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Maares M, Keil C, Thomsen S, Günzel D, Wiesner B, Haase H. Characterization of Caco-2 cells stably expressing the protein-based zinc probe eCalwy-5 as a model system for investigating intestinal zinc transport. J Trace Elem Med Biol 2018; 49:296-304. [PMID: 29395783 DOI: 10.1016/j.jtemb.2018.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/22/2017] [Accepted: 01/17/2018] [Indexed: 12/30/2022]
Abstract
Intestinal zinc resorption, in particular its regulation and mechanisms, are not yet fully understood. Suitable intestinal cell models are needed to investigate zinc uptake kinetics and the role of labile zinc in enterocytes in vitro. Therefore, a Caco-2 cell clone was produced, stably expressing the genetically encoded zinc biosensor eCalwy-5. The aim of the present study was to reassure the presence of characteristic enterocyte-specific properties in the Caco-2-eCalwy clone. Comparison of Caco-2-WT and Caco-2-eCalwy cells revealed only slight differences regarding subcellular localization of the tight junction protein occludin and alkaline phosphatase activity, which did not affect basic integrity of the intestinal barrier or the characteristic brush border membrane morphology. Furthermore, introduction of the additional zinc-binding protein in Caco-2 cells did not alter mRNA expression of the major intestinal zinc transporters (zip4, zip5, znt-1 and znt-5), but increased metallothionein 1a-expression and cellular resistance to higher zinc concentrations. Moreover, this study examines the effect of sensor expression level on its saturation with zinc. Fluorescence cell imaging indicated considerable intercellular heterogeneity in biosensor-expression. However, FRET-measurements confirmed that these differences in expression levels have no effect on fractional zinc-saturation of the probe.
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Affiliation(s)
- Maria Maares
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, Berlin, Germany
| | - Claudia Keil
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, Berlin, Germany
| | - Susanne Thomsen
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, Berlin, Germany
| | - Dorothee Günzel
- Institute of Clinical Physiology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | | | - Hajo Haase
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, Berlin, Germany; TraceAge-DFG Research Unit on Interactions of essential trace elements in healthy and diseased elderly, Potsdam-Berlin-Jena, Germany.
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52
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Fudge DH, Black R, Son L, LeJeune K, Qin Y. Optical Recording of Zn 2+ Dynamics in the Mitochondrial Matrix and Intermembrane Space with the GZnP2 Sensor. ACS Chem Biol 2018; 13:1897-1905. [PMID: 29912548 DOI: 10.1021/acschembio.8b00319] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The zinc ion (Zn2+) is emerging as an important signaling molecule. Here, we engineered an improved Zn2+ probe GZnP2 based on a previously developed fluorescent sensor GZnP1 to provide a higher fluorescent readout (2-fold higher) that is proportional to cellular labile Zn2+ concentrations. We further developed a set of GZnP2 derived imaging tools to determine the labile Zn2+ concentrations in the mitochondrial matrix, mitochondrial intermembrane space (IMS), and cytosol in four different cell lines (HeLa, Cos-7, HEK293, and INS-1). The labile Zn2+ concentration in the matrix was less than 1 pM, while the labile Zn2+ concentration in the IMS was comparable to the cytosol (∼100 pM). With these sensors, we showed that upon exposure to high Zn2+, only the cytosol and the IMS were overloaded with Zn2+, while the mitochondrial matrix was unable to sequester excess labile Zn2+ in depolarized INS-1 cells. This work highlighted the importance of distinguishing the labile Zn2+ concentrations and dynamics between the mitochondrial matrix and IMS.
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Affiliation(s)
- Dylan H. Fudge
- Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Raymond Black
- Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Lea Son
- Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Kate LeJeune
- Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
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53
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In vivo biosensors: mechanisms, development, and applications. ACTA ACUST UNITED AC 2018; 45:491-516. [DOI: 10.1007/s10295-018-2004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Abstract
In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.
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54
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Jiménez-Sánchez A, Lei EK, Kelley SO. A Multifunctional Chemical Probe for the Measurement of Local Micropolarity and Microviscosity in Mitochondria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Arturo Jiménez-Sánchez
- Department of Biochemistry; Faculty of Medicine; University of Toronto; Toronto Ontario M5S 1A8 Canada
| | - Eric K. Lei
- Department of Biochemistry; Faculty of Medicine; University of Toronto; Toronto Ontario M5S 1A8 Canada
| | - Shana O. Kelley
- Department of Biochemistry; Faculty of Medicine; University of Toronto; Toronto Ontario M5S 1A8 Canada
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy; Institute for Biomedical and Biomaterials Engineering; Departments of Biochemistry and Chemistry; University of Toronto; Toronto Ontario M5S 1A8 Canada
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55
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Jiménez-Sánchez A, Lei EK, Kelley SO. A Multifunctional Chemical Probe for the Measurement of Local Micropolarity and Microviscosity in Mitochondria. Angew Chem Int Ed Engl 2018; 57:8891-8895. [PMID: 29808513 DOI: 10.1002/anie.201802796] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/06/2018] [Indexed: 12/13/2022]
Abstract
The measurement of physicochemical parameters in living cells can provide information on individual cellular organelles, helping us to understand subcellular function in health and disease. While organelle-specific chemical probes have allowed qualitative evaluation of microenvironmental variations, the simultaneous quantification of mitochondrial local microviscosity (ηm ) and micropolarity (ϵm ), along with concurrent structural variations, has remained an unmet need. Herein, we describe a new multifunctional mitochondrial probe (MMP) for simultaneous monitoring of ηm and ϵm by fluorescence lifetime and emission intensity recordings, respectively. The MMP enables highly precise measurements of ηm and ϵm in the presence of a variety of agents perturbing cellular function, and the observed changes can also be correlated with alterations in mitochondrial network morphology and motility. This strategy represents a promising tool for the analysis of subtle changes in organellar structure.
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Affiliation(s)
- Arturo Jiménez-Sánchez
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Eric K Lei
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Shana O Kelley
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, Institute for Biomedical and Biomaterials Engineering, Departments of Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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56
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Parsons DS, Hogstrand C, Maret W. The C-terminal cytosolic domain of the human zinc transporter ZnT8 and its diabetes risk variant. FEBS J 2018; 285:1237-1250. [PMID: 29430817 PMCID: PMC5947572 DOI: 10.1111/febs.14402] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/22/2017] [Accepted: 02/05/2018] [Indexed: 12/21/2022]
Abstract
A significant aspect of the control of cellular zinc in eukarya is its subcellular re‐distribution. One of the four human vesicular zinc transporters, ZnT8, supplies the millimolar zinc concentrations of insulin granules in pancreatic β‐cells, affecting insulin processing, crystallisation and secretion. ZnT8 has a transmembrane and a C‐terminal cytosolic domain; the latter has important functions and purportedly mediates protein–protein interactions, senses cytosolic zinc and/or channels zinc to the transport site in the transmembrane domain (TMD). A common variant W325R in the C‐terminal domain (CTD) increases the risk to develop type 2 diabetes and affects autoantibody specificity in type 1 diabetes. To investigate the differences between the two protein variants, we purified and biophysically characterised both variants of the ZnT8 CTD [R325 variant of ZnT8 CTD (aa267–369) (ZnT8cR) and W325 variant of ZnT8 CTD (aa267–369) (ZnT8cW)]. The domains fold independently of the TMD. Remarkably, the ZnT8cW variant (diabetes protection in the full‐length protein) is less thermostable than the ZnT8cR variant (diabetes risk in the full‐length protein). The ZnT8cW monomers associate with higher affinity. Both CTD variants bind zinc with a stoichiometry that differs from bacterial homologues, emphasising the limitation of the latter as models for the structure and function of the human proteins. The relatively small but reproducible differences between the two ZnT8 CTD variants begin to provide a molecular basis for the different diabetes susceptibility caused by the full‐length ZnT8 proteins.
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Affiliation(s)
- Douglas S Parsons
- Metal Metabolism Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Christer Hogstrand
- Metal Metabolism Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Wolfgang Maret
- Metal Metabolism Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
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57
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58
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Kocyła A, Adamczyk J, Krężel A. Interdependence of free zinc changes and protein complex assembly – insights into zinc signal regulation. Metallomics 2018; 10:120-131. [DOI: 10.1039/c7mt00301c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Small and local changes in cellular free zinc concentration affect protein assembly.
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Affiliation(s)
- Anna Kocyła
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Justyna Adamczyk
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Artur Krężel
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
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59
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Fudge DH, Black R, Qin Y. Optical Recording of Cellular Zinc Dynamics with Zinc-Finger-Based Biosensors. Methods Mol Biol 2018; 1867:103-112. [PMID: 30155818 DOI: 10.1007/978-1-4939-8799-3_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In addition to serving as an essential structural component, zinc is also involved in intracellular and intercellular signaling pathways to impact a number of cellular functions. Genetically encoded zinc sensors that are specifically targeted to various subcellular compartments (ER, mitochondria, nucleus, plasma membrane, and vesicles) have been proven to provide accurate and sensitive visualization and quantification of zinc. Here we describe the methods to utilize both ratiometric and intensiometric genetically encoded zinc sensors designed based on zinc fingers for imaging and quantification of cellular free, labile zinc concentrations, [Zn2+]free. This chapter explains in detail how to quantify [Zn2+]free in live cells as well as how to monitor zinc influx in INS-1 cells stimulated with high glucose.
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Affiliation(s)
- Dylan H Fudge
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Ray Black
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, USA.
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60
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Hao Z, Zhu R, Chen PR. Genetically encoded fluorescent sensors for measuring transition and heavy metals in biological systems. Curr Opin Chem Biol 2017; 43:87-96. [PMID: 29275290 DOI: 10.1016/j.cbpa.2017.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Abstract
Great progress has been made in expanding the repertoire of genetically encoded fluorescent sensors for monitoring intracellular transition metals (TMs). This powerful toolkit permits dynamic and non-invasive detection of TMs with high spatial-temporal resolution, which enables us to better understand the roles of TM homeostasis in both physiological and pathological settings. Here we summarize the recent development of genetically encoded fluorescent sensors for intracellular detection of TMs such as zinc and copper, as well as heavy metals including lead, cadmium, mercury, and arsenic.
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Affiliation(s)
- Ziyang Hao
- Synthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Department of Chemistry, The University of Chicago, Chicago 60637, USA
| | - Rongfeng Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing, China.
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61
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Pratibha, Singh S, Sivakumar S, Verma S. Purine-Based Fluorescent Sensors for Imaging Zinc Ions in HeLa Cells. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pratibha
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur Uttar Pradesh India
| | - Swati Singh
- Department of Chemical Engineering; Material Science Programme; Indian Institute of Technology Kanpur; 208016 Kanpur Uttar Pradesh India
| | - Sri Sivakumar
- Department of Chemical Engineering; Material Science Programme; Indian Institute of Technology Kanpur; 208016 Kanpur Uttar Pradesh India
| | - Sandeep Verma
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur Uttar Pradesh India
- DST Thematic Unit of Excellence on Soft Nanofabrication; Indian Institute of Technology Kanpur; 208016 Kanpur Uttar Pradesh India
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62
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Koopman CD, Zimmermann WH, Knöpfel T, de Boer TP. Cardiac optogenetics: using light to monitor cardiac physiology. Basic Res Cardiol 2017; 112:56. [PMID: 28861604 PMCID: PMC5579185 DOI: 10.1007/s00395-017-0645-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/28/2017] [Indexed: 12/12/2022]
Abstract
Our current understanding of cardiac excitation and its coupling to contraction is largely based on ex vivo studies utilising fluorescent organic dyes to assess cardiac action potentials and signal transduction. Recent advances in optogenetic sensors open exciting new possibilities for cardiac research and allow us to answer research questions that cannot be addressed using the classic organic dyes. Especially thrilling is the possibility to use optogenetic sensors to record parameters of cardiac excitation and contraction in vivo. In addition, optogenetics provide a high spatial resolution, as sensors can be coupled to motifs and targeted to specific cell types and subcellular domains of the heart. In this review, we will give a comprehensive overview of relevant optogenetic sensors, how they can be utilised in cardiac research and how they have been applied in cardiac research up to now.
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Affiliation(s)
- Charlotte D Koopman
- Department of Medical Physiology, University Medical Center Utrecht, Yalelaan 50, 3584CM, Utrecht, The Netherlands.,Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, 3584CT, Utrecht, The Netherlands
| | - Wolfram H Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany.,DHZK (German Center for Cardiovascular Research), Partner Site, Göttingen, Germany
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London, UK.,Centre for Neurotechnology, Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Teun P de Boer
- Department of Medical Physiology, University Medical Center Utrecht, Yalelaan 50, 3584CM, Utrecht, The Netherlands.
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63
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Carter KP, Carpenter MC, Fiedler B, Jimenez R, Palmer AE. Critical Comparison of FRET-Sensor Functionality in the Cytosol and Endoplasmic Reticulum and Implications for Quantification of Ions. Anal Chem 2017; 89:9601-9608. [PMID: 28758723 DOI: 10.1021/acs.analchem.7b02933] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genetically encoded sensors based on fluorescence resonance energy transfer (FRET) are powerful tools for quantifying and visualizing analytes in living cells, and when targeted to organelles have the potential to define distribution of analytes in different parts of the cell. However, quantitative estimates of analyte distribution require rigorous and systematic analysis of sensor functionality in different locations. In this work, we establish methods to critically evaluate sensor performance in different organelles and carry out a side-by-side comparison of three different genetically encoded sensor platforms for quantifying cellular zinc ions (Zn2+). Calibration conditions are optimized for high dynamic range and stable FRET signals. Using a combination of single-cell microscopy and a novel microfluidic platform capable of screening thousands of cells in a few hours, we observe differential performance of these sensors in the cytosol compared to the ER of HeLa cells, and identify the formation of oxidative oligomers of the sensors in the ER. Finally, we use new methodology to re-evaluate the binding parameters of these sensors both in the test tube and in living cells. Ultimately, we demonstrate that sensor responses can be affected by different cellular environments, and provide a framework for evaluating future generations of organelle-targeted sensors.
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Affiliation(s)
- Kyle P Carter
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States.,BioFrontiers Institute, University of Colorado , Boulder, Colorado 80303, United States
| | - Margaret C Carpenter
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States.,BioFrontiers Institute, University of Colorado , Boulder, Colorado 80303, United States
| | - Brett Fiedler
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States.,JILA, University of Colorado and National Institute of Standards and Technology , Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States.,JILA, University of Colorado and National Institute of Standards and Technology , Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States.,BioFrontiers Institute, University of Colorado , Boulder, Colorado 80303, United States
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64
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Gerber PA, Rutter GA. The Role of Oxidative Stress and Hypoxia in Pancreatic Beta-Cell Dysfunction in Diabetes Mellitus. Antioxid Redox Signal 2017; 26:501-518. [PMID: 27225690 PMCID: PMC5372767 DOI: 10.1089/ars.2016.6755] [Citation(s) in RCA: 397] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE Metabolic syndrome is a frequent precursor of type 2 diabetes mellitus (T2D), a disease that currently affects ∼8% of the adult population worldwide. Pancreatic beta-cell dysfunction and loss are central to the disease process, although understanding of the underlying molecular mechanisms is still fragmentary. Recent Advances: Oversupply of nutrients, including glucose and fatty acids, and the subsequent overstimulation of beta cells, are believed to be an important contributor to insulin secretory failure in T2D. Hypoxia has also recently been implicated in beta-cell damage. Accumulating evidence points to a role for oxidative stress in both processes. Although the production of reactive oxygen species (ROS) results from enhanced mitochondrial respiration during stimulation with glucose and other fuels, the expression of antioxidant defense genes is unusually low (or disallowed) in beta cells. CRITICAL ISSUES Not all subjects with metabolic syndrome and hyperglycemia go on to develop full-blown diabetes, implying an important role in disease risk for gene-environment interactions. Possession of common risk alleles at the SLC30A8 locus, encoding the beta-cell granule zinc transporter ZnT8, may affect cytosolic Zn2+ concentrations and thus susceptibility to hypoxia and oxidative stress. FUTURE DIRECTIONS Loss of normal beta-cell function, rather than total mass, is increasingly considered to be the major driver for impaired insulin secretion in diabetes. Better understanding of the role of oxidative changes, its modulation by genes involved in disease risk, and effects on beta-cell identity may facilitate the development of new therapeutic strategies to this disease. Antioxid. Redox Signal. 26, 501-518.
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Affiliation(s)
- Philipp A. Gerber
- Department of Endocrinology, Diabetes and Clinical Nutrition, University Hospital Zurich, Zurich, Switzerland
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, London, United Kingdom
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65
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Abstract
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.
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Affiliation(s)
- Lynn Sanford
- University of Colorado Boulder, Boulder, CO, United States
| | - Amy Palmer
- University of Colorado Boulder, Boulder, CO, United States.
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66
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Li CR, Li SL, Yang ZY. Development of a coumarin-furan conjugate as Zn 2+ ratiometric fluorescent probe in ethanol-water system. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:214-222. [PMID: 27915158 DOI: 10.1016/j.saa.2016.11.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
In this study, a novel coumarin-derived compound bearing the furan moiety called 7-diethylamino-3-formylcoumarin (2'-furan formyl) hydrazone (1) has been designed, synthesized and evaluated as a Zn2+ ratiometric fluorescent probe in ethanol-water system. This probe 1 showed good selectivity and high sensitivity towards Zn2+ over other metal ions investigated, and a decrease in fluorescence emission intensity at 511nm accompanied by an enhancement in fluorescence emission intensity at 520nm of this probe 1 was observed in the presence of Zn2+ in ethanol-water (V : V=9 : 1) solution, which provided ratiometric fluorescence detection of Zn2+. Additionally, the ratiometric fluorescence response of 1 to Zn2+ was nearly completed within 0.5min, which suggested that this probe 1 could be utilized for sensing and monitoring Zn2+ in environmental and biological systems for real-time detection.
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Affiliation(s)
- Chao-Rui Li
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China
| | - Si-Liang Li
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China; School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou 730050, PR China
| | - Zheng-Yin Yang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China.
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Abstract
FRET-sensors have become important tools for intracellular imaging, but their dependence on external illumination presents some limitations, such as photobleaching and phototoxicity, which limit measurements over extended periods of time. Fluorescence measurements also suffer from autofluorescence and light scattering, which hampers in vivo imaging and measurements in strongly absorbing and scattering media such as blood. In principle, these issues can be resolved by using sensors based on bioluminescence resonance energy transfer (BRET). The recent development of brighter and more stable luciferases and the concomitant improvement in luciferase substrates have substantially decreased the sensitivity gap between fluorescence and bioluminescence. As a result, the application of BRET-sensors is no longer restricted to measurements on cell populations, but they can also be used for imaging of single living cells, and BRET has started to emerge as an attractive sensor format for point-of-care diagnostics. The aim of this chapter is to first provide a brief overview of the basic design principles for BRET-sensors. Next, important design considerations will be discussed in more detail by describing the development of three different classes of BRET-sensors, both from our own work and that of others. These examples are all based on the NanoLuc luciferase, a bright and very stable blue light-emitting luciferase developed by Promega that has quickly risen to prominence in the bioluminescence field.
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Affiliation(s)
- Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Stijn J A Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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68
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Zhang Y, Avalos JL. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28067471 DOI: 10.1002/wsbm.1373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023]
Abstract
Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans-omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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69
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Hessels AM, Taylor KM, Merkx M. Monitoring cytosolic and ER Zn(2+) in stimulated breast cancer cells using genetically encoded FRET sensors. Metallomics 2016; 8:211-7. [PMID: 26739447 PMCID: PMC4756312 DOI: 10.1039/c5mt00257e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Zn(2+)-specific ion channel ZIP7 has been implicated to play an important role in releasing Zn(2+) from the ER. External stimulation of breast cancer cells has been proposed to induce phosphorylation of ZIP7 by CK2α, resulting in ZIP7-mediated Zn(2+) release from the ER into the cytosol. Here, we examined whether changes in cytosolic and ER Zn(2+) concentrations can be detected upon such external stimuli. Two previously developed FRET sensors for Zn(2+), eZinCh-2 (Kd = 1 nM at pH 7.1) and eCALWY-4 (Kd = 0.63 nM at pH 7.1), were expressed in both the cytosol and the ER of wild-type MCF-7 and TamR cells. Treatment of MCF-7 and TamR cells with external Zn(2+) and pyrithione, one of the previously used triggers, resulted in an immediate increase in free Zn(2+) in both cytosol and ER, suggesting that Zn(2+) was directly transferred across the cellular membranes by pyrithione. Cells treated with a second trigger, EGF/ionomycin, showed no changes in intracellular Zn(2+) levels, neither in multicolor imaging experiments that allowed simultaneous imaging of cytosolic and ER Zn(2+), nor in experiments in which cytosolic and ER Zn(2+) were monitored separately. In contrast to previous work using small-molecule fluorescent dyes, these results indicate that EGF-ionomycin treatment does not result in significant changes in cytosolic Zn(2+) levels as a result from Zn(2+) release from the ER. These results underline the importance of using genetically encoded fluorescent sensors to complement and verify intracellular imaging experiments with synthetic fluorescent Zn(2+) dyes.
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Affiliation(s)
- Anne M Hessels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Kathryn M Taylor
- Breast Cancer Molecular Pharmacology Group, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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70
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Chabosseau P, Rutter GA. Zinc and diabetes. Arch Biochem Biophys 2016; 611:79-85. [DOI: 10.1016/j.abb.2016.05.022] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/09/2016] [Accepted: 05/31/2016] [Indexed: 01/09/2023]
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Abstract
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Genetically encoded
FRET-based sensor proteins have significantly
contributed to our current understanding of the intracellular functions
of Zn2+. However, the external excitation required for
these fluorescent sensors can give rise to photobleaching and phototoxicity
during long-term imaging, limits applications that suffer from autofluorescence
and light scattering, and is not compatible with light-sensitive cells.
For these applications, sensor proteins based on Bioluminescence Resonance
Energy Transfer (BRET) would provide an attractive alternative. In
this work, we used the bright and stable luciferase NanoLuc to create
the first genetically encoded BRET sensors for measuring intracellular
Zn2+. Using a new sensor approach, the NanoLuc domain was
fused to the Cerulean donor domain of two previously developed FRET
sensors, eCALWY and eZinCh-2. In addition to preserving the excellent
Zn2+ affinity and specificity of their predecessors, these
newly developed sensors enable both BRET- and FRET-based detection.
While the dynamic range of the BRET signal for the eCALWY-based BLCALWY-1
sensor was limited by the presence of two competing BRET pathways,
BRET/FRET sensors based on the eZinCh-2 scaffold (BLZinCh-1 and -2)
yielded robust 25–30% changes in BRET ratio. In addition, introduction
of a chromophore-silencing mutation resulted in a BRET-only sensor
(BLZinCh-3) with increased BRET response (50%) and an unexpected 10-fold
increase in Zn2+ affinity. The combination of robust ratiometric
response, physiologically relevant Zn2+ affinities, and
stable and bright luminescence signal offered by the BLZinCh sensors
allowed monitoring of intracellular Zn2+ in plate-based
assays as well as intracellular BRET-based imaging in single living
cells in real time.
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Affiliation(s)
- Stijn J. A. Aper
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems (ICMS),
Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Pieterjan Dierickx
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
- Division
of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems (ICMS),
Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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72
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Qin Y, Sammond DW, Braselmann E, Carpenter MC, Palmer AE. Development of an Optical Zn 2+ Probe Based on a Single Fluorescent Protein. ACS Chem Biol 2016; 11:2744-2751. [PMID: 27467056 DOI: 10.1021/acschembio.6b00442] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Various fluorescent probes have been developed to reveal the biological functions of intracellular labile Zn2+. Here, we present Green Zinc Probe (GZnP), a novel genetically encoded Zn2+ sensor design based on a single fluorescent protein (single-FP). The GZnP sensor is generated by attaching two zinc fingers (ZF) of the transcription factor Zap1 (ZF1 and ZF2) to the two ends of a circularly permuted green fluorescent protein (cpGFP). Formation of ZF folds induces interaction between the two ZFs, which induces a change in the cpGFP conformation, leading to an increase in fluorescence. A small sensor library is created to include mutations in the ZFs, cpGFP and linkers between ZF and cpGFP to improve signal stability, sensor brightness and dynamic range based on rational protein engineering, and computational design by Rosetta. Using a cell-based library screen, we identify sensor GZnP1, which demonstrates a stable maximum signal, decent brightness (QY = 0.42 at apo state), as well as specific and sensitive response to Zn2+ in HeLa cells (Fmax/Fmin = 2.6, Kd = 58 pM, pH 7.4). The subcellular localizing sensors mito-GZnP1 (in mitochondria matrix) and Lck-GZnP1 (on plasma membrane) display sensitivity to Zn2+ (Fmax/Fmin = 2.2). This sensor design provides freedom to be used in combination with other optical indicators and optogenetic tools for simultaneous imaging and advancing our understanding of cellular Zn2+ function.
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Affiliation(s)
- Yan Qin
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Deanne W. Sammond
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Esther Braselmann
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Margaret C. Carpenter
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Amy E. Palmer
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
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73
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Abstract
Genetically encoded fluorescent Zn(2+) indicators (GEZIs) are highly attractive research tools for studying Zn(2+) homeostasis and signaling in mammalian cells. Most current GEZIs are based on Förster resonance energy transfer (FRET) between a select pair of fluorescent proteins (FPs) fused with Zn(2+)-binding motifs. One drawback of such FRET-based GEZIs is their broad spectral profile bandwidths, creating challenges when monitoring multiple targets or parameters. To address this issue, we have engineered a group of intensiometric GEZIs based on single teal and red FPs that can be utilized to monitor subcellular Zn(2+) diffusion and glucose-induced Zn(2+) secretion in pancreatic INS-1E β-cells. These GEZIs offer the simplicity of intensiometric measurements, compatibility in multicolor imaging, large dynamic ranges, and relatively small molecular sizes, making them valuable additions to the molecular toolbox for imaging Zn(2+).
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Affiliation(s)
- Zhijie Chen
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
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74
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Carpenter MC, Lo MN, Palmer AE. Techniques for measuring cellular zinc. Arch Biochem Biophys 2016; 611:20-29. [PMID: 27580940 DOI: 10.1016/j.abb.2016.08.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 02/08/2023]
Abstract
The development and improvement of fluorescent Zn2+ sensors and Zn2+ imaging techniques have increased our insight into this biologically important ion. Application of these tools has identified an intracellular labile Zn2+ pool and cultivated further interest in defining the distribution and dynamics of labile Zn2+. The study of Zn2+ in live cells in real time using sensors is a powerful way to answer complex biological questions. In this review, we highlight newly engineered Zn2+ sensors, methods to test whether the sensors are accessing labile Zn2+, and recent studies that point to the challenges of using such sensors. Elemental mapping techniques can complement and strengthen data collected with sensors. Both mass spectrometry-based and X-ray fluorescence-based techniques yield highly specific, sensitive, and spatially resolved snapshots of metal distribution in cells. The study of Zn2+ has already led to new insight into all phases of life from fertilization of the egg to life-threatening cancers. In order to continue building new knowledge about Zn2+ biology it remains important to critically assess the available toolset for this endeavor.
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Affiliation(s)
- Margaret C Carpenter
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, United States.
| | - Maria N Lo
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, United States.
| | - Amy E Palmer
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, United States.
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75
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Aper SJ, Merkx M. Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn(2+) Sensor into a Light-Responsive Zn(2+) Binding Protein. ACS Synth Biol 2016; 5:698-709. [PMID: 27031076 DOI: 10.1021/acssynbio.6b00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein-based sensors and switches provide attractive tools for the real-time monitoring and control of molecular processes in complex biological environments. Fluorescent sensor proteins have been developed for a wide variety of small molecules, but the construction of genetically encoded light-responsive ligand binding proteins remains mostly unexplored. Here we present a generic approach to reengineer a previously developed FRET-based Zn(2+) sensor into a light-activatable Zn(2+) binding protein using a design strategy based on mutually exclusive domain interactions. These so-called VividZn proteins consist of two light-responsive Vivid domains that homodimerize upon illumination with blue light, thus preventing the binding of Zn(2+) between two Zn(2+) binding domains, Atox1 and WD4. Following optimization of the linker between WD4 and the N-terminus of one of the Vivid domains, VividZn variants were obtained that show a 9- to 55-fold decrease in Zn(2+) affinity upon illumination, which is fully reversible following dark adaptation. The Zn(2+) affinities of the switch could be rationally tuned between 1 pM and 2 nM by systematic variation of linker length and mutation of one of the Zn(2+) binding residues. Similarly, introduction of mutations in the Vivid domains allowed tuning of the switching kinetics between 10 min and 7 h. Low expression levels in mammalian cells precluded the demonstration of light-induced perturbation of cytosolic Zn(2+) levels. Nonetheless, our results firmly establish the use of intramolecular Vivid dimerization as an attractive light-sensitive input module to rationally engineer light-responsive protein switches based on mutually exclusive domain interactions.
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Affiliation(s)
- Stijn J.A. Aper
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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76
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Hessels AM, Merkx M. Simple Method for Proper Analysis of FRET Sensor Titration Data and Intracellular Imaging Experiments Based on Isosbestic Points. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anne M. Hessels
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
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