1
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Jeong HJ. Quenchbodies That Enable One-Pot Detection of Antigens: A Structural Perspective. Bioengineering (Basel) 2023; 10:1262. [PMID: 38002387 PMCID: PMC10669387 DOI: 10.3390/bioengineering10111262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Quenchbody (Q-body) is a unique, reagentless, fluorescent antibody whose fluorescent intensity increases in an antigen-concentration-dependent manner. Q-body-based homogeneous immunoassay is superior to conventional immunoassays as it does not require multiple immobilization, reaction, and washing steps. In fact, simply mixing the Q-body and the sample containing the antigen enables the detection of the target antigen. To date, various Q-bodies have been developed to detect biomarkers of interest, including haptens, peptides, proteins, and cells. This review sought to describe the principle of Q-body-based immunoassay and the use of Q-body for various immunoassays. In particular, the Q-bodies were classified from a structural perspective to provide useful information for designing Q-bodies with an appropriate objective.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University, Sejong-si 30016, Republic of Korea
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2
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Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
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Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
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3
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van Hoogstraten SWG, Kuik C, Arts JJC, Cillero-Pastor B. Molecular imaging of bacterial biofilms-a systematic review. Crit Rev Microbiol 2023:1-22. [PMID: 37452571 DOI: 10.1080/1040841x.2023.2223704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023]
Abstract
The formation of bacterial biofilms in the human body and on medical devices is a serious human health concern. Infections related to bacterial biofilms are often chronic and difficult to treat. Detailed information on biofilm formation and composition over time is essential for a fundamental understanding of the underlying mechanisms of biofilm formation and its response to anti-biofilm therapy. However, information on the chemical composition, structural components of biofilms, and molecular interactions regarding metabolism- and communication pathways within the biofilm, such as uptake of administered drugs or inter-bacteria communication, remains elusive. Imaging these molecules and their distribution in the biofilm increases insight into biofilm development, growth, and response to environmental factors or drugs. This systematic review provides an overview of molecular imaging techniques used for bacterial biofilm imaging. The techniques included mass spectrometry-based techniques, fluorescence-labelling techniques, spectroscopic techniques, nuclear magnetic resonance spectroscopy (NMR), micro-computed tomography (µCT), and several multimodal approaches. Many molecules were imaged, such as proteins, lipids, metabolites, and quorum-sensing (QS) molecules, which are crucial in intercellular communication pathways. Advantages and disadvantages of each technique, including multimodal approaches, to study molecular processes in bacterial biofilms are discussed, and recommendations on which technique best suits specific research aims are provided.
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Affiliation(s)
- S W G van Hoogstraten
- Laboratory for Experimental Orthopaedics, Department of Orthopaedic Surgery, CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - C Kuik
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - J J C Arts
- Laboratory for Experimental Orthopaedics, Department of Orthopaedic Surgery, CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
- Department of Biomedical Engineering, Orthopaedic Biomechanics, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - B Cillero-Pastor
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
- Department of Cell Biology-Inspired Tissue Engineering, The MERLN Institute for Technology-Inspired Regenerative Medicine, University of Maastricht, Maastricht, the Netherlands
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4
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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5
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Electron transfer in protein modifications: from detection to imaging. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1417-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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6
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Liu Y, Yuan G, Hassan MM, Abraham PE, Mitchell JC, Jacobson D, Tuskan GA, Khakhar A, Medford J, Zhao C, Liu CJ, Eckert CA, Doktycz MJ, Tschaplinski TJ, Yang X. Biological and Molecular Components for Genetically Engineering Biosensors in Plants. BIODESIGN RESEARCH 2022; 2022:9863496. [PMID: 37850147 PMCID: PMC10521658 DOI: 10.34133/2022/9863496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/08/2022] [Indexed: 10/19/2023] Open
Abstract
Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.
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Affiliation(s)
- Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - June Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Cheng Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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7
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Cumberbatch D, Mori T, Yang J, Mi D, Vinson P, Weaver CD, Johnson CH. A BRET Ca 2+ sensor enables high-throughput screening in the presence of background fluorescence. Sci Signal 2022; 15:eabq7618. [PMID: 35973028 PMCID: PMC9930640 DOI: 10.1126/scisignal.abq7618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The intrinsic fluorescence of samples confounds the use of fluorescence-based sensors. This is of particular concern in high-throughput screening (HTS) applications using large chemical libraries containing intrinsically fluorescent compounds. To overcome this problem, we developed a bioluminescence resonance energy transfer (BRET) Ca2+ sensor, CalfluxCTN. We demonstrated that it reliably reported changes in intracellular Ca2+ concentrations evoked by an agonist and an antagonist of the human muscarinic acetylcholine receptor M1 (hM1R) even in the presence of the fluorescent compound fluorescein, which interfered with a standard fluorescent HTS sensor (Fluo-8). In an HTS using a chemical library containing fluorescent compounds, CalfluxCTN accurately identified agonists and antagonists that were missed or miscategorized using Fluo-8. Moreover, we showed that a luciferase substrate that becomes activated only when inside cells generated long-lasting BRET signals in HTS, enabling results to be reliably compared among replicate samples for hours. Thus, the use of a self-luminescent sensor instead of a fluorescent sensor could facilitate the complete screening of chemical libraries in a high-throughput context and enable analysis of autofluorescent samples in many different applications.
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Affiliation(s)
- Derrick Cumberbatch
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Jie Yang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Dehui Mi
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | | | - C. David Weaver
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
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8
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Dysfunctional Heteroreceptor Complexes as Novel Targets for the Treatment of Major Depressive and Anxiety Disorders. Cells 2022; 11:cells11111826. [PMID: 35681521 PMCID: PMC9180493 DOI: 10.3390/cells11111826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/10/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Among mental diseases, major depressive disorder (MDD) and anxiety deserve a special place due to their high prevalence and their negative impact both on society and patients suffering from these disorders. Consequently, the development of novel strategies designed to treat them quickly and efficiently, without or at least having limited side effects, is considered a highly important goal. Growing evidence indicates that emerging properties are developed on recognition, trafficking, and signaling of G-protein coupled receptors (GPCRs) upon their heteromerization with other types of GPCRs, receptor tyrosine kinases, and ionotropic receptors such as N-methyl-D-aspartate (NMDA) receptors. Therefore, to develop new treatments for MDD and anxiety, it will be important to identify the most vulnerable heteroreceptor complexes involved in MDD and anxiety. This review focuses on how GPCRs, especially serotonin, dopamine, galanin, and opioid heteroreceptor complexes, modulate synaptic and volume transmission in the limbic networks of the brain. We attempt to provide information showing how these emerging concepts can contribute to finding new ways to treat both MDD and anxiety disorders.
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9
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Li MS, Wong HL, Ip YL, Peng Z, Yiu R, Yuan H, Wai Wong JK, Chan YK. Current and Future Perspectives on Microfluidic Tear Analytic Devices. ACS Sens 2022; 7:1300-1314. [PMID: 35579258 DOI: 10.1021/acssensors.2c00569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Most current invasive analytic devices for disease diagnosis and monitoring require the collection of blood, which causes great discomfort for patients and may potentially cause infection. This explains the great need for noninvasive devices that utilize other bodily fluids like sweat, saliva, tears, or urine. Among them, eye tears are easily accessible, less complex in composition, and less susceptible to dilution. Tears also contain valuable clinical information for the diagnosis of ocular and systemic diseases as the tear analyte level shows great correlation with the blood analyte level. These unique advantages make tears a promising platform for use in clinical settings. As the volume of tear film and the rate of tear flow are only microliters in size, the use of microfluidic technology in analytic devices allows minimal sample consumption. Hence, more and more microfluidic tear analytic devices have been proposed, and their working mechanisms can be broadly categorized into four main types: (a) electrochemical, (b) photonic crystals, (c) fluorescence, and (d) colorimetry. These devices are being developed toward the application of point-of-care tests with rapid yet accurate results. This review aims to provide a general overview of the recent developmental trend of microfluidic devices for tear analysis. Moreover, the fundamental principle behind each type of device along with their strengths and weaknesses will be discussed, especially in terms of their abilities and potential in being used in point-of-care settings.
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Affiliation(s)
- Man Shek Li
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
| | - Ho Lam Wong
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
| | - Yan Lam Ip
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
| | - Zhiting Peng
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
| | - Rachel Yiu
- Department of Ophthalmology, Grantham Hospital, Hong Kong West Cluster, Hong Kong SAR 000000
| | - Hao Yuan
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, P R China
| | - Jasper Ka Wai Wong
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
- Department of Ophthalmology, Grantham Hospital, Hong Kong West Cluster, Hong Kong SAR 000000
| | - Yau Kei Chan
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000
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10
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Kang C, Shrestha KL, Kwon S, Park S, Kim J, Kwon Y. Intein-Mediated Protein Engineering for Cell-Based Biosensors. BIOSENSORS 2022; 12:bios12050283. [PMID: 35624584 PMCID: PMC9138240 DOI: 10.3390/bios12050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022]
Abstract
Cell-based sensors provide a flexible platform for screening biologically active targets and for monitoring their interactions in live cells. Their applicability extends across a vast array of biological research and clinical applications. Particularly, cell-based sensors are becoming a potent tool in drug discovery and cell-signaling studies by allowing function-based screening of targets in biologically relevant environments and enabling the in vivo visualization of cellular signals in real-time with an outstanding spatiotemporal resolution. In this review, we aim to provide a clear view of current cell-based sensor technologies, their limitations, and how the recent improvements were using intein-mediated protein engineering. We first discuss the characteristics of cell-based sensors and present several representative examples with a focus on their design strategies, which differentiate cell-based sensors from in vitro analytical biosensors. We then describe the application of intein-mediated protein engineering technology for cell-based sensor fabrication. Finally, we explain the characteristics of intein-mediated reactions and present examples of how the intein-mediated reactions are used to improve existing methods and develop new approaches in sensor cell fabrication to address the limitations of current technologies.
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Abstract
Optical imaging is an indispensable tool in clinical diagnostics and fundamental biomedical research. Autofluorescence-free optical imaging, which eliminates real-time optical excitation to minimize background noise, enables clear visualization of biological architecture and physiopathological events deep within living subjects. Molecular probes especially developed for autofluorescence-free optical imaging have been proven to remarkably improve the imaging sensitivity, penetration depth, target specificity, and multiplexing capability. In this Review, we focus on the advancements of autofluorescence-free molecular probes through the lens of particular molecular or photophysical mechanisms that produce long-lasting luminescence after the cessation of light excitation. The versatile design strategies of these molecular probes are discussed along with a broad range of biological applications. Finally, challenges and perspectives are discussed to further advance the next-generation autofluorescence-free molecular probes for in vivo imaging and in vitro biosensors.
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Affiliation(s)
- Yuyan Jiang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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12
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Bioluminescence Resonance Energy Transfer (BRET) Imaging in Living Cells: Image Acquisition and Quantification. Methods Mol Biol 2021. [PMID: 34050482 DOI: 10.1007/978-1-0716-1258-3_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Bioluminescence resonance energy transfer (BRET) is an energy transfer phenomenon from a luciferase donor to a fluorescence acceptor and serves as an indicator of protein-protein interaction or protein proximity. BRET imaging is a powerful tool in the investigation of signaling proteins because it enables spatial analysis of such protein interactions. Here, we describe a method exerting high-resolution BRET imaging by combining bright-light output luciferases, such as NanoLuc , photon-counting EM-CCD, and unique algorithms for image correction and denoising.
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13
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Biosensors: A Sneak Peek into Plant Cell's Immunity. Life (Basel) 2021; 11:life11030209. [PMID: 33800034 PMCID: PMC7999283 DOI: 10.3390/life11030209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some respects, such as their use in following biotic stress response, employing more than one biosensor in the same chassis, and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players in the immune response: salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions, has so far been possible by using the most advanced genetically encoded biosensors in plants which allow the monitoring of calcium and the two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensor are also the most evolved in crops. In the last section, we examine the challenges in the use of biosensors and demonstrate some strategies to overcome them.
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14
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Interactomes: Experimental and In Silico Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:107-117. [DOI: 10.1007/978-3-030-80352-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Tian Y, Zhu P, Chen Y, Chen W, Du L, Wu C, Wang P. A sperm-cell-based biosensor using a fluorescence probe for responsive signal readout toward bitter flavor detection. Talanta 2020; 211:120731. [DOI: 10.1016/j.talanta.2020.120731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
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16
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Weihs F, Peh A, Dacres H. A red-shifted Bioluminescence Resonance Energy Transfer (BRET) biosensing system for rapid measurement of plasmin activity in human plasma. Anal Chim Acta 2019; 1102:99-108. [PMID: 32044001 DOI: 10.1016/j.aca.2019.12.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/20/2019] [Accepted: 12/16/2019] [Indexed: 01/29/2023]
Abstract
Proteases are key signalling molecules for many physiological processes and their dysregulation is implicated in the progression of a range of diseases. Sensitive methods to measure protease activities in complex biological samples are critical for rapid disease diagnoses. The proteolytic activity of plasmin reflects the fibrinolysis state of blood and its deregulation can indicate pathologies such as bleeding events. While Bioluminescence Resonance Energy Transfer (BRET) is a powerful and sensitive method for the detection of protease activity, the commonly applied blue-shifted BRET2 system, consisting of the Renilla luciferase Rluc2 and the large-stokes shift fluorescent protein GFP2, suffers from light absorption and light scattering in human plasma samples. To address this challenge, we developed a red-shifted BRET-based plasmin sensor by substituting BRET2 with the BRET6 system. BRET6 is composed of the red-shifted RLuc8.6 luciferase linked to the red light emitting fluorescent protein TurboFP635. The BRET6 biosensor exhibited 3-fold less light absorption in plasma samples compared to the BRET2 sensor leading to an up to a 5-fold increase in sensitivity for plasmin detection in plasma. The limits of detection for plasmin were determined to be 11.90 nM in 7.5% (v/v) plasma with a 10 min assay which enables biologically relevant plasmin activities of thrombolytic therapies to be detected. While a colorigenic plasmin activity assay achieved a similar detection limit of 10.91 nM in 7.5% (v/v) human plasma, it required a 2 h incubation period. The BRET6 sensor described here is faster and more specific than the colorigenic assay as it did not respond to unspiked human plasma samples.
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Affiliation(s)
- Felix Weihs
- CSIRO, Food Innovation Centre, 671 Sneydes Road, Werribee, VIC, 3030, Australia.
| | - Alex Peh
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACTON, Canberra, ACT, 2601, Australia; Universiti Putra Malaysia, Malaysia
| | - Helen Dacres
- CSIRO, Food Innovation Centre, 671 Sneydes Road, Werribee, VIC, 3030, Australia
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Kobayashi H, Picard LP, Schönegge AM, Bouvier M. Bioluminescence resonance energy transfer-based imaging of protein-protein interactions in living cells. Nat Protoc 2019; 14:1084-1107. [PMID: 30911173 DOI: 10.1038/s41596-019-0129-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/08/2019] [Indexed: 11/09/2022]
Abstract
Bioluminescence resonance energy transfer (BRET) is a transfer of energy between a luminescence donor and a fluorescence acceptor. Because BRET occurs when the distance between the donor and acceptor is <10 nm, and its efficiency is inversely proportional to the sixth power of distance, it has gained popularity as a proximity-based assay to monitor protein-protein interactions and conformational rearrangements in live cells. In such assays, one protein of interest is fused to a bioluminescent energy donor (luciferases from Renilla reniformis or Oplophorus gracilirostris), and the other protein is fused to a fluorescent energy acceptor (such as GFP or YFP). Because the BRET donor does not require an external light source, it does not lead to phototoxicity or autofluorescence. It therefore represents an interesting alternative to fluorescence-based imaging such as FRET. However, the low signal output of BRET energy donors has limited the spatiotemporal resolution of BRET imaging. Here, we describe how recent improvements in detection devices and BRET probes can be used to markedly improve the resolution of BRET imaging, thus widening the field of BRET imaging applications. The protocol described herein involves three main stages. First, cell preparation and transfection require 3 d, including cell culture time. Second, image acquisition takes 10-120 min per sample, after an initial 60 min for microscope setup. Finally, image analysis typically takes 1-2 h. The choices of energy donor, acceptor, luminescent substrates, cameras and microscope setup, as well as acquisition modes to be used for different applications, are also discussed.
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Affiliation(s)
- Hiroyuki Kobayashi
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Louis-Philippe Picard
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Anne-Marie Schönegge
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Michel Bouvier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada.
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18
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Cui Y, Zhang X, Yu M, Zhu Y, Xing J, Lin J. Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress. SCIENCE CHINA-LIFE SCIENCES 2019; 62:619-632. [DOI: 10.1007/s11427-018-9500-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/12/2019] [Indexed: 01/07/2023]
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19
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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20
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Liu S, Yu F, Hu Q, Wang T, Yu L, Du S, Yu W, Li N. Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis. J Proteome Res 2018; 17:3195-3213. [DOI: 10.1021/acs.jproteome.8b00320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Shichang Liu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Qin Hu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tingliang Wang
- Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lujia Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shengwang Du
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Weichuan Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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21
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A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging. Sci Rep 2018; 8:8984. [PMID: 29895862 PMCID: PMC5997707 DOI: 10.1038/s41598-018-27174-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/25/2018] [Indexed: 02/04/2023] Open
Abstract
Genetically encoded biosensors based on the principle of Förster resonance energy transfer comprise two major classes: biosensors based on fluorescence resonance energy transfer (FRET) and those based on bioluminescence energy transfer (BRET). The FRET biosensors visualize signaling-molecule activity in cells or tissues with high resolution. Meanwhile, due to the low background signal, the BRET biosensors are primarily used in drug screening. Here, we report a protocol to transform intramolecular FRET biosensors to BRET-FRET hybrid biosensors called hyBRET biosensors. The hyBRET biosensors retain all properties of the prototype FRET biosensors and also work as BRET biosensors with dynamic ranges comparable to the prototype FRET biosensors. The hyBRET biosensors are compatible with optogenetics, luminescence microplate reader assays, and non-invasive whole-body imaging of xenograft and transgenic mice. This simple protocol will expand the use of FRET biosensors and enable visualization of the multiscale dynamics of cell signaling in live animals.
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22
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Kamkaew A, Sun H, England CG, Cheng L, Liu Z, Cai W. Quantum dot-NanoLuc bioluminescence resonance energy transfer enables tumor imaging and lymph node mapping in vivo. Chem Commun (Camb) 2018; 52:6997-7000. [PMID: 27157466 DOI: 10.1039/c6cc02764d] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A small luciferase protein (Nluc) was conjugated to QDs as a bioluminescence resonance energy transfer (BRET) pair. The conjugate showed 76% BRET efficiency and lymph node mapping was successfully performed. The cRGD peptide was conjugated to QD-Nluc for tumor targeting. The self-illuminating QD-Nluc showed excellent energy transfer in a living system and offered an optimal tumor-to-background ratio (>85).
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Affiliation(s)
- Anyanee Kamkaew
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, WI 53705, USA.
| | - Haiyan Sun
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, WI 53705, USA.
| | - Christopher G England
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, WI 53705, USA.
| | - Liang Cheng
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, WI 53705, USA. and Institute of Functional Nano & Soft Materials (FUNSOM), Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Weibo Cai
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, WI 53705, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA
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Zhang Y, Robertson JB, Xie Q, Johnson CH. Monitoring Intracellular pH Change with a Genetically Encoded and Ratiometric Luminescence Sensor in Yeast and Mammalian Cells. Methods Mol Biol 2018; 1461:117-30. [PMID: 27424899 DOI: 10.1007/978-1-4939-3813-1_9] [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: 04/29/2023]
Abstract
"pHlash" is a novel bioluminescence-based pH sensor for measuring intracellular pH, which is developed based on Bioluminescence Resonance Energy Transfer (BRET). pHlash is a fusion protein between a mutant of Renilla luciferase (RLuc) and a Venus fluorophore. The spectral emission of purified pHlash protein exhibits pH dependence in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification. In this chapter, we describe an in vitro characterization of pHlash, and also in vivo assays including in yeast cells and in HeLa cells using pHlash as a cytoplasmic pH indicator.
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Affiliation(s)
- Yunfei Zhang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Modern Experiment Technology Center, Anhui University, Hefei, Anhui, 230601, China
| | - J Brian Robertson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Qiguang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei, China
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
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24
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Goto-Yamada S, Hikino K, Nishimura M, Nakagawa T, Mano S. Bimolecular Fluorescence Complementation with Improved Gateway-Compatible Vectors to Visualize Protein-Protein Interactions in Plant Cells. Methods Mol Biol 2018; 1794:245-258. [PMID: 29855962 DOI: 10.1007/978-1-4939-7871-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The bimolecular fluorescence complementation (BiFC) assay is a powerful, flexible, and simple tool to study protein-protein interactions in living cells. To accelerate the production and assessment of BiFC constructs, Gateway-compatible multicolor BiFC vectors were generated to enable the simultaneous production of multiple fusion genes that have the split N- or C-terminal fragment of fluorescent protein with the gene of interest in a high-throughput manner. Two different transient expression techniques for the assessment of BiFC in plant cells are described.
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Affiliation(s)
- Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazumi Hikino
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Tsuyoshi Nakagawa
- Department of Molecular and Functional Genomics, Interdisciplinary Centre for Science Research, Organization for Research and Academic Information, Shimane University, Matsue, Japan
| | - Shoji Mano
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan.
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25
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Yang J, Cumberbatch D, Centanni S, Shi SQ, Winder D, Webb D, Johnson CH. Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca ++ sensing. Nat Commun 2016; 7:13268. [PMID: 27786307 PMCID: PMC5476805 DOI: 10.1038/ncomms13268] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 09/13/2016] [Indexed: 11/09/2022] Open
Abstract
Optogenetic techniques allow intracellular manipulation of Ca++ by illumination of light-absorbing probe molecules such as channelrhodopsins and melanopsins. The consequences of optogenetic stimulation would optimally be recorded by non-invasive optical methods. However, most current optical methods for monitoring Ca++ levels are based on fluorescence excitation that can cause unwanted stimulation of the optogenetic probe and other undesirable effects such as tissue autofluorescence. Luminescence is an alternate optical technology that avoids the problems associated with fluorescence. Using a new bright luciferase, we here develop a genetically encoded Ca++ sensor that is ratiometric by virtue of bioluminescence resonance energy transfer (BRET). This sensor has a large dynamic range and partners optimally with optogenetic probes. Ca++ fluxes that are elicited by brief pulses of light to cultured cells expressing melanopsin and to neurons-expressing channelrhodopsin are quantified and imaged with the BRET Ca++ sensor in darkness, thereby avoiding undesirable consequences of fluorescence irradiation.
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Affiliation(s)
- Jie Yang
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Derrick Cumberbatch
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Samuel Centanni
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Shu-Qun Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Danny Winder
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Donna Webb
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
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26
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Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
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Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
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27
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In Vivo Analysis of Protein-Protein Interactions with Bioluminescence Resonance Energy Transfer (BRET): Progress and Prospects. Int J Mol Sci 2016; 17:ijms17101704. [PMID: 27727181 PMCID: PMC5085736 DOI: 10.3390/ijms17101704] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 11/17/2022] Open
Abstract
Proteins are the elementary machinery of life, and their functions are carried out mostly by molecular interactions. Among those interactions, protein-protein interactions (PPIs) are the most important as they participate in or mediate all essential biological processes. However, many common methods for PPI investigations are slightly unreliable and suffer from various limitations, especially in the studies of dynamic PPIs. To solve this problem, a method called Bioluminescence Resonance Energy Transfer (BRET) was developed about seventeen years ago. Since then, BRET has evolved into a whole class of methods that can be used to survey virtually any kinds of PPIs. Compared to many traditional methods, BRET is highly sensitive, reliable, easy to perform, and relatively inexpensive. However, most importantly, it can be done in vivo and allows the real-time monitoring of dynamic PPIs with the easily detectable light signal, which is extremely valuable for the PPI functional research. This review will take a comprehensive look at this powerful technique, including its principles, comparisons with other methods, experimental approaches, classifications, applications, early developments, recent progress, and prospects.
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28
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Chen M, Liu S, Li W, Zhang Z, Zhang X, Zhang XE, Cui Z. Three-Fragment Fluorescence Complementation Coupled with Photoactivated Localization Microscopy for Nanoscale Imaging of Ternary Complexes. ACS NANO 2016; 10:8482-8490. [PMID: 27584616 DOI: 10.1021/acsnano.6b03543] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many cellular processes are governed by molecular machineries that involve multiple protein interactions. However, visualizing and identifying multiprotein complexes such as ternary complexes inside cells is always challenging, particularly in the subdiffraction cellular space. Here, we developed a three-fragment fluorescence complementation system (TFFC) based on the splitting of a photoactivatable fluorescent protein, mIrisFP, for the imaging of ternary complexes inside living cells. Using a combination of TFFC and photoactivated localization microscopy (PALM), namely, the TFFC-PALM technique, we are able to identify the multi-interaction of a ternary complex with nanometer-level spatial resolution and single-molecule sensitivity. The TFFC-PALM system has been further applied to the analysis of the Gs ternary complex, which is composed of αs, β1, and γ2 subunits, providing further insights into the subcellular localization and function of G protein subunits at the single-molecule level. The TFFC-PALM represents a valuable method for the visualization and identification of ternary complexes inside cells at the nanometer scale.
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Affiliation(s)
- Minghai Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Sanying Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Xiaowei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
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29
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Namkung Y, Le Gouill C, Lukashova V, Kobayashi H, Hogue M, Khoury E, Song M, Bouvier M, Laporte SA. Monitoring G protein-coupled receptor and β-arrestin trafficking in live cells using enhanced bystander BRET. Nat Commun 2016; 7:12178. [PMID: 27397672 PMCID: PMC4942582 DOI: 10.1038/ncomms12178] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/08/2016] [Indexed: 12/14/2022] Open
Abstract
Endocytosis and intracellular trafficking of receptors are pivotal to maintain physiological functions and drug action; however, robust quantitative approaches are lacking to study such processes in live cells. Here we present new bioluminescence resonance energy transfer (BRET) sensors to quantitatively monitor G protein-coupled receptors (GPCRs) and β-arrestin trafficking. These sensors are based on bystander BRET and use the naturally interacting chromophores luciferase (RLuc) and green fluorescent protein (rGFP) from Renilla. The versatility and robustness of this approach are exemplified by anchoring rGFP at the plasma membrane or in endosomes to generate high dynamic spectrometric BRET signals on ligand-promoted recruitment or sequestration of RLuc-tagged proteins to, or from, specific cell compartments, as well as sensitive subcellular BRET imaging for protein translocation visualization. These sensors are scalable to high-throughput formats and allow quantitative pharmacological studies of GPCR trafficking in real time, in live cells, revealing ligand-dependent biased trafficking of receptor/β-arrestin complexes. Cellular signaling processes often involve trafficking of receptors and other proteins between subcellular compartments. Here the authors demonstrate a method based on the concept of Enhanced bystander Bioluminescence Resonance Energy Transfer (EbBRET) that allows efficient real time monitoring of endocytosis and trafficking.
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Affiliation(s)
- Yoon Namkung
- Department of Medicine, Research Institute of the McGill University Health Center (RI-MUHC), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Christian Le Gouill
- Department of Biochemistry and Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada H3C 1J4
| | - Viktoria Lukashova
- Department of Biochemistry and Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada H3C 1J4
| | - Hiroyuki Kobayashi
- Department of Biochemistry and Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada H3C 1J4
| | - Mireille Hogue
- Department of Biochemistry and Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada H3C 1J4
| | - Etienne Khoury
- Department of Medicine, Research Institute of the McGill University Health Center (RI-MUHC), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Mideum Song
- Department of Medicine, Research Institute of the McGill University Health Center (RI-MUHC), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Michel Bouvier
- Department of Biochemistry and Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada H3C 1J4
| | - Stéphane A Laporte
- Department of Medicine, Research Institute of the McGill University Health Center (RI-MUHC), McGill University, Montréal, Québec, Canada H4A 3J1.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada H3G 1Y6.,Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, Canada H3A 0C7
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30
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Xu T, Close D, Handagama W, Marr E, Sayler G, Ripp S. The Expanding Toolbox of In Vivo Bioluminescent Imaging. Front Oncol 2016; 6:150. [PMID: 27446798 PMCID: PMC4917529 DOI: 10.3389/fonc.2016.00150] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022] Open
Abstract
In vivo bioluminescent imaging (BLI) permits the visualization of engineered bioluminescence from living cells and tissues to provide a unique perspective toward the understanding of biological processes as they occur within the framework of an authentic in vivo environment. The toolbox of in vivo BLI includes an inventory of luciferase compounds capable of generating bioluminescent light signals along with sophisticated and powerful instrumentation designed to detect and quantify these light signals non-invasively as they emit from the living subject. The information acquired reveals the dynamics of a wide range of biological functions that play key roles in the physiological and pathological control of disease and its therapeutic management. This mini review provides an overview of the tools and applications central to the evolution of in vivo BLI as a core technology in the preclinical imaging disciplines.
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Affiliation(s)
- Tingting Xu
- The Center for Environmental Biotechnology, The University of Tennessee , Knoxville, TN , USA
| | - Dan Close
- 490 BioTech, Inc. , Knoxville, TN , USA
| | - Winode Handagama
- The Department of Biology, Maryville College , Maryville, TN , USA
| | - Enolia Marr
- The Center for Environmental Biotechnology, The University of Tennessee , Knoxville, TN , USA
| | - Gary Sayler
- The Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, USA; 490 BioTech, Inc., Knoxville, TN, USA
| | - Steven Ripp
- The Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, USA; 490 BioTech, Inc., Knoxville, TN, USA
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31
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Chen Y, Ren JQ, Zhang XG, Wu DY, Shen AG, Hu JM. Alkyne-Modulated Surface-Enhanced Raman Scattering-Palette for Optical Interference-Free and Multiplex Cellular Imaging. Anal Chem 2016; 88:6115-9. [DOI: 10.1021/acs.analchem.6b01374] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yong Chen
- Key
Laboratory of Analytical Chemistry for Biology and Medicine (Ministry
of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jia-Qiang Ren
- Key
Laboratory of Analytical Chemistry for Biology and Medicine (Ministry
of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xia-Guang Zhang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative
Innovation Center of Chemistry for Energy Materials, and Department
of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - De-Yin Wu
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative
Innovation Center of Chemistry for Energy Materials, and Department
of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Ai-Guo Shen
- Key
Laboratory of Analytical Chemistry for Biology and Medicine (Ministry
of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ji-Ming Hu
- Key
Laboratory of Analytical Chemistry for Biology and Medicine (Ministry
of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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Hirvonen LM, Suhling K. Photon Counting Imaging with an Electron-Bombarded Pixel Image Sensor. SENSORS (BASEL, SWITZERLAND) 2016; 16:E617. [PMID: 27136556 PMCID: PMC4883308 DOI: 10.3390/s16050617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/08/2016] [Accepted: 04/25/2016] [Indexed: 11/21/2022]
Abstract
Electron-bombarded pixel image sensors, where a single photoelectron is accelerated directly into a CCD or CMOS sensor, allow wide-field imaging at extremely low light levels as they are sensitive enough to detect single photons. This technology allows the detection of up to hundreds or thousands of photon events per frame, depending on the sensor size, and photon event centroiding can be employed to recover resolution lost in the detection process. Unlike photon events from electron-multiplying sensors, the photon events from electron-bombarded sensors have a narrow, acceleration-voltage-dependent pulse height distribution. Thus a gain voltage sweep during exposure in an electron-bombarded sensor could allow photon arrival time determination from the pulse height with sub-frame exposure time resolution. We give a brief overview of our work with electron-bombarded pixel image sensor technology and recent developments in this field for single photon counting imaging, and examples of some applications.
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Affiliation(s)
- Liisa M Hirvonen
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Klaus Suhling
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
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33
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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34
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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35
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Yuan ML, Jiang TY, Du LP, Li MY. Luminescence of coelenterazine derivatives with C-8 extended electronic conjugation. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Coriano C, Powell E, Xu W. Monitoring Ligand-Activated Protein-Protein Interactions Using Bioluminescent Resonance Energy Transfer (BRET) Assay. Methods Mol Biol 2016; 1473:3-15. [PMID: 27518618 DOI: 10.1007/978-1-4939-6346-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The bioluminescent resonance energy transfer (BRET) assay has been extensively used in cell-based and in vivo imaging systems for detecting protein-protein interactions in the native environment of living cells. These protein-protein interactions are essential for the functional response of many signaling pathways to environmental chemicals. BRET has been used as a toxicological tool for identifying chemicals that either induce or inhibit these protein-protein interactions. This chapter focuses on describing the toxicological applications of BRET and its optimization as a high-throughput detection system in live cells. Here we review the construction of BRET fusion proteins, describe the BRET methodology, and outline strategies to overcome obstacles that may arise. Furthermore, we describe the advantage of BRET over other resonance energy transfer methods for monitoring protein-protein interactions.
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Affiliation(s)
- Carlos Coriano
- Department of Oncology, University of Wisconsin-Madison, 7459 WIMR II, 1111 Highland Avenue, Madison, WI, 53705-2275, USA
| | - Emily Powell
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Xu
- Department of Oncology, University of Wisconsin-Madison, 7459 WIMR II, 1111 Highland Avenue, Madison, WI, 53705-2275, USA.
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37
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Hudson BD. Using Biosensors to Study Free Fatty Acid Receptor Pharmacology and Function. Handb Exp Pharmacol 2016; 236:79-100. [PMID: 27757763 DOI: 10.1007/164_2016_58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The free fatty acid (FFA) family of G protein coupled receptors (GPCRs) has generated significant interest for exploiting its members as potential drug targets. However, unravelling the complex pharmacology of this family of receptors has proven challenging. In recent years the use of biosensor technologies capable of assessing biological functions in living cells, and in real time, has greatly enhanced our ability to study GPCR pharmacology and function. These include genetically encoded sensors that change the intensity or wavelength of light emitted from a bioluminescent or fluorescent protein in response to a stimulus, as well as non-genetically encoded sensors able to measure more global cellular changes, such as mass redistribution within a cell. This chapter will examine how these sensors can be used to study GPCRs, and in particular how they are helping uncover the pharmacology of the FFA family of receptors.
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Affiliation(s)
- Brian D Hudson
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
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Abstract
Application of bioluminescence resonance energy transfer (BRET) assay has been of special value in measuring dynamic events such as protein-protein interactions (PPIs) in vitro or in vivo. It was only in the late 1990s the BRET assay using RLuc-YFP was introduced for biological research showing its use in determining interaction of two proteins involved in circadian rhythm. Several inherent attributes such as rapid and fairly sensitive ratiometric measurements, assessment of PPI irrespective of protein location in cellular compartment, and cost-effectiveness consenting to high-throughput assay development make BRET a popular genetic reporter-based assay for PPI studies. In BRET-based screening, within a defined proximity range of 10-100 Å, excited state energy of the luminescence molecule can excite the acceptor fluorophore in the form of resonance energy transfer, causing it to emit at its characteristic emission wavelength. Based on this principle, several such donor-acceptor pairs, using the Renilla luciferase or its mutants as donor and either GFP2, YFP, mOrange, TagRFP, or TurboFP as acceptor, have been reported for use.In recent years, BRET-related research has become significantly versatile in the assay format and its applicability by adopting the assay on multiple detection devices such as small-animal optical imaging platform or bioluminescence microscope. Beyond the scope of quantitative measurement of PPIs and protein dimerization, molecular optical imaging applications based on BRET assays have broadened its scope for screening of pharmacological compounds by unifying in vitro, live cell, and in vivo animal/plant measurement all on one platform. Taking examples from the literature, this chapter contributes to in-depth methodological details on how to perform in vitro and in vivo BRET experiments, and illustrates its advantages as a single-format assay.
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Affiliation(s)
- Shalini Dimri
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Soumya Basu
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Abhijit De
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.
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Abstract
Since their discovery, G protein-coupled receptors (GPCRs) constitute one of the most studied proteins leading to important discoveries and perspectives in terms of their biology and implication in physiology and pathophysiology. This is mostly linked to the remarkable advances in the development and application of the biophysical resonance energy transfer (RET)-based approaches, including bioluminescence and fluorescence resonance energy transfer (BRET and FRET, respectively). Indeed, BRET and FRET have been extensively applied to study different aspects of GPCR functioning such as their activation and regulation either statically or dynamically, in real-time and intact cells. Consequently, our view on GPCRs has considerably changed opening new challenges for the study of GPCRs in their native tissues in the aim to get more knowledge on how these receptors control the biological responses. Moreover, the technological aspect of this field of research promises further developments for robust and reliable new RET-based assays that may be compatible with high-throughput screening as well as drug discovery programs.
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Affiliation(s)
- Mohammed Akli Ayoub
- Biologie et Bioinformatique des Systèmes de Signalisation, Institut National de la Recherche Agronomique, UMR85, Unité Physiologie de la Reproduction et des Comportements; CNRS, UMR7247, Nouzilly, France; LE STUDIUM(®) Loire Valley Institute for Advanced Studies, Orléans, France.
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40
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Lin Y, Liu T, Liu J, Liu X, Ou Y, Zhang H, Li M, Sonnewald U, Song B, Xie C. Subtle Regulation of Potato Acid Invertase Activity by a Protein Complex of Invertase, Invertase Inhibitor, and SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE. PLANT PHYSIOLOGY 2015; 168:1807-19. [PMID: 26134163 PMCID: PMC4528764 DOI: 10.1104/pp.15.00664] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/25/2015] [Indexed: 05/19/2023]
Abstract
Slowing down cold-induced sweetening (CIS) of potato (Solanum tuberosum) tubers is of economic importance for the potato industry to ensure high-quality products. The conversion of sucrose to reducing sugars by the acid invertase StvacINV1 is thought to be critical for CIS. Identification of the specific StvacINV1 inhibitor StInvInh2B and the α- and β-subunits of the interacting protein SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE from the wild potato species Solanum berthaultii (SbSnRK1) has led to speculation that invertase activity may be regulated via a posttranslational mechanism that remains to be elucidated. Using bimolecular fluorescence complementation assays, this study confirmed the protein complex by pairwise interactions. In vitro kinase assays and protein phosphorylation analysis revealed that phosphorylation of SbSnRK1α is causal for StvacINV1 activity and that its active form blocks the inhibition of StInvInh2B by SbSnRK1β, whereas its inactive form restores the function of SbSnRK1β that prevents StInvInh2B from repressing StvacINV1. Overexpression of SbSnRK1α in CIS-sensitive potato confirmed that SbSnRK1α has significant effects on acid invertase-associated sucrose degradation. A higher level of SbSnRK1α expression was accompanied by elevated SbSnRK1α phosphorylation, reduced acid invertase activity, a higher sucrose-hexose ratio, and improved chip color. Our results lend new insights into a subtle regulatory mode of invertase activity and provide a novel approach for potato CIS improvement.
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Affiliation(s)
- Yuan Lin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Tengfei Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Jun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Xun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Yongbin Ou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Huiling Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Meng Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Uwe Sonnewald
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Botao Song
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
| | - Conghua Xie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Y.L., T.L., J.L., X.L., Y.O., H.Z., M.L., B.S., C.X.); andBiochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany (U.S.)
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41
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Lim JH, Park GC, Lee SM, Lee JH, Lim B, Hwang SM, Kim JH, Park H, Joo J, Kim YP. Surface-Tunable Bioluminescence Resonance Energy Transfer via Geometry-Controlled ZnO Nanorod Coordination. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3469-3475. [PMID: 25802061 DOI: 10.1002/smll.201403700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/24/2015] [Indexed: 06/04/2023]
Abstract
The use of ZnO nanorods (NRs) as an effective coordinator and biosensing platform to create bioluminescence resonance energy transfer (BRET) is reported. Herein, a hydrothermal approach is applied to obtain morphologically controlled ZnO NRs, which are directly bound to luciferase (Luc) and carboxy-modified quantum dot (QD) acting as a donor-acceptor pair for BRET. BRET efficiency varies significantly with the geometry of ZnO NRs, which modulates the coordination between hexahistidine-tagged Luc (Luc-His6 ) and QD, owing to the combined effect of the total surface area consisting of (001) and (100) planes and their surface polarities. Unlike typical QD-BRET reactions with metal ions (e.g., zinc ions), a geometry-controlled ZnO NR platform can facilitate the design of surface-initiated BRET sensors without being supplemented by copious metal ions: the geometry-controlled ZnO NR platform can therefore pave the way for nanostructure-based biosensors with enhanced analytical performance.
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Affiliation(s)
- Jun Hyung Lim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Geun Chul Park
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Seung Muk Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Butaek Lim
- Department of Life Science and Institute of Nano Science and Technology, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Soo Min Hwang
- Institute for Superconducting and Electronic Materials, University of Wollongong, North Wollongong, NSW, 2500, Australia
| | - Jung Ho Kim
- Institute for Superconducting and Electronic Materials, University of Wollongong, North Wollongong, NSW, 2500, Australia
| | - Hansoo Park
- School of Integrative Engineering, Chung-Ang University, Seoul, 156-756, Korea
| | - Jinho Joo
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Young-Pil Kim
- Department of Life Science and Institute of Nano Science and Technology, Hanyang University, Seoul, 133-791, Republic of Korea
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Jia K, Ionescu RE. Measurement of Bacterial Bioluminescence Intensity and Spectrum: Current Physical Techniques and Principles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 154:19-45. [PMID: 25981856 DOI: 10.1007/10_2015_324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed.
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Affiliation(s)
- Kun Jia
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France
| | - Rodica Elena Ionescu
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France.
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Hirvonen LM, Jiggins S, Sergent N, Zanda G, Suhling K. Photon counting imaging with an electron-bombarded CCD: towards a parallel-processing photoelectronic time-to-amplitude converter. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:123102. [PMID: 25554267 DOI: 10.1063/1.4901935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We have used an electron-bombarded CCD for optical photon counting imaging. The photon event pulse height distribution was found to be linearly dependent on the gain voltage. We propose on this basis that a gain voltage sweep during exposure in an electron-bombarded sensor would allow photon arrival time determination with sub-frame exposure time resolution. This effectively uses an electron-bombarded sensor as a parallel-processing photoelectronic time-to-amplitude converter, or a two-dimensional photon counting streak camera. Several applications that require timing of photon arrival, including Fluorescence Lifetime Imaging Microscopy, may benefit from such an approach. A simulation of a voltage sweep performed with experimental data collected with different acceleration voltages validates the principle of this approach. Moreover, photon event centroiding was performed and a hybrid 50% Gaussian/Centre of Gravity + 50% Hyperbolic cosine centroiding algorithm was found to yield the lowest fixed pattern noise. Finally, the camera was mounted on a fluorescence microscope to image F-actin filaments stained with the fluorescent dye Alexa 488 in fixed cells.
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Affiliation(s)
- Liisa M Hirvonen
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Stephen Jiggins
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Nicolas Sergent
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Gianmarco Zanda
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Klaus Suhling
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
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44
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Abstract
Taking advantage of BRET, a mutant firefly luciferase with higher pH- and thermo-stability than the wild-type could be coupled with the red-emitting fluorescent protein of mCherry in both a fused and unfused format. The BRET pair allows >40% of the light emitted to be red shifted over 600 nm to the mCherry acceptor wavelength. Taking the expected quantum yield for mCherry (0.22), a good fit to predicted light transfer is shown, with no other losses. Two measurements are considered for ATP determination: (a) a ratiometric technique for ATP measurement using both donor and acceptor emission intensities, making the calibration slope independent of protein concentration in a broad range. This measurement was limited by the BRET efficiency and the low quantum yield of the mCherry acceptor, but this detection limit might be improved with other fluorescent proteins with higher quantum yield. The fused BRET pair also resulted in a small increase in the BRET ratio. (b) An ATP dependent shift in the wavelength maximum using just the acceptor mCherry emission was also proposed for ATP determination. This did not require a high BRET efficiency and only uses emission above 600 nm to obtain the acceptor emission maximum, but not its intensity; it is independent of protein concentration across a broad range. This offers a novel and robust method for determination of ATP between 10(-11) to 10(-5) M with an easy baseline calibration with ATP concentration >10(-4) M.
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Affiliation(s)
- Golnaz Borghei
- Institute of Biotechnology, Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK.
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45
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Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria. mBio 2014; 5:e01050-14. [PMID: 24846380 PMCID: PMC4030481 DOI: 10.1128/mbio.01050-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells, thus allowing the detection of protein-protein interactions in live bacterial cells. This BRET system added another useful tool to address important questions in microbiological studies.
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Wu N, Dacres H, Anderson A, Trowell SC, Zhu Y. Comparison of static and microfluidic protease assays using modified bioluminescence resonance energy transfer chemistry. PLoS One 2014; 9:e88399. [PMID: 24551097 PMCID: PMC3925127 DOI: 10.1371/journal.pone.0088399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022] Open
Abstract
Background Fluorescence and bioluminescence resonance energy transfer (F/BRET) are two forms of Förster resonance energy transfer, which can be used for optical transduction of biosensors. BRET has several advantages over fluorescence-based technologies because it does not require an external light source. There would be benefits in combining BRET transduction with microfluidics but the low luminance of BRET has made this challenging until now. Methodology We used a thrombin bioprobe based on a form of BRET (BRETH), which uses the BRET1 substrate, native coelenterazine, with the typical BRET2 donor and acceptor proteins linked by a thrombin target peptide. The microfluidic assay was carried out in a Y-shaped microfluidic network. The dependence of the BRETH ratio on the measurement location, flow rate and bioprobe concentration was quantified. Results were compared with the same bioprobe in a static microwell plate assay. Principal Findings The BRETH thrombin bioprobe has a lower limit of detection (LOD) than previously reported for the equivalent BRET1–based version but it is substantially brighter than the BRET2 version. The normalised BRETH ratio of the bioprobe changed 32% following complete cleavage by thrombin and 31% in the microfluidic format. The LOD for thrombin in the microfluidic format was 27 pM, compared with an LOD of 310 pM, using the same bioprobe in a static microwell assay, and two orders of magnitude lower than reported for other microfluidic chip-based protease assays. Conclusions These data demonstrate that BRET based microfluidic assays are feasible and that BRETH provides a useful test bed for optimising BRET-based microfluidics. This approach may be convenient for a wide range of applications requiring sensitive detection and/or quantification of chemical or biological analytes.
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Affiliation(s)
- Nan Wu
- CSIRO Materials Science and Engineering and Food Futures Flagship, Clayton South, Australia
| | - Helen Dacres
- CSIRO Ecosystem Sciences and Food Futures Flagship, Canberra, Australia
| | - Alisha Anderson
- CSIRO Ecosystem Sciences and Food Futures Flagship, Canberra, Australia
| | | | - Yonggang Zhu
- CSIRO Ecosystem Sciences and Food Futures Flagship, Canberra, Australia
- * E-mail:
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Ma X, Cheng Z, Jin Y, Liang X, Yang X, Dai Z, Tian J. SM5-1-conjugated PLA nanoparticles loaded with 5-fluorouracil for targeted hepatocellular carcinoma imaging and therapy. Biomaterials 2014; 35:2878-89. [PMID: 24411331 DOI: 10.1016/j.biomaterials.2013.12.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/18/2013] [Indexed: 12/19/2022]
Abstract
SM5-1 is a humanized mouse antibody which has a high binding specificity for a membrane protein of about 230 kDa overexpressed in hepatocellular carcinoma (HCC), melanoma and breast cancer. In this study, SM5-1-conjugated poly D, L (lactide-coglycolide) (PLA) PLA containing Cy7 (PLA-Cy7-SM5-1) was prepared to study the targeting specificity of the bioconjugate to HCC-LM3-fLuc cell. Then, SM5-1-conjugated PLA containing 5-fluorouracil (5-FU) (PLA-5FU-SM5-1) and PLA containing 5-FU (PLA-5FU) were prepared for treatment of subcutaneous HCC-LM3-fLuc tumor mice. The results showed that PLA-5FU-SM5-1, PLA-5FU and 5-FU induced a 45.07%, 23.56% and 19.05% tumor growth inhibition rate, respectively, on day 31 post-treatment as determined by bioluminescent intensity. In addition, in order to evaluate the antitumor efficacy of PLA-5FU-SM5-1, HCC-LM3-fLuc cells were injected into the liver to establish the experimental orthotopic liver tumor models. The experiments showed that PLA-5FU-SM5-1, PLA-5FU and 5-FU induced a 53.24%, 31.00%, and 18.11% tumor growth inhibition rate, respectively, on day 31 post-treatment determined by the bioluminescent intensity of the abdomen in tumor-bearing mice. Furthermore, we have calculated the three-dimensional location of the liver cancer in mice using a multilevel adaptive finite element algorithm based on bioluminescent intensity decay calibration. The reconstruction results demonstrated that PLA-5FU-SM5-1 inhibited the tumor rapid progression, which were consistent with the results of subcutaneous tumor mice experiments and in vitro cell experiment results.
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Affiliation(s)
- Xibo Ma
- Key Laboratory of Molecular Imaging of Chinese Academy of Sciences, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen Cheng
- Molecular Imaging Program at Stanford (MIPS), Bio-X Program, Department of Radiology, Stanford University, California 94305-5344, USA
| | - Yushen Jin
- Nanomedicine and Biosensor Laboratory, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Xiaolong Liang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Xin Yang
- Key Laboratory of Molecular Imaging of Chinese Academy of Sciences, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhifei Dai
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Jie Tian
- Key Laboratory of Molecular Imaging of Chinese Academy of Sciences, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.
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Hanson MR, Sattarzadeh A. Fluorescent labeling and confocal microscopic imaging of chloroplasts and non-green plastids. Methods Mol Biol 2014; 1132:125-43. [PMID: 24599850 DOI: 10.1007/978-1-62703-995-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
While chlorophyll has served as an excellent label for plastids in green tissue, the development of fluorescent proteins has allowed their ready visualization in all tissues of the plants, revealing new features of their morphology and motility. Gene regulatory sequences in plastid transgenes can be optimized through the use of fluorescent protein reporters. Fluorescent labeling of plastids simultaneously with other subcellular locations reveals dynamic interactions and mutant phenotypes. Transient expression of fluorescent protein fusions is particularly valuable to determine whether or not a protein of unknown function is targeted to the plastid. Particle bombardment and agroinfiltration methods described here are convenient for imaging fluorescent proteins in plant organelles. With proper selection of fluorophores for labeling the components of the plant cell, confocal microscopy can produce extremely informative images at high resolution at depths not feasible by standard epifluorescence microscopy.
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Affiliation(s)
- Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Waadt R, Schlücking K, Schroeder JI, Kudla J. Protein fragment bimolecular fluorescence complementation analyses for the in vivo study of protein-protein interactions and cellular protein complex localizations. Methods Mol Biol 2014; 1062:629-58. [PMID: 24057390 PMCID: PMC4073779 DOI: 10.1007/978-1-62703-580-4_33] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The analyses of protein-protein interactions are crucial for understanding cellular processes including signal transduction, protein trafficking, and movement. Protein fragment complementation assays are based on the reconstitution of protein function when non-active protein fragments are brought together by interacting proteins that were genetically fused to these protein fragments. Bimolecular fluorescence complementation (BiFC) relies on the reconstitution of fluorescent proteins and enables both the analysis of protein-protein interactions and the visualization of protein complex formations in vivo. Transient expression of proteins is a convenient approach to study protein functions in planta or in other organisms and minimizes the need for time-consuming generation of stably expressing transgenic organisms. Here we describe protocols for BiFC analyses in Nicotiana benthamiana and Arabidopsis thaliana leaves transiently transformed by Agrobacterium infiltration. Further, we discuss different BiFC applications and provide examples for proper BiFC analyses in planta.
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Affiliation(s)
- Rainer Waadt
- University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive #0116, La Jolla, CA 92093-0116, USA
| | - Kathrin Schlücking
- Universität Münster, Molekulargenetik und Zellbiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
| | - Julian I. Schroeder
- University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive #0116, La Jolla, CA 92093-0116, USA
| | - Jörg Kudla
- Universität Münster, Molekulargenetik und Zellbiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
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De A, Jasani A, Arora R, Gambhir SS. Evolution of BRET Biosensors from Live Cell to Tissue-Scale In vivo Imaging. Front Endocrinol (Lausanne) 2013; 4:131. [PMID: 24065957 PMCID: PMC3779814 DOI: 10.3389/fendo.2013.00131] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/05/2013] [Indexed: 11/13/2022] Open
Abstract
Development of bioluminescence resonance energy transfer (BRET) based genetic sensors for sensing biological functions such as protein-protein interactions (PPIs) in vivo has a special value in measuring such dynamic events at their native environment. Since its inception in the late nineties, BRET related research has gained significant momentum in terms of adding versatility to the assay format and wider applicability where it has been suitably used. Beyond the scope of quantitative measurement of PPIs and protein dimerization, molecular imaging applications based on BRET assays have broadened its scope for screening pharmacologically important compounds by in vivo imaging as well. In this mini-review we focus on an in-depth analysis of engineered BRET systems developed and their successful application to cell-based assays as well as in vivo non-invasive imaging in live subjects.
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Affiliation(s)
- Abhijit De
- Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
- *Correspondence: Abhijit De, Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai 410210, India e-mail:
| | - Akshi Jasani
- Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohit Arora
- Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjiv S. Gambhir
- MIPS, Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA
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