1
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Fluorescence resonance energy transfer-based nanomaterials for the sensing in biological systems. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.12.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Abstract
Embryonic cells grow in environments that provide a plethora of physical cues, including mechanical forces that shape the development of the entire embryo. Despite their prevalence, the role of these forces in embryonic development and their integration with chemical signals have been mostly neglected, and scrutiny in modern molecular embryology tilted, instead, towards the dissection of molecular pathways involved in cell fate determination and patterning. It is now possible to investigate how mechanical signals induce downstream genetic regulatory networks to regulate key developmental processes in the embryo. Here, we review the insights into mechanical control of early vertebrate development, including the role of forces in tissue patterning and embryonic axis formation. We also highlight recent in vitro approaches using individual embryonic stem cells and self-organizing multicellular models of human embryos, which have been instrumental in expanding our understanding of how mechanics tune cell fate and cellular rearrangements during human embryonic development.
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3
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Schlembach I, Grünberger A, Rosenbaum MA, Regestein L. Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes. Trends Biotechnol 2021; 39:1093-1109. [PMID: 33573846 PMCID: PMC7612867 DOI: 10.1016/j.tibtech.2021.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial mixed cultures are gaining increasing attention as biotechnological production systems, since they offer a large but untapped potential for future bioprocesses. Effects of secondary metabolite induction and advantages of labor division for the degradation of complex substrates offer new possibilities for process intensification. However, mixed cultures are highly complex, and, consequently, many biotic and abiotic parameters are required to be identified, characterized, and ideally controlled to establish a stable bioprocess. In this review, we discuss the advantages and disadvantages of existing measurement techniques for identifying, characterizing, monitoring, and controlling mixed cultures and highlight promising examples. Moreover, existing challenges and emerging technologies are discussed, which lay the foundation for novel analytical workflows to monitor mixed-culture bioprocesses.
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Affiliation(s)
- Ivan Schlembach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
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4
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Intracellular Ionic Strength Sensing Using NanoLuc. Int J Mol Sci 2021; 22:ijms22020677. [PMID: 33445497 PMCID: PMC7826950 DOI: 10.3390/ijms22020677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.
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5
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Carrasco-López C, García-Echauri SA, Kichuk T, Avalos JL. Optogenetics and biosensors set the stage for metabolic cybergenetics. Curr Opin Biotechnol 2020; 65:296-309. [DOI: 10.1016/j.copbio.2020.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
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6
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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: 12] [Impact Index Per Article: 2.4] [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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7
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Junker NO, Vaghefikia F, Albarghash A, Höfig H, Kempe D, Walter J, Otten J, Pohl M, Katranidis A, Wiegand S, Fitter J. Impact of Molecular Crowding on Translational Mobility and Conformational Properties of Biological Macromolecules. J Phys Chem B 2019; 123:4477-4486. [PMID: 31059260 DOI: 10.1021/acs.jpcb.9b01239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effects of molecular crowding on structural and dynamical properties of biological macromolecules do depend on the concentration of crowding agents but also on the molecular mass and the structural compactness of the crowder molecules. By employing fluorescence correlation spectroscopy (FCS), we investigated the translational mobility of several biological macromolecules ranging from 17 kDa to 2.7 MDa. Polyethylene glycol and Ficoll polymers of different molecular masses were used in buffer solutions to mimic a crowded environment. The reduction in translational mobility of the biological tracer molecules was analyzed as a function of crowder volume fractions and was generally more pronounced in PEG as compared to Ficoll solutions. For several crowding conditions, we observed a molecular sieving effect, in which the diffusion coefficient of larger tracer molecules is reduced to a larger extent than predicted by the Stokes-Einstein relation. By employing a FRET-based biosensor, we also showed that a multiprotein complex is significantly compacted in the presence of macromolecular crowders. Importantly, with respect to sensor in vivo applications, ligand concentration determining sensors would need a crowding specific calibration in order to deliver correct cytosolic ligand concentration.
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Affiliation(s)
- Niklas O Junker
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Farzaneh Vaghefikia
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Alyazan Albarghash
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Henning Höfig
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Daryan Kempe
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Julia Walter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | | | | | | | - Simone Wiegand
- Physikalische Chemie , Universität zu Köln , 50923 Köln , Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
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8
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Botman D, de Groot DH, Schmidt P, Goedhart J, Teusink B. In vivo characterisation of fluorescent proteins in budding yeast. Sci Rep 2019; 9:2234. [PMID: 30783202 PMCID: PMC6381139 DOI: 10.1038/s41598-019-38913-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/14/2018] [Indexed: 02/05/2023] Open
Abstract
Fluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins.
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Affiliation(s)
- Dennis Botman
- Systems Bioinformatics/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Daan Hugo de Groot
- Systems Bioinformatics/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Phillipp Schmidt
- Systems Bioinformatics/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Bioinformatics/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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9
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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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10
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Liu B, Mavrova SN, van den Berg J, Kristensen SK, Mantovanelli L, Veenhoff LM, Poolman B, Boersma AJ. Influence of Fluorescent Protein Maturation on FRET Measurements in Living Cells. ACS Sens 2018; 3:1735-1742. [PMID: 30168711 PMCID: PMC6167724 DOI: 10.1021/acssensors.8b00473] [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] [Indexed: 11/28/2022]
Abstract
![]()
Förster resonance
energy transfer (FRET)-based sensors are
a valuable tool to quantify cell biology, yet it remains necessary
to identify and prevent potential artifacts in order to exploit their
full potential. We show here that artifacts arising from slow donor
mCerulean3 maturation can be substantially diminished by constitutive
expression in both prokaryotic and eukaryotic cells, which can also
be achieved by incorporation of faster-maturing FRET donors. We developed
an improved version of the donor mTurquoise2 that matures faster than
the parent protein. Our analysis shows that using equal maturing fluorophores
in FRET-based sensors or using constitutive low expression conditions
helps to reduce maturation-induced artifacts, without the need of
additional noise-inducing spectral corrections. In general, we show
that monitoring and controlling the maturation of fluorescent proteins
in living cells is important and should be addressed in in
vivo applications of genetically encoded FRET sensors.
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Affiliation(s)
- Boqun Liu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sara N. Mavrova
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jonas van den Berg
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian K. Kristensen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luca Mantovanelli
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University
Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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11
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Höfig H, Otten J, Steffen V, Pohl M, Boersma AJ, Fitter J. Genetically Encoded Förster Resonance Energy Transfer-Based Biosensors Studied on the Single-Molecule Level. ACS Sens 2018; 3:1462-1470. [PMID: 29979038 DOI: 10.1021/acssensors.8b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors for the quantification of ligand molecules change the magnitude of FRET between two fluorescent proteins upon binding a target metabolite. When highly sensitive sensors are being designed, extensive sensor optimization is essential. However, it is often difficult to verify the ideas of modifications made to a sensor during the sensor optimization process because of the limited information content of ensemble FRET measurements. In contrast, single-molecule detection provides detailed information and higher accuracy. Here, we investigated a set of glucose and crowding sensors on the single-molecule level. We report the first comprehensive single-molecule study of FRET-based biosensors with reasonable counting statistics and identify characteristics in the single-molecule FRET histograms that constitute fingerprints of sensor performance. Hence, our single-molecule approach extends the toolbox of methods aiming to understand and optimize the design of FRET-based biosensors.
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Affiliation(s)
- Henning Höfig
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Otten
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Victoria Steffen
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Arnold J. Boersma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, Netherlands
| | - Jörg Fitter
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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12
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Faccio G, Salentinig S. Enzyme-Triggered Dissociation of a FRET-Based Protein Biosensor Monitored by Synchrotron SAXS. Biophys J 2017; 113:1731-1737. [PMID: 29045867 DOI: 10.1016/j.bpj.2017.08.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022] Open
Abstract
Protein biosensors are widely used for the monitoring of metabolite concentration and enzymatic activities inside living cells and in in vitro applications. Neutrophil elastase (NE) is a serine protease of relevance in inflammatory diseases whose activity can lead to pathological conditions if unregulated. This study focuses on the structural characterization of a biosensor for NE activity based on Förster resonance energy transfer (FRET). The cleavage by NE results in dissociation of the FRET fluorescent protein pair and alteration of the fluorescent emission spectrum. We have used small angle x-ray scattering at a high intensity synchrotron source, combined with model-free analysis of the scattering data, to demonstrate the structure of the biosensor and the effect of its exposure to NE on size and shape. These investigations, together with biochemical studies, established the nanostructure-activity relationship that may contribute to the detailed understanding of the FRET-based biosensor and guide the rational design of new biosensor constructs.
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Affiliation(s)
- Greta Faccio
- Laboratory for Biointerfaces, Department "Materials Meet Life", Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.
| | - Stefan Salentinig
- Laboratory for Biointerfaces, Department "Materials Meet Life", Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.
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13
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Sander K, Asano KG, Bhandari D, Van Berkel GJ, Brown SD, Davison B, Tschaplinski TJ. Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:270. [PMID: 29213318 PMCID: PMC5707896 DOI: 10.1186/s13068-017-0960-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are prominent candidate biocatalysts that, together, can enable the direct biotic conversion of lignocellulosic biomass to ethanol. The imbalance and suboptimal turnover rates of redox cofactors are currently hindering engineering efforts to achieve higher bioproductivity in both organisms. Measuring relevant intracellular cofactor concentrations will help understand redox state of these cofactors and help identify a strategy to overcome these limitations; however, metabolomic determinations of these labile metabolites have historically proved challenging. RESULTS Through our validations, we verified the handling and storage stability of these metabolites, and verified extraction matrices and extraction solvent were not suppressing mass spectrometry signals. We recovered adenylate energy charge ratios (a main quality indicator) above 0.82 for all extractions. NADH/NAD+ values of 0.26 and 0.04 for an adhE-deficient strain of C. thermocellum and its parent, respectively, reflect the expected shift to a more reduced redox potential when a species lacks the ability to re-oxidize NADH by synthesizing ethanol. This method failed to yield reliable results with C. bescii and poor-growing strains of T. saccharolyticum. CONCLUSIONS Our validated protocols demonstrate and validate the extraction and analysis of selected redox and energy-related metabolites from two candidate consolidated bioprocessing biocatalysts, C. thermocellum and T. saccharolyticum. This development and validation highlights the important, but often neglected, need to optimize and validate metabolomic protocols when adapting them to new cell or tissue types.
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Affiliation(s)
- Kyle Sander
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Keiji G. Asano
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Deepak Bhandari
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Gary J. Van Berkel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Steven D. Brown
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Skokie, IL USA
| | - Brian Davison
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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14
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Abstract
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Knowledge of the
ionic strength in cells is required to understand
the in vivo biochemistry of the charged biomacromolecules.
Here, we present the first sensors to determine the ionic strength
in living cells, by designing protein probes based on Förster
resonance energy transfer (FRET). These probes allow observation of
spatiotemporal changes in the ionic strength on the single-cell level.
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Affiliation(s)
- Boqun Liu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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15
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Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A. Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Rupprecht C, Wingen M, Potzkei J, Gensch T, Jaeger KE, Drepper T. A novel FbFP-based biosensor toolbox for sensitive in vivo determination of intracellular pH. J Biotechnol 2017; 258:25-32. [PMID: 28501596 DOI: 10.1016/j.jbiotec.2017.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 02/07/2023]
Abstract
The intracellular pH is an important modulator of various bio(techno)logical processes such as enzymatic conversion of metabolites or transport across the cell membrane. Changes of intracellular pH due to altered proton distribution can thus cause dysfunction of cellular processes. Consequently, accurate monitoring of intracellular pH allows elucidating the pH-dependency of (patho)physiological and biotechnological processes. In this context, genetically encoded biosensors represent a powerful tool to determine intracellular pH values non-invasively and with high spatiotemporal resolution. We have constructed a toolbox of novel genetically encoded FRET-based pH biosensors (named Fluorescence Biosensors for pH or FluBpH) that utilizes the FMN-binding fluorescent protein EcFbFP as donor domain. In contrast to many fluorescent proteins of the GFP family, EcFbFP exhibits a remarkable tolerance towards acidic pH (pKa∼3.2). To cover the broad range of physiologically relevant pH values, three EYFP variants exhibiting pKa values of 5.7, 6.1 and 7.5 were used as pH-sensing FRET acceptor domains. The resulting biosensors FluBpH 5.7, FluBpH 6.1 and FluBpH 7.5 were calibrated in vitro and in vivo to accurately evaluate their pH indicator properties. To demonstrate the in vivo applicability of FluBpH, changes of intracellular pH were ratiometrically measured in E. coli cells during acid stress.
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Affiliation(s)
- Christian Rupprecht
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Marcus Wingen
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Janko Potzkei
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; GO-Bio Projekt SenseUP, Forschungszentrum Jülich, D-52425 Jülich GmbH, Germany
| | - Thomas Gensch
- Institute of Complex Systems ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis. SENSORS 2016; 16:s16101604. [PMID: 27690044 PMCID: PMC5087393 DOI: 10.3390/s16101604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/15/2016] [Accepted: 09/20/2016] [Indexed: 12/12/2022]
Abstract
Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET)-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP) flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP), Citrine). Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum) strain DM1933 in a BioLector® microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization.
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18
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Steffen V, Otten J, Radek A, Wiechert W, Noack S, Pohl M. FRET-Based Biosensors for Online Measurement of Lysine Production. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201650264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Liemburg-Apers DC, Schirris TJJ, Russel FGM, Willems PHGM, Koopman WJH. Mitoenergetic Dysfunction Triggers a Rapid Compensatory Increase in Steady-State Glucose Flux. Biophys J 2016; 109:1372-86. [PMID: 26445438 DOI: 10.1016/j.bpj.2015.08.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/13/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022] Open
Abstract
ATP can be produced in the cytosol by glycolytic conversion of glucose (GLC) into pyruvate. The latter can be metabolized into lactate, which is released by the cell, or taken up by mitochondria to fuel ATP production by the tricarboxylic acid cycle and oxidative phosphorylation (OXPHOS) system. Altering the balance between glycolytic and mitochondrial ATP generation is crucial for cell survival during mitoenergetic dysfunction, which is observed in a large variety of human disorders including cancer. To gain insight into the kinetic properties of this adaptive mechanism we determined here how acute (30 min) inhibition of OXPHOS affected cytosolic GLC homeostasis. GLC dynamics were analyzed in single living C2C12 myoblasts expressing the fluorescent biosensor FLII(12)Pglu-700μδ6 (FLII). Following in situ FLII calibration, the kinetic properties of GLC uptake (V1) and GLC consumption (V2) were determined independently and used to construct a minimal mathematical model of cytosolic GLC dynamics. After validating the model, it was applied to quantitatively predict V1 and V2 at steady-state (i.e., when V1 = V2 = Vsteady-state) in the absence and presence of OXPHOS inhibitors. Integrating model predictions with experimental data on lactate production, cell volume, and O2 consumption revealed that glycolysis and mitochondria equally contribute to cellular ATP production in control myoblasts. Inhibition of OXPHOS induced a twofold increase in Vsteady-state and glycolytic ATP production flux. Both in the absence and presence of OXPHOS inhibitors, GLC was consumed at near maximal rates, meaning that GLC consumption is rate-limiting under steady-state conditions. Taken together, we demonstrate here that OXPHOS inhibition increases steady-state GLC uptake and consumption in C2C12 myoblasts. This activation fully compensates for the reduction in mitochondrial ATP production, thereby maintaining the balance between cellular ATP supply and demand.
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Affiliation(s)
- Dania C Liemburg-Apers
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter H G M Willems
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Werner J H Koopman
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands.
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20
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Ng HL, Lin MZ. Structure-guided wavelength tuning in far-red fluorescent proteins. Curr Opin Struct Biol 2016; 39:124-133. [PMID: 27468111 PMCID: PMC5548387 DOI: 10.1016/j.sbi.2016.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/28/2016] [Accepted: 07/13/2016] [Indexed: 12/11/2022]
Abstract
In recent years, protein engineers have succeeded in tuning the excitation spectra of natural fluorescent proteins from green wavelengths into orange and red wavelengths, resulting in the creation of a series of fluorescent proteins with emission in the far-red portions of the optical spectrum. These results have arisen from the synergistic combination of structural knowledge of fluorescent proteins, chemical intuition, and high-throughput screening methods. Here we review structural features found in autocatalytic far-red fluorescent proteins, and discuss how they add to our understanding of the biophysical mechanisms of wavelength tuning in biological chromophores.
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Affiliation(s)
- Ho-Leung Ng
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA; University of Hawaii Cancer Center, Honolulu, HI, USA.
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Pediatrics, Stanford University, Stanford, CA, USA.
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21
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Grosch JH, Sieben M, Lattermann C, Kauffmann K, Büchs J, Spieß AC. Enzyme activity deviates due to spatial and temporal temperature profiles in commercial microtiter plate readers. Biotechnol J 2016; 11:519-29. [DOI: 10.1002/biot.201500422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/08/2015] [Accepted: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
| | - Michaela Sieben
- RWTH Aachen University, AVT - Biochemical Engineering; Aachen Germany
| | | | - Kira Kauffmann
- RWTH Aachen University, AVT - Enzyme Process Technology; Aachen Germany
| | - Jochen Büchs
- RWTH Aachen University, AVT - Enzyme Process Technology; Aachen Germany
| | - Antje C. Spieß
- RWTH Aachen University, AVT - Enzyme Process Technology; Aachen Germany
- DWI - Leibniz-Institute for Interactive Materials; Aachen Germany
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22
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Schulenburg C, Faccio G, Jankowska D, Maniura-Weber K, Richter M. A FRET-based biosensor for the detection of neutrophil elastase. Analyst 2016; 141:1645-8. [DOI: 10.1039/c5an01747e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The direct and specific detection of biomarkers activity is crucial as it can allow monitoring the state of tissue or wound, as well as the progression of the inflammatory process.
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Affiliation(s)
- C. Schulenburg
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - G. Faccio
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - D. Jankowska
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - K. Maniura-Weber
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - M. Richter
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
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23
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Faccio G, Bannwarth MB, Schulenburg C, Steffen V, Jankowska D, Pohl M, Rossi RM, Maniura-Weber K, Boesel LF, Richter M. Encapsulation of FRET-based glucose and maltose biosensors to develop functionalized silica nanoparticles. Analyst 2016; 141:3982-4. [DOI: 10.1039/c5an02573g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silicate nanoparticles with immobilized FRET-based biosensors were developed for the detection of glucose and maltose.
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24
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Liu D, Evans T, Zhang F. Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 2015; 31:35-43. [DOI: 10.1016/j.ymben.2015.06.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
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25
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Ermilov EA, Schlak M, Steffen R, Liu XQ, Liu JY, Röder B. Energy transfer properties of a novel boron dipyrromethene–perylenediimide donor–acceptor dyad. RSC Adv 2015. [DOI: 10.1039/c5ra10077a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The boron dipyrromethene–perylenediimide dyad has been prepared and studied for its light-harvesting properties with various steady-state and time-resolved spectroscopic methods.
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Affiliation(s)
- Eugeny A. Ermilov
- Institut für Physik
- Photobiophysik
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | - Martin Schlak
- Institut für Physik
- Photobiophysik
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | - Ronald Steffen
- Institut für Physik
- Photobiophysik
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | - Xiao-Qiong Liu
- State Key Laboratory of Photocatalysis on Energy and Environment & Fujian Engineering Research Center of Functional Materials
- College of Chemistry
- Fuzhou University
- Fuzhou 350002
- P. R. China
| | - Jian-Yong Liu
- State Key Laboratory of Photocatalysis on Energy and Environment & Fujian Engineering Research Center of Functional Materials
- College of Chemistry
- Fuzhou University
- Fuzhou 350002
- P. R. China
| | - Beate Röder
- Institut für Physik
- Photobiophysik
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
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