quantitatively measure the limits of resolution and the relative induction levels mediated by a small molecule photocaged effector for the first time. Well-defined patterns of reporter genes were reproducibly formed within 6-36 h with feature sizes as small as 300 microm. After photo-patterning, NvOC-Dox can be rapidly removed, rendering cells photoinsensitive and allowing one to monitor GFP product formation in real time. Patterned co-expression of the cell surface ligand ephrin A5 on cell monolayers creates well-defined patterns that are sufficient to direct and segregate co-cultured cells via either attractive or repulsive signaling cues. The ability to direct the arrangement of cells on living cell monolayers through the action of light may serve as a model system for engineering artificial tissues.
Collapse
Affiliation(s)
- Daniel J. Sauers
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Murali K. Temburni
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - John B. Biggins
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Luke M. Ceo
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Deni S. Galileo
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - John T. Koh
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| |
Collapse
|
48
|
Richards JL, Seward GK, Wang YH, Dmochowski IJ. Turning the 10-23 DNAzyme on and off with light. Chembiochem 2010; 11:320-4. [PMID: 20077457 PMCID: PMC2908382 DOI: 10.1002/cbic.200900702] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Indexed: 11/10/2022]
Affiliation(s)
- Julia L. Richards
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Garry K. Seward
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Yu-Hsiu Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| |
Collapse
|
49
|
Sebej P, Solomek T, Hroudná L, Brancová P, Klán P. Photochemistry of 2-nitrobenzylidene acetals. J Org Chem 2010; 74:8647-58. [PMID: 19824651 DOI: 10.1021/jo901756r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Photolysis of dihydroxy compounds (diols) protected as 2-nitrobenzylidene acetals (ONBA) and subsequent acid- or base-catalyzed hydrolysis of the 2-nitrosobenzoic acid ester intermediates result in an efficient and high-yielding release of the substrates. We investigated the scope and limitations of ONBA photochemistry and expanded upon earlier described two-step procedures to show that the protected diols of many structural varieties can also be liberated in a one-pot procedure. In view of the fact that the acetals of nonsymmetrically substituted diols are converted into one of the corresponding 2-nitrosobenzoic acid ester isomers with moderate to high regioselectivity, the mechanism of their formation was studied using various experimental techniques. The experimental data were found to be in agreement with DFT-based quantum chemical calculations that showed the preferential cleavage occurs on the acetal C-O bond in the vicinity of more electron-withdrawing (or less electron-donating) groups. The study also revealed considerable complexity in the cleavage mechanism and that the structural variations in the substrate can significantly alter the reaction pathway. This deprotection strategy was found to be also applicable for 2-thioethanol when released from the corresponding monothioacetal in the presence of a reducing agent, such as ascorbic acid.
Collapse
Affiliation(s)
- Peter Sebej
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5/A8, 625 00 Brno, Czech Republic
| | | | | | | | | |
Collapse
|
50
|
Wang P, Zhou L, Zhang X, Liang X. Facilitated photochemical cleavage of benzylic C–O bond. Application to photolabile hydroxyl-protecting group design. Chem Commun (Camb) 2010; 46:1514-6. [DOI: 10.1039/b922021f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|