1
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Dong F, Lojko P, Bazzone A, Bernhard F, Borodina I. Transporter function characterization via continuous-exchange cell-free synthesis and solid supported membrane-based electrophysiology. Bioelectrochemistry 2024; 159:108732. [PMID: 38810322 DOI: 10.1016/j.bioelechem.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Functional characterization of transporters is impeded by the high cost and technical challenges of current transporter assays. Thus, in this work, we developed a new characterization workflow that combines cell-free protein synthesis (CFPS) and solid supported membrane-based electrophysiology (SSME). For this, membrane protein synthesis was accomplished in a continuous exchange cell-free system (CECF) in the presence of nanodiscs. The resulting transporters expressed in nanodiscs were incorporated into proteoliposomes and assayed in the presence of different substrates using the surface electrogenic event reader. As a proof of concept, we validated this workflow to express and characterize five diverse transporters: the drug/H+-coupled antiporters EmrE and SugE, the lactose permease LacY, the Na+/H+ antiporter NhaA from Escherichia coli, and the mitochondrial carrier AAC2 from Saccharomyces cerevisiae. For all transporters kinetic parameters, such as KM, IMAX, and pH dependency, were evaluated. This robust and expedite workflow (e.g., can be executed within only five workdays) offers a convenient direct functional assessment of transporter protein activity and has the ability to facilitate applications of transporters in medical and biotechnological research.
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Affiliation(s)
- Fang Dong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Pawel Lojko
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | | | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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2
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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3
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Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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4
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Hui CY, Ma BC, Hu SY, Wu C. Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:123016. [PMID: 38008253 DOI: 10.1016/j.envpol.2023.123016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Shun-Yu Hu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Can Wu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
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5
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Jensen GC, Janis MK, Jara J, Abbasi N, Zastrow ML. Zinc-Induced Fluorescence Turn-On in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins. Biochemistry 2023; 62:2828-2840. [PMID: 37699411 PMCID: PMC11057272 DOI: 10.1021/acs.biochem.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to the near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 (All1280g2) from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue-light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. All1280g2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent All1280g2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here, we show that All1280g2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with a blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn2+ significantly enhances All1280g2-PEB fluorescence across a biologically relevant pH range from 6.0 to 9.0, with pH-dependent dissociation constants from 1 μM to ∼20-80 nM. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement. Mutation of the cysteine residue within the DXCF motif to alanine abolishes the zinc-induced fluorescence enhancement. Collectively, these results support the presence of a unique fluorescence-enhancing Zn2+ binding site in All1280g2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Jazzmin Jara
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Nasir Abbasi
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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6
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Jensen GC, Janis MK, Jara J, Abbasi N, Zastrow ML. Zinc-Induced Fluorescence Turn-on in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552977. [PMID: 37609204 PMCID: PMC10441388 DOI: 10.1101/2023.08.11.552977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. GAF2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that, unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent GAF2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here we show that GAF2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn 2+ significantly enhances GAF2-PEB fluorescence across a biologically relevant pH range from 6.0-9.0 and with pH-dependent µM to nM dissociation constants. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement, respectively. Mutation of the cysteine residue within the DXCF motif to alanine abolishes zinc-induced fluorescence enhancement. Collectively, these results support the presence of a fluorescence enhancing Zn 2+ binding site in GAF2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.
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Affiliation(s)
- Gary C. Jensen
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Makena K. Janis
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Jazzmin Jara
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Nasir Abbasi
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Melissa L. Zastrow
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
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7
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Mamontova AV, Simonyan TR, Bogdanov AM. Prospects of Genetically Encoded Flim Indicators for the Quantitative Assessment of Intracellular Parameters. Mol Biol 2022. [DOI: 10.1134/s0026893322050090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Zou W, Nguyen HN, Zastrow ML. Mutant Flavin-Based Fluorescent Protein Sensors for Detecting Intracellular Zinc and Copper in Escherichia coli. ACS Sens 2022; 7:3369-3378. [PMID: 36282086 PMCID: PMC9888404 DOI: 10.1021/acssensors.2c01376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs) are a class of fluorescent reporters that undergo oxygen-independent fluorophore incorporation, which is an important advantage over green fluorescent proteins (GFPs) and mFruits. A FbFP derived from Chlamydomonas reinhardtii (CreiLOV) is a promising platform for designing new metal sensors. Some FbFPs are intrinsically quenched by metal ions, but the question of where metals bind and how to tune metal affinity has not been addressed. We used site-directed mutagenesis of CreiLOV to probe a hypothesized copper(II) binding site that led to fluorescence quenching. Most mutations changed the fluorescence quenching level, supporting the proposed site. One key mutation introducing a second cysteine residue in place of asparagine (CreiLOVN41C) significantly altered metal affinity and selectivity, yielding a zinc sensor. The fluorescence intensity and lifetime of CreiLOVN41C were reversibly quenched by Zn2+ ions with a biologically relevant affinity (apparent dissociation constant, Kd, of 1 nM). Copper quenching of CreiLOVN41C was retained but with several orders of magnitude higher affinity than CreiLOV (Kd = 0.066 fM for Cu2+, 5.4 fM for Cu+) and partial reversibility. We also show that CreiLOVN41C is an excellent intensity- and lifetime-based zinc sensor in aerobic and anaerobic live bacterial cells. Zn2+-induced fluorescence quenching is reversible over several cycles in Escherichia coli cell suspensions and can be imaged by fluorescence microscopy. CreiLOVN41C is a novel oxygen-independent metal sensor that significantly expands the current fluorescent protein-based toolbox of metal sensors and will allow for studies of anaerobic and low oxygen systems previously precluded by the use of oxygen-dependent GFPs.
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Affiliation(s)
- Wenping Zou
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N. Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L. Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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9
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Brennan CK, Yao Z, Ionkina AA, Rathbun CM, Sathishkumar B, Prescher JA. Multiplexed bioluminescence imaging with a substrate unmixing platform. Cell Chem Biol 2022; 29:1649-1660.e4. [PMID: 36283402 PMCID: PMC9675729 DOI: 10.1016/j.chembiol.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Bioluminescent tools can illuminate cellular features in whole organisms. Multi-component tracking remains challenging, though, owing to a lack of well-resolved probes and long imaging times. To address the need for more rapid, quantitative, and multiplexed bioluminescent readouts, we developed an analysis pipeline featuring sequential substrate administration and serial image acquisition. Light output from each luciferin is layered on top of the previous image, with minimal delay between substrate delivery. A MATLAB algorithm was written to analyze bioluminescent images generated from the rapid imaging protocol and deconvolute (i.e., unmix) signals from luciferase-luciferin pairs. Mixtures comprising three to five luciferase reporters were readily distinguished in under 50 min; this same experiment would require days using conventional workflows. We further showed that the algorithm can be used to accurately quantify luciferase levels in heterogeneous mixtures. Based on its speed and versatility, the multiplexed imaging platform will expand the scope of bioluminescence technology.
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Affiliation(s)
- Caroline K Brennan
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Zi Yao
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Anastasia A Ionkina
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Colin M Rathbun
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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10
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Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
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Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
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11
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Hartmann FSF, Udugama IA, Seibold GM, Sugiyama H, Gernaey KV. Digital models in biotechnology: Towards multi-scale integration and implementation. Biotechnol Adv 2022; 60:108015. [PMID: 35781047 DOI: 10.1016/j.biotechadv.2022.108015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022]
Abstract
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.
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Affiliation(s)
- Fabian S F Hartmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Isuru A Udugama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
| | - Gerd M Seibold
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
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12
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Kim H, Choi G, Suk ME, Kim TJ. Resource for FRET-Based Biosensor Optimization. Front Cell Dev Biol 2022; 10:885394. [PMID: 35794864 PMCID: PMC9251444 DOI: 10.3389/fcell.2022.885394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
After the development of Cameleon, the first fluorescence resonance energy transfer (FRET)-based calcium indicator, a variety of FRET-based genetically encoded biosensors (GEBs) have visualized numerous target players to monitor their cell physiological dynamics spatiotemporally. Many attempts have been made to optimize GEBs, which require labor-intensive effort, novel approaches, and precedents to develop more sensitive and versatile biosensors. However, researchers face considerable trial and error in upgrading biosensors because examples and methods of improving FRET-based GEBs are not well documented. In this review, we organize various optimization strategies after assembling the existing cases in which the non-fluorescent components of biosensors are upgraded. In addition, promising areas to which optimized biosensors can be applied are briefly discussed. Therefore, this review could serve as a resource for researchers attempting FRET-based GEB optimization.
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Affiliation(s)
- Heonsu Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
| | - Gyuho Choi
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Myung Eun Suk
- Department of Mechanical Engineering, IT Convergence College of Materials and Components Engineering, Dong-Eui University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
| | - Tae-Jin Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Biological Sciences, Pusan National University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
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13
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Visualizing the pH in Escherichia coli Colonies via the Sensor Protein mCherryEA Allows High-Throughput Screening of Mutant Libraries. mSystems 2022; 7:e0021922. [PMID: 35430898 PMCID: PMC9238402 DOI: 10.1128/msystems.00219-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cytoplasmic pH in bacteria is tightly regulated by diverse active mechanisms and interconnected regulatory processes. Many processes and regulators underlying pH homeostasis have been identified via phenotypic screening of strain libraries for nongrowth at low or high pH values. Direct screens with respect to changes of the internal pH in mutant strain collections are limited by laborious methods, which include fluorescent dyes and radioactive probes. Genetically encoded biosensors equip single organisms or strain libraries with an internal sensor molecule during the generation of the strain. Here, we used the pH-sensitive mCherry variant mCherryEA as a ratiometric pH biosensor. We visualized the internal pH of Escherichia coli colonies on agar plates by the use of a GelDoc imaging system. Combining this imaging technology with robot-assisted colony picking and spotting allowed us to screen and select mutants with altered internal pH values from a small transposon mutagenesis-derived E. coli library. Identification of the transposon (Tn) insertion sites in strains with altered internal pH levels revealed that the transposon was inserted into trkH (encoding a transmembrane protein of the potassium uptake system) or rssB (encoding the adaptor protein RssB, which mediates the proteolytic degradation of the general stress response regulator RpoS), two genes known to be associated with pH homeostasis and pH stress adaptation. This successful screening approach demonstrates that the pH sensor-based analysis of arrayed colonies on agar plates is a sensitive approach for the rapid identification of genes involved in pH homeostasis or pH stress adaptation in E. coli. IMPORTANCE Phenotypic screening of strain libraries on agar plates has become a versatile tool to understand gene functions and to optimize biotechnological platform organisms. Screening is supported by genetically encoded biosensors that allow to easily measure intracellular processes. For this purpose, transcription factor-based biosensors have emerged as the sensor type of choice. Here, the target stimulus initiates the activation of a response gene (e.g., a fluorescent protein), followed by transcription, translation, and maturation. Due to this mechanistic principle, biosensor readouts are delayed and cannot report the actual intracellular state of the cell in real time. To capture rapid intracellular processes adequately, fluorescent reporter proteins are extensively applied. However, these sensor types have not previously been used for phenotypic screenings. To take advantage of their properties, we established here an imaging method that allows application of a rapid ratiometric sensor protein for assessing the internal pH of colonies in a high-throughput manner.
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14
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Dey SK, Filonov GS, Olarerin-George AO, Jackson BT, Finley LWS, Jaffrey SR. Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat Chem Biol 2022; 18:180-190. [PMID: 34937909 PMCID: PMC8967656 DOI: 10.1038/s41589-021-00925-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/18/2021] [Indexed: 02/02/2023]
Abstract
Fluorogenic RNA aptamers are used to genetically encode fluorescent RNA and to construct RNA-based metabolite sensors. Unlike naturally occurring aptamers that efficiently fold and undergo metabolite-induced conformational changes, fluorogenic aptamers can exhibit poor folding, which limits their cellular fluorescence. To overcome this, we evolved a naturally occurring well-folded adenine riboswitch into a fluorogenic aptamer. We generated a library of roughly 1015 adenine aptamer-like RNAs in which the adenine-binding pocket was randomized for both size and sequence, and selected Squash, which binds and activates the fluorescence of green fluorescent protein-like fluorophores. Squash exhibits markedly improved in-cell folding and highly efficient metabolite-dependent folding when fused to a S-adenosylmethionine (SAM)-binding aptamer. A Squash-based ratiometric sensor achieved quantitative SAM measurements, revealed cell-to-cell heterogeneity in SAM levels and revealed metabolic origins of SAM. These studies show that the efficient folding of naturally occurring aptamers can be exploited to engineer well-folded cell-compatible fluorogenic aptamers and devices.
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Affiliation(s)
- Sourav Kumar Dey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.,Present address: Sartorius, Ann Arbor, Michigan, USA
| | | | - Benjamin T. Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lydia W. S. Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.,
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15
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van der Linden FH, Mahlandt EK, Arts JJG, Beumer J, Puschhof J, de Man SMA, Chertkova AO, Ponsioen B, Clevers H, van Buul JD, Postma M, Gadella TWJ, Goedhart J. A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium. Nat Commun 2021; 12:7159. [PMID: 34887382 PMCID: PMC8660884 DOI: 10.1038/s41467-021-27249-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
The most successful genetically encoded calcium indicators (GECIs) employ an intensity or ratiometric readout. Despite a large calcium-dependent change in fluorescence intensity, the quantification of calcium concentrations with GECIs is problematic, which is further complicated by the sensitivity of all GECIs to changes in the pH in the biological range. Here, we report on a sensing strategy in which a conformational change directly modifies the fluorescence quantum yield and fluorescence lifetime of a circular permutated turquoise fluorescent protein. The fluorescence lifetime is an absolute parameter that enables straightforward quantification, eliminating intensity-related artifacts. An engineering strategy that optimizes lifetime contrast led to a biosensor that shows a 3-fold change in the calcium-dependent quantum yield and a fluorescence lifetime change of 1.3 ns. We dub the biosensor Turquoise Calcium Fluorescence LIfeTime Sensor (Tq-Ca-FLITS). The response of the calcium sensor is insensitive to pH between 6.2-9. As a result, Tq-Ca-FLITS enables robust measurements of intracellular calcium concentrations by fluorescence lifetime imaging. We demonstrate quantitative imaging of calcium concentrations with the turquoise GECI in single endothelial cells and human-derived organoids.
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Affiliation(s)
- Franka H van der Linden
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eike K Mahlandt
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Janine J G Arts
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Hematology at Sanquin Research and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Saskia M A de Man
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anna O Chertkova
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Bas Ponsioen
- Center for Molecular Medicine, Oncode Institute, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Jaap D van Buul
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Hematology at Sanquin Research and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Marten Postma
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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16
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Vaughan HJ, Green JJ. Recent Advances in Gene Therapy for Cancer Theranostics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100300. [PMID: 34738046 PMCID: PMC8562678 DOI: 10.1016/j.cobme.2021.100300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is great interest in developing gene therapies for many disease indications, including cancer. However, successful delivery of nucleic acids to tumor cells is a major challenge, and in vivo efficacy is difficult to predict. Cancer theranostics is an approach combining anti-tumor therapy with imaging or diagnostic capabilities, with the goal of monitoring successful delivery and efficacy of a therapeutic agent in a tumor. Successful theranostics must maintain a high degree of anticancer targeting and efficacy while incorporating high-contrast imaging agents that are nontoxic and compatible with clinical imaging modalities. This review highlights recent advancements in theranostic strategies, including imaging technologies and genetic engineering approaches. Graphical Abstract.
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Affiliation(s)
- Hannah J. Vaughan
- Department of Biomedical Engineering, Institute for NanoBioTechnology, and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA
| | - Jordan J. Green
- Department of Biomedical Engineering, Institute for NanoBioTechnology, and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA
- Departments of Ophthalmology, Oncology, Neurosurgery, Materials Science & Engineering, and Chemical & Biomolecular Engineering, and the Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA
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17
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Miyata Y, Fuse H, Tokumoto S, Hiki Y, Deviatiiarov R, Yoshida Y, Yamada TG, Cornette R, Gusev O, Shagimardanova E, Funahashi A, Kikawada T. Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells. Sci Rep 2021; 11:19698. [PMID: 34611198 PMCID: PMC8492635 DOI: 10.1038/s41598-021-98905-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/16/2021] [Indexed: 01/01/2023] Open
Abstract
Pv11 is an insect cell line established from the midge Polypedilum vanderplanki, whose larval form exhibits an extreme desiccation tolerance known as anhydrobiosis. Pv11 itself is also capable of anhydrobiosis, which is induced by trehalose treatment. Here we report the successful construction of a genome editing system for Pv11 cells and its application to the identification of signaling pathways involved in anhydrobiosis. Using the Cas9-mediated gene knock-in system, we established Pv11 cells that stably expressed GCaMP3 to monitor intracellular Ca2+ mobilization. Intriguingly, trehalose treatment evoked a transient increase in cytosolic Ca2+ concentration, and further experiments revealed that the calmodulin-calcineurin-NFAT pathway contributes to tolerance of trehalose treatment as well as desiccation tolerance, while the calmodulin-calmodulin kinase-CREB pathway conferred only desiccation tolerance on Pv11 cells. Thus, our results show a critical contribution of the trehalose-induced Ca2+ surge to anhydrobiosis and demonstrate temporally different roles for each signaling pathway.
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Affiliation(s)
- Yugo Miyata
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroto Fuse
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yusuke Hiki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Ruslan Deviatiiarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Richard Cornette
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Takahiro Kikawada
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
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18
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FLIM-Based Intracellular and Extracellular pH Measurements Using Genetically Encoded pH Sensor. BIOSENSORS-BASEL 2021; 11:bios11090340. [PMID: 34562930 PMCID: PMC8468847 DOI: 10.3390/bios11090340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 02/04/2023]
Abstract
The determination of pH in live cells and tissues is of high importance in physiology and cell biology. In this report, we outline the process of the creation of SypHerExtra, a genetically encoded fluorescent sensor that is capable of measuring extracellular media pH in a mildly alkaline range. SypHerExtra is a protein created by fusing the previously described pH sensor SypHer3s with the neurexin transmembrane domain that targets its expression to the cytoplasmic membrane. We showed that with excitation at 445 nm, the fluorescence lifetime of both SypHer3s and SypHerExtra strongly depend on pH. Using FLIM microscopy in live eukaryotic cells, we demonstrated that SypHerExtra can be successfully used to determine extracellular pH, while SypHer3s can be applied to measure intracellular pH. Thus, these two sensors are suitable for quantitative measurements using the FLIM method, to determine intracellular and extracellular pH in a range from pH 7.5 to 9.5 in different biological systems.
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19
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Abstract
The imaging of chromatin, genomic loci, RNAs, and proteins is very important to study their localization, interaction, and coordinated regulation. Recently, several clustered regularly interspaced short palindromic repeats (CRISPR) based imaging methods have been established. The refurbished tool kits utilizing deactivated Cas9 (dCas9) and dCas13 have been established to develop applications of CRISPR-Cas technology beyond genome editing. Here, we review recent advancements in CRISPR-based methods that enable efficient imaging and visualization of chromatin, genomic loci, RNAs, and proteins. RNA aptamers, Pumilio, SuperNova tagging system, molecular beacons, halotag, bimolecular fluorescence complementation, RNA-guided endonuclease in situ labeling, and oligonucleotide-based imaging methods utilizing fluorescent proteins, organic dyes, or quantum dots have been developed to achieve improved fluorescence and signal-to-noise ratio for the imaging of chromatin or genomic loci. RNA-guided RNA targeting CRISPR systems (CRISPR/dCas13) and gene knock-in strategies based on CRISPR/Cas9 mediated site-specific cleavage and DNA repair mechanisms have been employed for efficient RNA and protein imaging, respectively. A few CRISPR-Cas-based methods to investigate the coordinated regulation of DNA-protein, DNA-RNA, or RNA-protein interactions for understanding chromatin dynamics, transcription, and protein function are also available. Overall, the CRISPR-based methods offer a significant improvement in elucidating chromatin organization and dynamics, RNA visualization, and protein imaging. The current and future advancements in CRISPR-based imaging techniques can revolutionize genome biology research for various applications.
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Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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20
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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21
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Reinartz I, Sarter M, Otten J, Höfig H, Pohl M, Schug A, Stadler AM, Fitter J. Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations. SENSORS 2021; 21:s21124144. [PMID: 34208740 PMCID: PMC8234384 DOI: 10.3390/s21124144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/27/2022]
Abstract
Inspired by the modular architecture of natural signaling proteins, ligand binding proteins are equipped with two fluorescent proteins (FPs) in order to obtain Förster resonance energy transfer (FRET)-based biosensors. Here, we investigated a glucose sensor where the donor and acceptor FPs were attached to a glucose binding protein using a variety of different linker sequences. For three resulting sensor constructs the corresponding glucose induced conformational changes were measured by small angle X-ray scattering (SAXS) and compared to recently published single molecule FRET results (Höfig et al., ACS Sensors, 2018). For one construct which exhibits a high change in energy transfer and a large change of the radius of gyration upon ligand binding, we performed coarse-grained molecular dynamics simulations for the ligand-free and the ligand-bound state. Our analysis indicates that a carefully designed attachment of the donor FP is crucial for the proper transfer of the glucose induced conformational change of the glucose binding protein into a well pronounced FRET signal change as measured in this sensor construct. Since the other FP (acceptor) does not experience such a glucose induced alteration, it becomes apparent that only one of the FPs needs to have a well-adjusted attachment to the glucose binding protein.
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Affiliation(s)
- Ines Reinartz
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany;
- HIDSS4Health-Helmholtz Information and Data Science School for Health, 76344 Eggenstein-Leopoldshafen, Germany
| | - Mona Sarter
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-8/JCNS-1, 52428 Jülich, Germany;
| | - Julia Otten
- Forschungszentrum Jülich, IBG-1, 52426 Jülich, Germany; (J.O.); (M.P.)
| | - Henning Höfig
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-6, 52428 Jülich, Germany
| | - Martina Pohl
- Forschungszentrum Jülich, IBG-1, 52426 Jülich, Germany; (J.O.); (M.P.)
| | - Alexander Schug
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52428 Jülich, Germany;
- Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Andreas M. Stadler
- Forschungszentrum Jülich, IBI-8/JCNS-1, 52428 Jülich, Germany;
- Institut für Physikalische Chemie, RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg Fitter
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-6, 52428 Jülich, Germany
- Correspondence: ; Tel.: +49-241-80-27209
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22
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Rathbun CM, Ionkina AA, Yao Z, Jones KA, Porterfield WB, Prescher JA. Rapid Multicomponent Bioluminescence Imaging via Substrate Unmixing. ACS Chem Biol 2021; 16:682-690. [PMID: 33729750 DOI: 10.1021/acschembio.0c00959] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Studies of biological function demand probes that can report on processes in real time and in physiological environments. Bioluminescent tools are uniquely suited for this purpose, as they enable sensitive imaging in cells and tissues. Bioluminescent reporters can also be monitored continuously over time without detriment, as excitation light is not required. Rather, light emission derives from luciferase-luciferin reactions. Several engineered luciferases and luciferins have expanded the scope of bioluminescence imaging in recent years. Multicomponent tracking remains challenging, though, due to a lack of streamlined methods to visualize combinations of bioluminescent reporters. Conventional approaches image one luciferase at a time. Consequently, short-term changes in cell growth or gene expression cannot be easily captured. Here, we report a strategy for rapid, multiplexed imaging with a wide range of luciferases and luciferins. Sequential addition of orthogonal luciferins, followed by substrate unmixing, enabled facile detection of multiple luciferases in vitro and in vivo. Multicomponent imaging in mice was also achieved on the minutes-to-hours time scale.
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23
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Pham H, Miller LW. Lanthanide-based resonance energy transfer biosensors for live-cell applications. Methods Enzymol 2021; 651:291-311. [PMID: 33888207 DOI: 10.1016/bs.mie.2021.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lanthanide-based, Förster resonance energy transfer (LRET) biosensors enable sensitive, time-gated luminescence (TGL) imaging or multiwell plate analysis of protein-protein interactions (PPIs) in living mammalian cells. LRET biosensors are polypeptides that consist of an alpha-helical linker sequence sandwiched between a lanthanide complex-binding domain and a fluorescent protein (FP) with two interacting domains residing at each terminus. Interaction between the terminal affinity domains brings the lanthanide complex and FP in close proximity such that lanthanide-to-FP, LRET-sensitized emission is increased. A recent proof-of-concept study examined model biosensors that incorporated the affinity partners FKBP12 and the rapamycin-binding domain of m-Tor (FRB) as well as p53 (1-92) and HDM2 (1-128). The sensors contained an Escherichia coli dihydrofolate reductase (eDHFR) domain that binds with high selectivity and affinity to Tb(III) complexes coupled to the ligand trimethoprim (TMP). When cell lines that stably expressed the sensors were treated with TMP-Tb(III), TGL microscopy revealed dramatic differences (>500%) in donor- or acceptor-denominated, Tb(III)-to-GFP LRET ratios between open (unbound) and closed (bound) states of the biosensors. Much larger signal changes (>2500%) and Z'-factors of 0.5 or more were observed when cells were grown in 96-well or 384-well plates and analyzed using a TGL plate reader. In this chapter, we elaborate on the design and performance of LRET biosensors and provide detailed protocols to guide their use for live-cell microscopic imaging studies and high-throughput library screening.
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Affiliation(s)
- Ha Pham
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States.
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Zhu R, Zhang G, Jing M, Han Y, Li J, Zhao J, Li Y, Chen PR. Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction. Nat Commun 2021; 12:581. [PMID: 33495458 PMCID: PMC7835342 DOI: 10.1038/s41467-020-20754-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022] Open
Abstract
Formaldehyde (FA) has long been considered as a toxin and carcinogen due to its damaging effects to biological macromolecules, but its beneficial roles have been increasingly appreciated lately. Real-time monitoring of this reactive molecule in living systems is highly desired in order to decipher its physiological and/or pathological functions, but a genetically encoded FA sensor is currently lacking. We herein adopt a structure-based study of the underlying mechanism of the FA-responsive transcription factor HxlR from Bacillus subtilis, which shows that HxlR recognizes FA through an intra-helical cysteine-lysine crosslinking reaction at its N-terminal helix α1, leading to conformational change and transcriptional activation. By leveraging this FA-induced intra-helical crosslinking and gain-of-function reorganization, we develop the genetically encoded, reaction-based FA sensor-FAsor, allowing spatial-temporal visualization of FA in mammalian cells and mouse brain tissues.
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Affiliation(s)
- Rongfeng Zhu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, China
| | - Gong Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, China
| | - Miao Jing
- Peking-Tsinghua Center for Life Sciences, 100871, Beijing, China
- State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, 100871, Beijing, China
- Chinese Institute for Brain Research, 102206, Beijing, China
| | - Yu Han
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Jiaofeng Li
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Jingyi Zhao
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Sciences, 100871, Beijing, China
- State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, 100871, Beijing, China.
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, 100871, Beijing, China.
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25
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Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Dijon NC, Nesheva DN, Holliday ND. Luciferase Complementation Approaches to Measure GPCR Signaling Kinetics and Bias. Methods Mol Biol 2021; 2268:249-274. [PMID: 34085274 DOI: 10.1007/978-1-0716-1221-7_17] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An understanding of the kinetic contributions to G protein-coupled receptor pharmacology and signaling is increasingly important in compound profiling. Nonequilibrium conditions are commonly present in vivo, for example, as the drug competes with dynamic changes in hormone or neurotransmitter concentration for the receptor. Under such conditions individual binding kinetic properties of the ligands can influence duration of action, local ligand concentration, and functional properties such as the degree of insurmountable inhibition. Mapping the kinetic patterns of GPCR signaling events elicited by agonists, rather than a peak response at a single timepoint, is often key to predicting their functional impact. This is also a path to a better understanding of the origins of ligand bias, and whether such ligands demonstrate their effects through selection of distinct GPCR conformations, or via their kinetic properties. Recent developments in complementation approaches, based on a small bright shrimp luciferase Nanoluc, provide a new route to kinetic analysis of GPCR signaling in living cells that is amenable to the throughput required for compound profiling. In the NanoBiT luciferase complementation system, GPCRs and effector proteins are tagged with Nanoluc fragments optimized for their low interacting affinity and stability. The interactions brought about by GPCR recruitment of the effector are reproduced by a rapid and reversible increase in NanoBiT luminescence, in the presence of its substrate furimazine. Here we discuss the methods for optimizing and validating the GPCR NanoBiT assays, and protocols for their application to study endpoint and kinetic aspects of agonist and antagonist pharmacology. We also describe how timecourse families of agonist concentration response curves, derived from a single NanoBiT assay experiment, can be used to evaluate the kinetic components in operational model derived parameters of ligand bias.
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Affiliation(s)
- Nicola C Dijon
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK
| | - Desislava N Nesheva
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK
| | - Nicholas D Holliday
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK. .,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK. .,Excellerate Bioscience, Biocity, Nottingham, UK.
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27
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Montecinos-Franjola F, Lin JY, Rodriguez EA. Fluorescent proteins for in vivo imaging, where's the biliverdin? Biochem Soc Trans 2020; 48:2657-2667. [PMID: 33196077 DOI: 10.1042/bst20200444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10-18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.
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Affiliation(s)
| | - John Y Lin
- School of Medicine, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
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28
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Fu L, Qian Y, Zhou J, Zheng L, Wang Y. Fluorescence-based quantitative platform for ultrasensitive food allergen detection: From immunoassays to DNA sensors. Compr Rev Food Sci Food Saf 2020; 19:3343-3364. [PMID: 33337031 DOI: 10.1111/1541-4337.12641] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/12/2020] [Accepted: 09/01/2020] [Indexed: 01/10/2023]
Abstract
Food allergies are global health issue with an increasing prevalence that affect food safety; hence, food allergen detection, labeling, and management are considered to be important priorities in the food industry. In this critical review, we provide a comprehensive overview of several fluorescence-based platforms based on different biorecognition ligands, such as antibodies, DNA, aptamers, and cells, for food allergen quantification. Traditional analytical methods are generally unsuitable for food manufacturers to accomplish the real-time identification of food allergens in food products. Therefore, it is important to develop simple, rapid, inexpensive, accurate, and sensitive methods to improve user accessibility. A fluorescence-based quantitative platform provides an excellent detection platform for food allergens because of its high sensitivity. This review summarizes the traditional antibody-based fluorescent techniques for food allergen detection, such as the time-resolved fluoroimmunoassay , immunofluorescence imaging, fluorescence enzyme-linked immune sorbent assay, flow injection fluoroimmunoassay, and fluorescence immunosensors. However, these methods suffer from disadvantages such as the significant rate of false-positive and false-negative results due to antibody cross-reactivity with nontarget food components in the complex food matrix and epitope degradation during food processing. Hence, different types of fluorescence-based immunoassays are suitable for standardization and quantification of allergens in fresh foods. In addition, we summarize new fluorescence-based quantitative platforms, including fluorescence genosensors, fluorescence cell sensors, and fluorescence aptamer sensors. With the advantages of high sensitivity and simple operation, fluorescence biosensors will have great potential in the future and could provide portable methods for multiallergen real-time detection in complex food systems.
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Affiliation(s)
- Linglin Fu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Yifan Qian
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Jinru Zhou
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Lei Zheng
- School of Food Science and Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Yanbo Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
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29
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Funck D, Baumgarten L, Stift M, von Wirén N, Schönemann L. Differential Contribution of P5CS Isoforms to Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:565134. [PMID: 33101333 PMCID: PMC7545825 DOI: 10.3389/fpls.2020.565134] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/09/2020] [Indexed: 05/24/2023]
Abstract
Proline accumulation is a widespread response of plants to salt stress as well as drought and cold stress. In most plant species, two isoforms of pyrroline-5-carboxylate synthetase (P5CS) catalyze the first step in proline biosynthesis from glutamate. In Arabidopsis, these isoforms differ in their spatial and temporal expression patterns, suggesting sub-functionalization. P5CS1 has been identified as the major contributor to stress-induced proline accumulation, whereas P5CS2 has been considered important for embryo development and growth. In contrast to previous results, our analysis of P5CS1- and P5CS2-GFP fusion proteins indicates that both enzymes were exclusively localized in the cytosol. The comparison of the susceptibility of p5cs1 and p5cs2 mutants to infection with Pseudomonas syringae and salt stress provided novel information on the contribution of the two P5CS isoforms to proline accumulation and stress tolerance. In agreement with previous studies, salt-stressed p5cs1 mutants accumulated very little proline, indicating that P5CS1 contributed more to stress-induced proline accumulation, whereas its impact on stress tolerance was rather weak. Germination and establishment of p5cs2 mutants were impaired under ambient conditions, further supporting that P5CS2 is most important for growth and development, whereas its contribution to stress-induced proline accumulation was smaller than that of P5CS1. In contrast to p5cs1 mutants or wildtype plants, p5cs2 mutants were only weakly affected by sudden exposure to a high NaCl concentration. These findings show that proline content, which was intermediate in leaves of p5cs2 mutants, was not directly correlated with stress tolerance in our experiments. In rosettes of NaCl-exposed p5cs2 mutants, nearly no accumulation of Na+ was observed, and the plants showed neither chlorosis nor reduction of photosynthesis. Based on these data, we suggest a function of P5CS2 or P5CS2-mediated proline synthesis in regulating Na+ accumulation in leaves and thereby salt stress tolerance.
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Affiliation(s)
- Dietmar Funck
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Lukas Baumgarten
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Luise Schönemann
- Department of Biology, University of Konstanz, Konstanz, Germany
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30
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Cambronne XA, Kraus WL. Location, Location, Location: Compartmentalization of NAD + Synthesis and Functions in Mammalian Cells. Trends Biochem Sci 2020; 45:858-873. [PMID: 32595066 DOI: 10.1016/j.tibs.2020.05.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
The numerous biological roles of NAD+ are organized and coordinated via its compartmentalization within cells. The spatial and temporal partitioning of this intermediary metabolite is intrinsic to understanding the impact of NAD+ on cellular signaling and metabolism. We review evidence supporting the compartmentalization of steady-state NAD+ levels in cells, as well as how the modulation of NAD+ synthesis dynamically regulates signaling by controlling subcellular NAD+ concentrations. We further discuss potential benefits to the cell of compartmentalizing NAD+, and methods for measuring subcellular NAD+ levels.
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Affiliation(s)
- Xiaolu A Cambronne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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31
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Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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32
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Nguyen D, Behrens DM, Sen S, Najdahmadi A, Pham JN, Speciale G, Lawrence MM, Majumdar S, Weiss GA, Botvinick EL. Photostable and Proteolysis-Resistant Förster Resonance Energy Transfer-Based Calcium Biosensor. Anal Chem 2020; 92:7683-7689. [PMID: 32352281 DOI: 10.1021/acs.analchem.0c00573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular sensors from protein engineering offer new methods to sensitively bind to and detect target analytes for a wide range of applications. For example, these sensors can be integrated into probes for implantation, and then yield new and valuable physiological information. Here, a new Förster resonance energy transfer (FRET)-based sensor is integrated with an optical fiber to yield a device measuring free Ca2+. This membrane encapsulated optical fiber (MEOF) device is composed of a sensor matrix that fills poly(tetrafluoroethylene) (PTFE) with an engineered troponin C (TnC) protein fused to a pair of FRET fluorophores. The FRET efficiency is modulated upon Ca2+ ion binding. The probe further comprises a second, size-excluding filter membrane that is synthesized by filling the pores of a PTFE matrix with a poly(ethylene glycol) dimethacrylate (PEGDMA) hydrogel; this design ensures protection from circulating proteases and the foreign body response. The two membranes are stacked and placed on a thin, silica optical fiber for optical excitation and detection. Results show the biosensor responds to changes in Ca2+ concentration within minutes with a sensitivity ranging from 0.01 to 10 mM Ca2+, allowing discrimination of hyper- and hypocalcemia. Furthermore, the system reversibly binds Ca2+ to allow continuous monitoring. This work paves the way for the use of engineered structure-switching proteins for continuous optical monitoring in a large number of applications.
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Affiliation(s)
- Dat Nguyen
- Department of Biomedical Engineering, University of California, Irvine, California 92697-2730, United States
| | - Danielle M Behrens
- Department of Biomedical Engineering, University of California, Irvine, California 92697-2730, United States
| | - Sanjana Sen
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Avid Najdahmadi
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92612-1475, United States
| | - Jessica N Pham
- Department of Chemistry, University of California, Irvine, California 92697-2015, United States
| | - Gaetano Speciale
- Department of Chemistry, University of California, Irvine, California 92697-2015, United States
| | - Micah M Lawrence
- Department of Biomedical Engineering, University of California, Irvine, California 92697-2730, United States
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, California 92697-2015, United States
| | - Gregory A Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2015, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-4625, United States
| | - Elliot L Botvinick
- Department of Biomedical Engineering, University of California, Irvine, California 92697-2730, United States.,Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92612-1475, United States.,Department of Surgery, University of California, Irvine, California 92697-2730, United States
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33
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Watabe T, Terai K, Sumiyama K, Matsuda M. Booster, a Red-Shifted Genetically Encoded Förster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein/Yellow Fluorescent Protein-Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools. ACS Sens 2020; 5:719-730. [PMID: 32101394 DOI: 10.1021/acssensors.9b01941] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been developed for the visualization of signaling molecule activities. Currently, most of them are comprised of cyan and yellow fluorescent proteins (CFP and YFP), precluding the use of multiple FRET biosensors within a single cell. Moreover, the FRET biosensors based on CFP and YFP are incompatible with the optogenetic tools that operate at blue light. To overcome these problems, here, we have developed FRET biosensors with red-shifted excitation and emission wavelengths. We chose mKOκ and mKate2 as the favorable donor and acceptor pair by calculating the Förster distance. By optimizing the order of fluorescent proteins and modulatory domains of the FRET biosensors, we developed a FRET biosensor backbone named "Booster". The performance of the protein kinase A (PKA) biosensor based on the Booster backbone (Booster-PKA) was comparable to that of AKAR3EV, a previously developed FRET biosensor comprising CFP and YFP. For the proof of concept, we first showed simultaneous monitoring of activities of two protein kinases with Booster-PKA and ERK FRET biosensors based on CFP and YFP. Second, we showed monitoring of PKA activation by Beggiatoa photoactivated adenylyl cyclase, an optogenetic generator of cyclic AMP. Finally, we presented PKA activity in living tissues of transgenic mice expressing Booster-PKA. Collectively, the results demonstrate the effectiveness and versatility of Booster biosensors as an imaging tool in vitro and in vivo.
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Affiliation(s)
- Tetsuya Watabe
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Terai
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0874, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
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34
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Zou W, Le K, Zastrow ML. Live‐Cell Copper‐Induced Fluorescence Quenching of the Flavin‐Binding Fluorescent Protein CreiLOV. Chembiochem 2020; 21:1356-1363. [DOI: 10.1002/cbic.201900669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Wenping Zou
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Khoa Le
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Melissa L. Zastrow
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
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35
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Thirukkumaran OM, Wang C, Asouzu NJ, Fron E, Rocha S, Hofkens J, Lavis LD, Mizuno H. Improved HaloTag Ligand Enables BRET Imaging With NanoLuc. Front Chem 2020; 7:938. [PMID: 31993413 PMCID: PMC6970966 DOI: 10.3389/fchem.2019.00938] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) from an exceptionally bright luciferase, NanoLuc, to a fluorescent HaloTag ligand is gaining momentum to monitor molecular interactions. The recommended use of HaloTag618 ligand for the NanoLuc-HaloTag BRET pair is versatile for ensemble experiments due to their well-separated emission bands. However, this system is not applicable for single-cell BRET imaging because of its low BRET efficiency and in turn weak acceptor signals. Here we explored the unprecedented potential of rhodamine based HaloTag ligands, containing azetidine rings, as BRET acceptors. Through a comprehensive evaluation of various commercial and Janelia Fluor HaloTag ligands for improved BRET efficiency and minimal donor signal bleed-through, we identified JF525 to be the best acceptor for microscopic BRET imaging. We successfully employed BRET imaging with JF525 to monitor the interaction of protein kinase A catalytic and regulatory subunit. Single-cell BRET imaging with HaloTag JF525 can henceforth open doors to comprehend and interpret molecular interactions.
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Affiliation(s)
- Ovia Margaret Thirukkumaran
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium.,Chem Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Congrong Wang
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Nnamdi Joseph Asouzu
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Eduard Fron
- Chem Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Susana Rocha
- Chem Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Johan Hofkens
- Chem Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Luke D Lavis
- Howard Hughes Medical Institute, Ashburn, VA, United States
| | - Hideaki Mizuno
- Laboratory for Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
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36
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Mikuni T. Genome editing-based approaches for imaging protein localization and dynamics in the mammalian brain. Neurosci Res 2020; 150:2-7. [DOI: 10.1016/j.neures.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/15/2019] [Accepted: 04/24/2019] [Indexed: 01/15/2023]
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37
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Howell AH, Peters WS, Knoblauch M. The diffusive injection micropipette (DIMP). JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153060. [PMID: 31765880 DOI: 10.1016/j.jplph.2019.153060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2023]
Abstract
The microinjection of fluorescent probes into live cells is an essential component in the toolbox of modern cell biology. Microinjection techniques include the penetration of the plasma membrane and, if present, the cell wall with micropipettes, and the application of pressure or electrical currents to drive the micropipette contents into the cell. These procedures interfere with cellular functions and therefore may induce artifacts. We designed the diffusive injection micropipette (DIMP) that avoids most of the possible artifacts due to the drastically reduced volume of its fluid contents and the utilization of diffusion for cargo delivery into the target cell. DIMPs were successfully tested in plant, fungal, and animal cells. Using the continuity of cytoplasmic dynamics over ten minutes after impalement of Nicotiana trichome cells as a criterion for non-invasiveness, we found DIMPs significantly less disruptive than conventional pressure microinjection. The design of DIMPs abolishes major sources of artifacts that cannot be avoided by other microinjection techniques. Moreover, DIMPs are inexpensive, easy to produce, and can be applied without specific equipment other than a micromanipulator. With these features, DIMPs may become the tool of choice for studies that require the least invasive delivery possible of materials into live cells.
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Affiliation(s)
- Alexander H Howell
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Winfried S Peters
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
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38
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Lv X, Gao P. An optical sensor for selective detection of phenol via double cross-linker precipitation polymerization. RSC Adv 2020; 10:25402-25407. [PMID: 35517451 PMCID: PMC9055332 DOI: 10.1039/d0ra03708g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/27/2020] [Indexed: 11/21/2022] Open
Abstract
Based on the electron-transfer mechanism between the template and quantum dots (QDs), an optical sensor was structured.
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Affiliation(s)
- Xiaodong Lv
- School of Electrical Engineering and Control Science
- Nanjing Tech University
- Nanjing 211899
- China
| | - Peng Gao
- School of Electrical Engineering
- Tongling University
- Tongling 244000
- China
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39
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Scida K, Plaxco KW, Jamieson BG. High frequency, real-time neurochemical and neuropharmacological measurements in situ in the living body. Transl Res 2019; 213:50-66. [PMID: 31361988 DOI: 10.1016/j.trsl.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 12/18/2022]
Abstract
The beautiful and complex brain machinery is perfectly synchronized, and our bodies have evolved to protect it against a myriad of potential threats. Shielded physically by the skull and chemically by the blood brain barrier, the brain processes internal and external information so that we can efficiently relate to the world that surrounds us while simultaneously and unconsciously controlling our vital functions. When coupled with the brittle nature of its internal chemical and electric signals, the brain's "armor" render accessing it a challenging and delicate endeavor that has historically limited our understanding of its structural and neurochemical intricacies. In this review, we briefly summarize the advancements made over the past 10 years to decode the brain's neurochemistry and neuropharmacology in situ, at the site of interest in the brain, with special focus on what we consider game-changing emerging technologies (eg, genetically encoded indicators and electrochemical aptamer-based sensors) and the challenges these must overcome before chronic, in situ chemosensing measurements become routine.
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Affiliation(s)
- Karen Scida
- Diagnostic Biochips, Inc., Glen Burnie, Maryland
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
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40
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Özyurt C, Üstükarcı H, Evran S, Telefoncu A. MerR‐fluorescent protein chimera biosensor for fast and sensitive detection of Hg
2+
in drinking water. Biotechnol Appl Biochem 2019; 66:731-737. [DOI: 10.1002/bab.1805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/12/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Canan Özyurt
- Department of Biochemistry Faculty of Science Ege University Bornova‐Izmir 35100 Turkey
- Department of Chemistry and Chemical Processing Technologies Lapseki Vocational School Canakkale Onsekiz Mart University Canakkale Lapseki Turkey
| | - Handan Üstükarcı
- Department of Biochemistry Faculty of Science Ege University Bornova‐Izmir 35100 Turkey
| | - Serap Evran
- Department of Biochemistry Faculty of Science Ege University Bornova‐Izmir 35100 Turkey
| | - Azmi Telefoncu
- Department of Biochemistry Faculty of Science Ege University Bornova‐Izmir 35100 Turkey
- Bio‐sensing and Bioinformatics Nanotechnologies R & D Trade & Ind. Ltd Co TECHNOPARK EGE, Ege University 35100 Izmir Turkey
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41
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Otten J, Tenhaef N, Jansen RP, Döbber J, Jungbluth L, Noack S, Oldiges M, Wiechert W, Pohl M. A FRET-based biosensor for the quantification of glucose in culture supernatants of mL scale microbial cultivations. Microb Cell Fact 2019; 18:143. [PMID: 31434564 PMCID: PMC6704555 DOI: 10.1186/s12934-019-1193-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/14/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND In most microbial cultivations D-glucose is the main carbon and energy source. However, quantification of D-glucose especially in small scale is still challenging. Therefore, we developed a FRET-based glucose biosensor, which can be applied in microbioreactor-based cultivations. This sensor consists of a glucose binding protein sandwiched between two fluorescent proteins, constituting a FRET pair. Upon D-glucose binding the sensor undergoes a conformational change which is translated into a FRET-ratio change. RESULTS The selected sensor shows an apparent Kd below 1.5 mM D-glucose and a very high sensitivity of up to 70% FRET-ratio change between the unbound and the glucose-saturated state. The soluble sensor was successfully applied online to monitor the glucose concentration in an Escherichia coli culture. Additionally, this sensor was utilized in an at-line process for a Corynebacterium glutamicum culture as an example for a process with cell-specific background (e.g. autofluorescence) and medium-induced quenching. Immobilization of the sensor via HaloTag® enabled purification and covalent immobilization in one step and increased the stability during application, significantly. CONCLUSION A FRET-based glucose sensor was used to quantify D-glucose consumption in microtiter plate based cultivations. To the best of our knowledge, this is the first method reported for online quantification of D-glucose in microtiter plate based cultivations. In comparison to D-glucose analysis via an enzymatic assay and HPLC, the sensor performed equally well, but enabled much faster measurements, which allowed to speed up microbial strain development significantly.
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Affiliation(s)
- Julia Otten
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Niklas Tenhaef
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Roman P. Jansen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Johannes Döbber
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lisa Jungbluth
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Noack
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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42
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Optimizing the fluorescent protein toolbox and its use. Curr Opin Biotechnol 2019; 58:183-191. [DOI: 10.1016/j.copbio.2019.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
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43
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Kost LA, Ivanova VO, Balaban PM, Lukyanov KA, Nikitin ES, Bogdanov AM. Red Fluorescent Genetically Encoded Voltage Indicators with Millisecond Responsiveness. SENSORS (BASEL, SWITZERLAND) 2019; 19:E2982. [PMID: 31284557 PMCID: PMC6651345 DOI: 10.3390/s19132982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 01/09/2023]
Abstract
Genetically encoded fluorescent indicators typically consist of the sensitive and reporter protein domains connected with the amino acid linkers. The final performance of a particular indicator may depend on the linker length and composition as strong as it depends on the both domains nature. Here we aimed to optimize interdomain linkers in VSD-FR189-188-a recently described red fluorescent protein-based voltage indicator. We have tested 13 shortened linker versions and monitored the dynamic range, response speed and polarity of the corresponding voltage indicator variants. While the new indicators didn't show a contrast enhancement, some of them carrying very short interdomain linkers responded 25-fold faster than the parental VSD-FR189-188. Also we found the critical linker length at which fluorescence response to voltage shift changes its polarity from negative to positive slope. Our observations thus make an important contribution to the designing principles of the fluorescent protein-derived voltage indicators.
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Affiliation(s)
- Liubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Violetta O Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Pavel M Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Evgeny S Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
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44
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Hochreiter B, Kunze M, Moser B, Schmid JA. Advanced FRET normalization allows quantitative analysis of protein interactions including stoichiometries and relative affinities in living cells. Sci Rep 2019; 9:8233. [PMID: 31160659 PMCID: PMC6547726 DOI: 10.1038/s41598-019-44650-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
FRET (Fluorescence Resonance Energy Transfer) measurements are commonly applied to proof protein-protein interactions. However, standard methods of live cell FRET microscopy and signal normalization only allow a principle assessment of mutual binding and are unable to deduce quantitative information of the interaction. We present an evaluation and normalization procedure for 3-filter FRET measurements, which reflects the process of complex formation by plotting FRET-saturation curves. The advantage of this approach relative to traditional signal normalizations is demonstrated by mathematical simulations. Thereby, we also identify the contribution of critical parameters such as the total amount of donor and acceptor molecules and their molar ratio. When combined with a fitting procedure, this normalization facilitates the extraction of key properties of protein complexes such as the interaction stoichiometry or the apparent affinity of the binding partners. Finally, the feasibility of our method is verified by investigating three exemplary protein complexes. Altogether, our approach offers a novel method for a quantitative analysis of protein interactions by 3-filter FRET microscopy, as well as flow cytometry. To facilitate the application of this method, we created macros and routines for the programs ImageJ, R and MS-Excel, which we make publicly available.
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Affiliation(s)
- Bernhard Hochreiter
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Markus Kunze
- Medical University Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Vienna, Austria
| | - Bernhard Moser
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Johannes A Schmid
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria.
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45
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Himmelstoß SF, Hirsch T. A critical comparison of lanthanide based upconversion nanoparticles to fluorescent proteins, semiconductor quantum dots, and carbon dots for use in optical sensing and imaging. Methods Appl Fluoresc 2019; 7:022002. [PMID: 30822759 DOI: 10.1088/2050-6120/ab0bfa] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The right choice of a fluorescent probe is essential for successful luminescence imaging and sensing and especially concerning in vivo and in vitro applications, the development of new classes have gained more and more attention in the last years. One of the most promising class are upconversion nanoparticles (UCNPs)-inorganic nanocrystals capable to convert near-infrared light in high energy radiation. In this review we will compare UCNPs with other fluorescent probes in terms of (a) the optical properties of the probes, such as their brightness, photostability and excitation wavelength; (b) their chemical properties such as the dispersibility, stability under experimental or physiological conditions, availability of chemical modification strategies for labelling; and (c) the potential toxicity and biocompatibility of the probe. Thereby we want to provide a better understanding of the advantages and drawbacks of UCNPs and address future challenges in the design of the nanocrystals.
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Affiliation(s)
- Sandy F Himmelstoß
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
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46
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Yang XA, Zweifach A. Temperature-Dependent Expression of a CFP-YFP FRET Diacylglycerol Sensor Enables Multiple-Read Screening for Compounds That Affect C1 Domains. SLAS DISCOVERY 2019; 24:682-692. [PMID: 30802416 DOI: 10.1177/2472555219830086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intramolecular CFP-YFP fluorescence resonance energy transfer (FRET) sensors expressed in cells are powerful research tools but have seen relatively little use in screening. We exploited the discovery that the expression of a CFP-YFP FRET diacylglycerol sensor (DAGR) increases over time when cells are incubated at room temperature to assess requirements for robust measurements using a Molecular Devices Spectramax i3x fluorescence plate reader. Expression levels resulting in YFP fluorescence >10-fold higher than untransfected cells and phorbol ester-stimulated FRET ratio changes of 60% or more were required to consistently give robust Z' > 0.5. As a means of confirming that these conditions are suitable for screening, we developed a novel multiple-read protocol to assay the NCI's Mechanistic Set III for agonists and antagonists of C1 domain activation. Sixteen compounds prevented C1 domain translocation. However, none blocked phorbol ester-stimulated protein kinase C (PKC) activity assessed using a phospho-specific antibody-six actually stimulated PKC activity. Cytometry, which produces higher Z' for a given FRET ratio change, might have been a better approach for discovering antagonists, as it would have allowed lower phorbol ester concentrations to be used. We conclude that CFP-YFP FRET measured in a Spectramax i3x plate reader can be used for screening under the conditions we defined. Our strategy of varying expression level and FRET ratio could be useful to others for determining conditions needed for robust cell-based intramolecular CFP-YFP FRET measurements on their instrumentation.
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Affiliation(s)
- Xiuyi Alexander Yang
- 1 Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT, USA
| | - Adam Zweifach
- 1 Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT, USA
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47
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Nguyen PTM, Ishiwata-Kimata Y, Kimata Y. Monitoring ADP/ATP ratio in yeast cells using the fluorescent-protein reporter PercevalHR. Biosci Biotechnol Biochem 2019; 83:824-828. [PMID: 30704350 DOI: 10.1080/09168451.2019.1574204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
PercevalHR (Perceval High Resolution) is an artificially designed fluorescent protein, which changes its excitation spectrum based on the ADP/ATP ratio of the environment. Here we demonstrated that PercevalHR can be used for monitoring energy status of Saccharomyces cerevisiae cells, which are affected by diauxic shift and mitochondria inhibition, in a non-invasive and non-destructive manner.
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Affiliation(s)
- Phuong Thi Mai Nguyen
- a Graduate School of Science and Technology , Nara Institute of Science and Technology , Nara , Japan
| | - Yuki Ishiwata-Kimata
- a Graduate School of Science and Technology , Nara Institute of Science and Technology , Nara , Japan
| | - Yukio Kimata
- a Graduate School of Science and Technology , Nara Institute of Science and Technology , Nara , Japan
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48
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Chapnick DA, Bunker E, Liu X, Old WM. Temporal Metabolite, Ion, and Enzyme Activity Profiling Using Fluorescence Microscopy and Genetically Encoded Biosensors. Methods Mol Biol 2019; 1978:343-353. [PMID: 31119673 DOI: 10.1007/978-1-4939-9236-2_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living cells employ complex and highly dynamic signaling networks and transcriptional circuits to maintain homeostasis and respond appropriately to constantly changing environments. These networks enable cells to maintain tight control on intracellular concentrations of ions, metabolites, proteins, and other biomolecules and ensure a careful balance between a cell's energetic needs and catabolic processes required for growth. Establishing molecular mechanisms of genetic and pharmacological perturbations remains challenging, due to the interconnected nature of these networks and the extreme sensitivity of cellular systems to their external environment. Live cell imaging with genetically encoded fluorescent biosensors provides a powerful new modality for nondestructive spatiotemporal tracking of ions, small molecules, enzymatic activities, and molecular interactions in living systems, from cells, tissues, and even living organisms. By deploying large panels of cell lines, each with distinct biosensors, many critical biochemical pathways can be monitored in a highly parallel and high-throughput fashion to identify pharmacological vulnerabilities and combination therapies unique to a given cell type or genetic background. Here we describe the experimental and analytical methods required to conduct multiplexed parallel fluorescence microscopy experiments on live cells expressing stable transgenic synthetic protein biosensors.
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Affiliation(s)
| | - Eric Bunker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA.
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49
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Single-Molecule Studies on a FRET Biosensor: Lessons from a Comparison of Fluorescent Protein Equipped versus Dye-Labeled Species. Molecules 2018; 23:molecules23123105. [PMID: 30486450 PMCID: PMC6320824 DOI: 10.3390/molecules23123105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 11/16/2022] Open
Abstract
Bacterial periplasmic binding proteins (PBPs) undergo a pronounced ligand-induced conformational change which can be employed to monitor ligand concentrations. The most common strategy to take advantage of this conformational change for a biosensor design is to use a Förster resonance energy transfer (FRET) signal. This can be achieved by attaching either two fluorescent proteins (FPs) or two organic fluorescent dyes of different colors to the PBPs in order to obtain an optical readout signal which is closely related to the ligand concentration. In this study we compare a FP-equipped and a dye-labeled version of the glucose/galactose binding protein MglB at the single-molecule level. The comparison demonstrates that changes in the FRET signal upon glucose binding are more pronounced for the FP-equipped sensor construct as compared to the dye-labeled analog. Moreover, the FP-equipped sensor showed a strong increase of the FRET signal under crowding conditions whereas the dye-labeled sensor was not influenced by crowding. The choice of a labeling scheme should therefore be made depending on the application of a FRET-based sensor.
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50
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Tebo AG, Pimenta FM, Zoumpoulaki M, Kikuti C, Sirkia H, Plamont MA, Houdusse A, Gautier A. Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors. ACS Chem Biol 2018; 13:2392-2397. [PMID: 30088915 DOI: 10.1021/acschembio.8b00417] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.
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Affiliation(s)
- Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Frederico M. Pimenta
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martha Zoumpoulaki
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Carlos Kikuti
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Helena Sirkia
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Anne Houdusse
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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