1
|
He R, Dong T, Chu J, Wang Y, Wang X, Song Y, Sun Y. Phaser-Trim: A Phase Separation Based Genetically Encoded Reporter for H3K9 Trimethylation in Living Cells. Anal Chem 2024. [PMID: 39101551 DOI: 10.1021/acs.analchem.4c00992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Histone methylation is a key epigenetic modification that regulates the chromatin structure and gene expression for proper cellular and physiological processes. Aberrant histone methylation patterns are implicated in many diseases. Therefore, monitoring histone methylation dynamics in living cells and species is essential for elucidating its regulatory mechanisms and identifying potential therapeutic targets. However, current methods for detecting histone methylation are limited by their low sensitivity and specificity. To overcome this challenge, we have developed a genetically encoded biosensor named Phaser-Trim (Phase separation based genetically encoded reporter for H3K9 Trimethylation) to detect the dynamic changes of H3K9me3 in living cells and species through the generation and disappearance of phase-separated droplets. Phaser-Trim demonstrates advantages of clear phenotypic characteristics, convenient operation, quantitative accuracy, biocompatibility, high specificity, and superior imaging performance with high signal-to-background ratio (SBR) for in vivo animal imaging. Using Phaser-Trim, we have successfully detected the dynamics of the H3K9me3 level during the differentiation of neural stem cells in Drosophila. Furthermore, Phaser-Trim also holds promise for application in high-throughput screening systems to facilitate the discovery of novel anticancer drugs.
Collapse
Affiliation(s)
- Renxi He
- National Biomedical Imaging Center, College of Future Technology, State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Tian Dong
- National Biomedical Imaging Center, College of Future Technology, State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Jingyi Chu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yao Wang
- National Biomedical Imaging Center, College of Future Technology, State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xiaotian Wang
- National Biomedical Imaging Center, College of Future Technology, State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yan Song
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yujie Sun
- National Biomedical Imaging Center, College of Future Technology, State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| |
Collapse
|
2
|
Richardson A, Alster J, Khoroshyy P, Psencik J, Valenta J, Tuma R, Critchley K. Direct Synthesis and Characterization of Hydrophilic Cu-Deficient Copper Indium Sulfide Quantum Dots. ACS OMEGA 2024; 9:17114-17124. [PMID: 38645370 PMCID: PMC11025077 DOI: 10.1021/acsomega.3c09531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/21/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024]
Abstract
Copper indium sulfide (CIS) nanocrystals constitute a promising alternative to cadmium- and lead-containing nanoparticles. We report a synthetic method that yields hydrophilic, core-only CIS quantum dots, exhibiting size-dependent, copper-deficient composition and optical properties that are suitable for direct coupling to biomolecules and nonradiative energy transfer applications. To assist such applications, we complemented previous studies covering the femtosecond-picosecond time scale with the investigation of slower radiative and nonradiative processes on the nanosecond time scale, using both time-resolved emission and transient absorption. As expected for core particles, relaxation occurs mainly nonradiatively, resulting in low, size-dependent photoluminescence quantum yield. The nonradiative relaxation from the first excited band is wavelength-dependent with lifetimes between 25 and 150 ns, reflecting the size distribution of the particles. Approximately constant lifetimes of around 65 ns were observed for nonradiative relaxation from the defect states at lower energies. The photoluminescence exhibited a large Stokes shift. The band gap emission decays on the order of 10 ns, while the defect emission is further red-shifted, and the lifetimes are on the order of 100 ns. Both sets of radiative lifetimes are wavelength-dependent, increasing toward longer wavelengths. Despite the low radiative quantum yield, the aqueous solubility and long lifetimes of the defect states are compatible with the proposed role of CIS quantum dots as excitation energy donors to biological molecules.
Collapse
Affiliation(s)
- Amanda Richardson
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Jan Alster
- Department
of Chemical Physics, Faculty of Mathematics and Physics, Charles University, Prague 121 16, Czech Republic
| | - Petro Khoroshyy
- Department
of Chemical Physics, Faculty of Mathematics and Physics, Charles University, Prague 121 16, Czech Republic
| | - Jakub Psencik
- Department
of Chemical Physics, Faculty of Mathematics and Physics, Charles University, Prague 121 16, Czech Republic
| | - Jan Valenta
- Department
of Chemical Physics, Faculty of Mathematics and Physics, Charles University, Prague 121 16, Czech Republic
| | - Roman Tuma
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
- Faculty
of Science, University of South Bohemia, Ceske Budejovice 370 05, Czech Republic
| | - Kevin Critchley
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| |
Collapse
|
3
|
Zhang H, Liu L, Li M. Mini-review of DNA Methylation Detection Techniques and Their Potential Applications in Disease Diagnosis, Prognosis, and Treatment. ACS Sens 2024; 9:1089-1103. [PMID: 38365574 DOI: 10.1021/acssensors.3c02328] [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: 02/18/2024]
Abstract
DNA methylation is the dominant epigenetic mechanism for regulating gene expression in mammals, playing crucial roles in development, differentiation, and tissue homeostasis. Aberrations in DNA methylation are closely associated with the potential onset of various diseases. Consequently, numerous DNA methylation detection techniques have been successively developed. These methods not only facilitate the exploration of disease mechanisms but also hold significant promise for the development of diagnostic and prognostic strategies. In this Perspective, we present a comprehensive overview of commonly employed DNA methylation detection techniques as well as biosensing based on their underlying analytical techniques. For its medical applications, we begin by examining the pathogenesis of different diseases and then proceed to discuss how relevant technologies are applied in the context of these specific medical conditions. Additionally, we briefly discuss the current limitations of these techniques and highlight future challenges in advancing methylation detection and analysis methodologies.
Collapse
Affiliation(s)
- Huaming Zhang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Liu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
Lin HH, Kuo MW, Fan TC, Yu AL, Yu J. YULINK regulates vascular formation in zebrafish and HUVECs. Biol Res 2023; 56:7. [PMID: 36843032 PMCID: PMC9969694 DOI: 10.1186/s40659-023-00415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/18/2023] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND The distinct arterial and venous cell fates are dictated by a combination of various genetic factors which form diverse types of blood vessels such as arteries, veins, and capillaries. We report here that YULINK protein is involved in vasculogenesis, especially venous formation. METHODS In this manuscript, we employed gene knockdown, yeast two-hybrid, FLIM-FRET, immunoprecipitation, and various imaging technologies to investigate the role of YULINK gene in zebrafish and human umbilical vein endothelial cells (HUVECs). RESULTS Knockdown of YULINK during the arterial-venous developmental stage of zebrafish embryos led to the defective venous formation and abnormal vascular plexus formation. Knockdown of YULINK in HUVECs impaired their ability to undergo cell migration and differentiation into a capillary-like tube formation. In addition, the phosphorylated EPHB4 was decreased in YULINK knockdown HUVECs. Yeast two-hybrid, FLIM-FRET, immunoprecipitation, as well as imaging technologies showed that YULINK colocalized with endosome related proteins (EPS15, RAB33B or TICAM2) and markers (Clathrin and RHOB). VEGF-induced VEGFR2 internalization was also compromised in YULINK knockdown HUVECs, demonstrating to the involvement of YULINK. CONCLUSION This study suggests that YULINK regulates vasculogenesis, possibly through endocytosis in zebrafish and HUVECs.
Collapse
Affiliation(s)
- Hsin-Hung Lin
- grid.28665.3f0000 0001 2287 1366Chemical Biology and Molecular Biophysics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Ming-Wei Kuo
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Tan-Chi Fan
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Alice L. Yu
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California, San Diego, CA USA
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333, Taoyuan, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
5
|
Rhynchosia volubilis Promotes Cell Survival via cAMP-PKA/ERK-CREB Pathway. Pharmaceuticals (Basel) 2022; 15:ph15010073. [PMID: 35056130 PMCID: PMC8778899 DOI: 10.3390/ph15010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Rhynchosia volubilis, a small black bean, has been used as a traditional remedy to treat diseases and maintain health in East Asia, but its cellular effects and molecular mechanisms are not fully understood. The purpose of this study was to investigate the effect of ethanol extract from Rhynchosia volubilis (EERV) on cell survival and to elucidate the biochemical signaling pathways. Our results showed that EERV stimulated the cyclic AMP (cAMP) signal revealed by a fluorescent protein (FP)-based intensiometric sensor. Using a Förster resonance energy transfer (FRET)-based sensor, we further revealed that EERV could activate PKA and ERK signals, which are downstream effectors of cAMP. In addition, we reported that EERV could induce the phosphorylation of CREB, a key signal for cell survival. Thus, our results suggested that EERV protects against apoptosis by activating the cell survival pathway through the cAMP-PKA/ERK-CREB pathway.
Collapse
|
6
|
Liu Z, Ramirez A, Liu X. Live Cell Imaging of Spatiotemporal Ca 2+ Fluctuation Responses to Anticancer Drugs. Methods Mol Biol 2022; 2488:227-236. [PMID: 35347692 DOI: 10.1007/978-1-0716-2277-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic triterpenoids, 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO) and its derivatives are known to have potent anti-cancer and anti-inflammatory activities. The mechanisms of actions of CDDO and its derivatives as potential therapeutics remain elusive. Previous studies found that CDDO-Me triggers apoptosis by inducing extracellular Ca2+ influx followed by endoplasmic reticulum (ER)-derived vacuolation. Since Ca2+ activity in cells is dynamic and needs to be tracked in real time in living cells, we report a high-throughput and high-content imaging method to track CDDO-induced Ca2+ fluctuation in both ER and cytosol with MATLAB script for data analysis and visualization.
Collapse
Affiliation(s)
- Zeyu Liu
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Adrian Ramirez
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
7
|
Gong Y, Wei C, Cheng L, Ma F, Lu S, Peng Q, Liu L, Wang Y. Tracking the Dynamic Histone Methylation of H3K27 in Live Cancer Cells. ACS Sens 2021; 6:4369-4378. [PMID: 34878766 PMCID: PMC9013700 DOI: 10.1021/acssensors.1c01670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Histone methylations play a crucial role in chromatin remodeling and genome regulations. However, there is a lack of tools to visualize these histone modifications with high spatiotemporal resolutions in live cells. We have developed a biosensor based on fluorescence resonance energy transfer (FRET) and incorporated it into nucleosomes, capable of monitoring the trimethylation of H3K27 (H3K27me3) in live cells. We also revealed that the performance of the FRET biosensor can be significantly improved by adjusting the linkers within the biosensor. An improved biosensor enables the live-cell imaging of different histone methylation status, induced by the suppressive H3.3K27M or existing in breast cancer cells with varying genetic backgrounds. We have further applied the biosensor to reveal the dynamic coupling between H3K27me3 changes and caspase activity representing the initiation of apoptosis in cancer cells by imaging both H3K27me3 and caspase activity simultaneously in the same live cells. Thus, this new FRET biosensor can provide a powerful tool to visualize the epigenetic regulation in live cells with high spatial temporal resolutions.
Collapse
Affiliation(s)
- Ya Gong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Chujun Wei
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Leonardo Cheng
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Fengyi Ma
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Qin Peng
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Longwei Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093-0435, United States
| |
Collapse
|
8
|
Fujimoto KJ. Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins. Front Mol Biosci 2021; 8:752700. [PMID: 34604313 PMCID: PMC8480471 DOI: 10.3389/fmolb.2021.752700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
The photo-functional chromophore retinal exhibits a wide variety of optical absorption properties depending on its intermolecular interactions with surrounding proteins and other chromophores. By utilizing these properties, microbial and animal rhodopsins express biological functions such as ion-transport and signal transduction. In this review, we present the molecular mechanisms underlying light absorption in rhodopsins, as revealed by quantum chemical calculations. Here, symmetry-adapted cluster-configuration interaction (SAC-CI), combined quantum mechanical and molecular mechanical (QM/MM), and transition-density-fragment interaction (TDFI) methods are used to describe the electronic structure of the retinal, the surrounding protein environment, and the electronic coupling between chromophores, respectively. These computational approaches provide successful reproductions of experimentally observed absorption and circular dichroism (CD) spectra, as well as insights into the mechanisms of unique optical properties in terms of chromophore-protein electrostatic interactions and chromophore-chromophore electronic couplings. On the basis of the molecular mechanisms revealed in these studies, we also discuss strategies for artificial design of the optical absorption properties of rhodopsins.
Collapse
Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| |
Collapse
|
9
|
Xu W, Pei G, Liu H, Ju X, Wang J, Ding Q, Li P. Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome. Cell Rep 2021; 36:109482. [PMID: 34297909 PMCID: PMC8285250 DOI: 10.1016/j.celrep.2021.109482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Bearing a relatively large single-stranded RNA genome in nature, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. In this study, we develop an innovative interaction screening strategy based on phase separation in cellulo, namely compartmentalization of protein-protein interactions in cells (CoPIC). Utilizing CoPIC screening, we map the interaction network among RTC-related viral proteins. We identify a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC leads to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient and robust interaction screening strategy, and they indicate the existence of a complex interaction network among RTC-related factors, thus opening up opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.
Collapse
Affiliation(s)
- Weifan Xu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Gaofeng Pei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongrui Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Ju
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiang Ding
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
10
|
Nakamura A, Goto Y, Kondo Y, Aoki K. Shedding light on developmental ERK signaling with genetically encoded biosensors. Development 2021; 148:271153. [PMID: 34338283 DOI: 10.1242/dev.199767] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The extracellular signal-regulated kinase (ERK) pathway governs cell proliferation, differentiation and migration, and therefore plays key roles in various developmental and regenerative processes. Recent advances in genetically encoded fluorescent biosensors have unveiled hitherto unrecognized ERK activation dynamics in space and time and their functional importance mainly in cultured cells. However, ERK dynamics during embryonic development have still only been visualized in limited numbers of model organisms, and we are far from a sufficient understanding of the roles played by developmental ERK dynamics. In this Review, we first provide an overview of the biosensors used for visualization of ERK activity in live cells. Second, we highlight the applications of the biosensors to developmental studies of model organisms and discuss the current understanding of how ERK dynamics are encoded and decoded for cell fate decision-making.
Collapse
Affiliation(s)
- Akinobu Nakamura
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,IRCC International Research Collaboration Center, National Institutes of Natural Sciences, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
| |
Collapse
|
11
|
Goto Y, Kondo Y, Aoki K. Visualization and Manipulation of Intracellular Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:225-234. [PMID: 33398816 DOI: 10.1007/978-981-15-8763-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cells respond to a wide range of extracellular stimuli, and process the input information through an intracellular signaling system comprised of biochemical and biophysical reactions, including enzymatic and protein-protein interactions. It is essential to understand the molecular mechanisms underlying intracellular signal transduction in order to clarify not only physiological cellular functions but also pathological processes such as tumorigenesis. Fluorescent proteins have revolutionized the field of life science, and brought the study of intracellular signaling to the single-cell and subcellular levels. Much effort has been devoted to developing genetically encoded fluorescent biosensors based on fluorescent proteins, which enable us to visualize the spatiotemporal dynamics of cell signaling. In addition, optogenetic techniques for controlling intracellular signal transduction systems have been developed and applied in recent years by regulating intracellular signaling in a light-dependent manner. Here, we outline the principles of biosensors for probing intracellular signaling and the optogenetic tools for manipulating them.
Collapse
Affiliation(s)
- Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan.
| |
Collapse
|
12
|
|
13
|
Optogenetic Imaging of Protein Activity Using Two-Photon Fluorescence Lifetime Imaging Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:295-308. [PMID: 33398821 DOI: 10.1007/978-981-15-8763-4_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Spatiotemporal dynamics of cellular proteins, including protein-protein interactions and conformational changes, is essential for understanding cellular functions such as synaptic plasticity, cell motility, and cell division. One of the best ways to understand the mechanisms of signal transduction is to visualize protein activity with high spatiotemporal resolution in living cells within tissues. Optogenetic probes such as fluorescent proteins, in combination with Förster Resonance Energy Transfer (FRET) techniques, enable the measurement of protein-protein interactions and conformational changes in response to signaling events in living cells. Of the various FRET detection systems, two-photon fluorescence lifetime imaging microscopy (2pFLIM) is one of the methods best suited to monitoring FRET in subcellular compartments of living cells located deep within tissues, such as brain slices. This review will introduce the principle of 2pFLIM-FRET and the use of chromoproteins for imaging intracellular protein activities and protein-protein interactions. Also, we will discuss two examples of 2pFLIM-FRET application: imaging actin polymerization in synapses of hippocampal neurons in brain sections and detecting small GTPase Cdc42 activity in astrocytes.
Collapse
|
14
|
Liu L, He F, Yu Y, Wang Y. Application of FRET Biosensors in Mechanobiology and Mechanopharmacological Screening. Front Bioeng Biotechnol 2020; 8:595497. [PMID: 33240867 PMCID: PMC7680962 DOI: 10.3389/fbioe.2020.595497] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022] Open
Abstract
Extensive studies have shown that cells can sense and modulate the biomechanical properties of the ECM within their resident microenvironment. Thus, targeting the mechanotransduction signaling pathways provides a promising way for disease intervention. However, how cells perceive these mechanical cues of the microenvironment and transduce them into biochemical signals remains to be answered. Förster or fluorescence resonance energy transfer (FRET) based biosensors are a powerful tool that can be used in live-cell mechanotransduction imaging and mechanopharmacological drug screening. In this review, we will first introduce FRET principle and FRET biosensors, and then, recent advances on the integration of FRET biosensors and mechanobiology in normal and pathophysiological conditions will be discussed. Furthermore, we will summarize the current applications and limitations of FRET biosensors in high-throughput drug screening and the future improvement of FRET biosensors. In summary, FRET biosensors have provided a powerful tool for mechanobiology studies to advance our understanding of how cells and matrices interact, and the mechanopharmacological screening for disease intervention.
Collapse
Affiliation(s)
| | | | | | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
15
|
Mikuni T, Uchigashima M. Methodological approaches to understand the molecular mechanism of structural plasticity of dendritic spines. Eur J Neurosci 2020; 54:6902-6911. [PMID: 32248570 DOI: 10.1111/ejn.14734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022]
Abstract
Dendritic spines are tiny protrusions emanating from the neuronal dendrites, typically housing single excitatory postsynapses. Structural plasticity of dendritic spines is considered to be essential for synaptic functional plasticity and also reorganization of neural circuits during learning and memory. Structural plasticity of spines is mediated by complex biochemical signaling with various spatial and temporal scales. A variety of methods based on pharmacological, genetic, molecular, imaging and optical approaches has been developed and applied to dissect the complex signal transduction pathways. In this review, we overview both conventional and new methodological approaches to identify, monitor and manipulate key molecules for structural plasticity of dendritic spines, ultimately aiming to understand the molecular mechanism of learning and memory in behaving animals.
Collapse
Affiliation(s)
- Takayasu Mikuni
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
| | - Motokazu Uchigashima
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan
| |
Collapse
|
16
|
In Vivo Imaging of the Coupling between Neuronal and CREB Activity in the Mouse Brain. Neuron 2019; 105:799-812.e5. [PMID: 31883788 DOI: 10.1016/j.neuron.2019.11.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/16/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023]
Abstract
Sensory experiences cause long-term modifications of neuronal circuits by modulating activity-dependent transcription programs that are vital for regulation of long-term synaptic plasticity and memory. However, it has not been possible to precisely determine the interaction between neuronal activity patterns and transcription factor activity. Here we present a technique using two-photon fluorescence lifetime imaging (2pFLIM) with new FRET biosensors to chronically image in vivo signaling of CREB, an activity-dependent transcription factor important for synaptic plasticity, at single-cell resolution. Simultaneous imaging of the red-shifted CREB sensor and GCaMP permitted exploration of how experience shapes the interplay between CREB and neuronal activity in the neocortex of awake mice. Dark rearing increased the sensitivity of CREB activity to Ca2+ elevations and prolonged the duration of CREB activation to more than 24 h in the visual cortex. This technique will allow researchers to unravel the transcriptional dynamics underlying experience-dependent plasticity in the brain.
Collapse
|
17
|
Wei J, Hameed M, Wang X, Zhang J, Guo S, Anwar MN, Pang L, Liu K, Li B, Shao D, Qiu Y, Zhong D, Zhou B, Ma Z. Antiviral activity of phage display-selected peptides against Japanese encephalitis virus infection in vitro and in vivo. Antiviral Res 2019; 174:104673. [PMID: 31812636 DOI: 10.1016/j.antiviral.2019.104673] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022]
Abstract
Japanese Encephalitis virus (JEV) is a zoonotic flavivirus that is the most significant etiological agent of childhood viral neurological infections. However, no specific antiviral drug is currently available to treat JEV infections. The JEV envelope (E) protein is a class II viral fusion protein that mediates host cell entry, making interference with the interaction between the E protein of JEV and its cognate receptors an attractive strategy for anti-JEV drug development. In this study, we identified a peptide derived from a phage display peptide library against the E protein of JEV, designated P1, that potentially inhibits in vitro and in vivo JEV infections. P1 inhibits JEV infection in BHK-21 cells with 50% inhibitory capacity at a concentration of 35.9 μM. The time-of-addition assay indicates that JEV replication is significantly inhibited during pre-infection and co-infection of P1 with JEV while post-infection treatments with P1 have very little impact on JEV proliferation, showing that P1 inhibits JEV infection at early stages and indicating the potential prophylactic effect of P1. We adapted an in vitro BiFC assay system and demonstrated that P1 interacts with JEV E proteins and blocks their entry into cells. We also evaluated the therapeutic efficacy of P1 in a lethal JEV mouse model exhibiting systemic and brain infections. Interestingly, P1 treatment protected C57BL/6 mice against mortality, markedly reduced the viral loads in blood and brain, and diminished the histopathological lesions in the brain cells. In addition to controlling systemic infection, P1 has a very low level of cytotoxicity and acts in a sequence-specific manner, as scrambled peptide sP1 does not show any antiviral activity. In conclusion, our in vitro and in vivo experimental findings show that P1 possesses antiviral activity against JEV infections, is safe to use, and has potential for further development as an antiviral treatment against JEV infections.
Collapse
Affiliation(s)
- Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Xin Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Junjie Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China; Shanghai Vocational and Technical College of Agriculture and Forestry, Shanghai, 201600, People's Republic of China
| | - Shuang Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Linlin Pang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Dengke Zhong
- Shanghai Vocational and Technical College of Agriculture and Forestry, Shanghai, 201600, People's Republic of China.
| | - Bin Zhou
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China.
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China.
| |
Collapse
|
18
|
Morciano G, Imamura H, Patergnani S, Pedriali G, Giorgi C, Pinton P. Measurement of ATP concentrations in mitochondria of living cells using luminescence and fluorescence approaches. Methods Cell Biol 2019; 155:199-219. [PMID: 32183959 DOI: 10.1016/bs.mcb.2019.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Adenosine 5'-triphosphate (ATP) is the central metabolite in the energy metabolism of cells and is hydrolyzed to ADP and inorganic phosphate to provide free energy in various cellular processes. ATP also functions as an intracellular signaling molecule. Thus, it is important to know the ATP concentration within cells to understand cellular activities. Here, we describe two methods to detect ATP concentrations in the cytoplasm and mitochondrial matrix using genetically encoded luminescent or fluorescent biosensors. These methods enable quantitative investigation of ATP concentration dynamics in living cells, single cells and cell populations.
Collapse
Affiliation(s)
- Giampaolo Morciano
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, (RA), Italy; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology and LTTA Center, University of Ferrara, Ferrara, Italy
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Simone Patergnani
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, (RA), Italy; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology and LTTA Center, University of Ferrara, Ferrara, Italy
| | - Gaia Pedriali
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, (RA), Italy; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology and LTTA Center, University of Ferrara, Ferrara, Italy
| | - Carlotta Giorgi
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology and LTTA Center, University of Ferrara, Ferrara, Italy
| | - Paolo Pinton
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, (RA), Italy; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology and LTTA Center, University of Ferrara, Ferrara, Italy.
| |
Collapse
|
19
|
Fluorescent Radiosensitizing Gold Nanoparticles. Int J Mol Sci 2019; 20:ijms20184618. [PMID: 31540386 PMCID: PMC6770707 DOI: 10.3390/ijms20184618] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/16/2019] [Accepted: 09/16/2019] [Indexed: 01/26/2023] Open
Abstract
Ultrasmall polyaminocarboxylate-coated gold nanoparticles (NPs), Au@DTDTPA and Au@TADOTAGA, that have been recently developed exhibit a promising potential for image-guided radiotherapy. In order to render the radiosensitizing effect of these gold nanoparticles even more efficient, the study of their localization in cells is required to better understand the relation between the radiosensitizing properties of the agents and their localization in cells and in tumors. To achieve this goal, post-functionalization of Au@DTDTPA nanoparticles by near-infrared (NIF) organic dyes (aminated derivative of cyanine 5, Cy5-NH2) was performed. The immobilization of organic Cy5-NH2 dyes onto the gold nanoparticles confers to these radiosensitizers fluorescence properties which can be exploited for monitoring their internalization in cancerous cells, for determining their localization in cells by fluorescence microscopy (a common and powerful imaging tool in biology), and for following up on their accumulation in tumors after intravenous injection.
Collapse
|
20
|
In Vivo Quantification of Intramolecular FRET Using RacFRET Biosensors. Methods Mol Biol 2019. [PMID: 31432484 DOI: 10.1007/978-1-4939-9686-5_13] [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
Genetically encoded FRET biosensors are powerful tools to visualize protein activity and signaling events in vivo. Compared with a biochemical approach, FRET biosensors allow a noninvasive spatial-temporal detection of signaling processes in live cells and animal tissues. While the concept of this technique is relatively simple, the experimental procedure is complicated and consists of several steps: (1) biosensor optimization; (2) data acquisition; and (3) image processing with each step posing its own challenge. In this chapter, we discuss steps (2) and (3) with the emphasis on the intramolecular RacFRET biosensor. We describe the design principle of the biosensor, the experimental imaging setup for acquiring FRET data in zebrafish embryos expressing the RacFRET biosensor, and the step-by-step ratio image generation protocol using Fiji software. We discuss important considerations during FRET data acquisition and analysis. Finally, we provide a macro code for the automated ratio image generation.
Collapse
|
21
|
ShadowR: a novel chromoprotein with reduced non-specific binding and improved expression in living cells. Sci Rep 2019; 9:12072. [PMID: 31427680 PMCID: PMC6700193 DOI: 10.1038/s41598-019-48604-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/08/2019] [Indexed: 01/08/2023] Open
Abstract
Here we developed an orange light-absorbing chromoprotein named ShadowR as a novel acceptor for performing fluorescence lifetime imaging microscopy-based Förster resonance energy transfer (FLIM-FRET) measurement in living cells. ShadowR was generated by replacing hydrophobic amino acids located at the surface of the chromoprotein Ultramarine with hydrophilic amino acids in order to reduce non-specific interactions with cytosolic proteins. Similar to Ultramarine, ShadowR shows high absorption capacity and no fluorescence. However, it exhibits reduced non-specific binding to cytosolic proteins and is highly expressed in HeLa cells. Using tandem constructs and a LOVTRAP system, we showed that ShadowR can be used as a FRET acceptor in combination with donor mRuby2 or mScarlet in HeLa cells. Thus, ShadowR is a useful, novel FLIM-FRET acceptor.
Collapse
|
22
|
Optical Sensors Based on II-VI Quantum Dots. NANOMATERIALS 2019; 9:nano9020192. [PMID: 30717393 PMCID: PMC6410100 DOI: 10.3390/nano9020192] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 02/07/2023]
Abstract
Fundamentals of quantum dots (QDs) sensing phenomena show the predominance of these fluorophores over standard organic dyes, mainly because of their unique optical properties such as sharp and tunable emission spectra, high emission quantum yield and broad absorption. Moreover, they also indicate no photo bleaching and can be also grown as no blinking emitters. Due to these properties, QDs may be used e.g., for multiplex testing of the analyte by simultaneously detecting multiple or very weak signals. Physico-chemical mechanisms used for analyte detection, like analyte stimulated QDs aggregation, nonradiative Förster resonance energy transfer (FRET) exhibit a number of QDs, which can be applied in sensors. Quantum dots-based sensors find use in the detection of ions, organic compounds (e.g., proteins, sugars, volatile substances) as well as bacteria and viruses.
Collapse
|
23
|
Shao S, Li Z, Cheng H, Wang S, Perkins NG, Sarkar P, Wei W, Xue M. A Chemical Approach for Profiling Intracellular AKT Signaling Dynamics from Single Cells. J Am Chem Soc 2018; 140:13586-13589. [PMID: 30351133 DOI: 10.1021/jacs.8b08931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present here a novel chemical method to continuously analyze intracellular AKT signaling activities at single-cell resolution, without genetic manipulations. A pair of cyclic peptide-based fluorescent probes were developed to recognize the phosphorylated Ser474 site and a distal epitope on AKT. A Förster resonance energy transfer signal is generated upon concurrent binding of the two probes onto the same AKT protein, which is contingent upon the Ser474 phosphorylation. Intracellular delivery of the probes enabled dynamic measurements of the AKT signaling activities. We further implemented this detection strategy on a microwell single-cell platform, and interrogated the AKT signaling dynamics in a human glioblastoma cell line. We resolved unique features of the single-cell signaling dynamics following different perturbations. Our study provided the first example of monitoring the temporal evolution of cellular signaling heterogeneities and unveiled biological information that was inaccessible to other methods.
Collapse
Affiliation(s)
- Shiqun Shao
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| | - Zhonghan Li
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| | - Hanjun Cheng
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Siwen Wang
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| | - Nicole G Perkins
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| | - Priyanka Sarkar
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| | - Wei Wei
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Min Xue
- Department of Chemistry , University of California, Riverside , Riverside , California 92521 , United States
| |
Collapse
|
24
|
Petrovics R, Söveges B, Egyed A, Knorr G, Kormos A, Imre T, Török G, Zeke A, Kocsmár É, Lotz G, Kele P, Németh K. A rapid and concise setup for the fast screening of FRET pairs using bioorthogonalized fluorescent dyes. Org Biomol Chem 2018; 16:2997-3005. [PMID: 29629719 DOI: 10.1039/c8ob00213d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
One of the most popular means to follow interactions between bio(macro)molecules is Förster resonance energy transfer (FRET). There is large interest in widening the selection of fluorescent FRET pairs especially in the region of the red/far red range, where minimal autofluorescence is encountered. A set of bioorthogonally applicable fluorescent dyes, synthesized recently in our lab, were paired (Cy3T/Cy5T; Cy1A/Cy3T and Cy1A/CBRD1A) based on their spectral characteristics in order to test their potential in FRET applications. For fast elaboration of the selected pairs we have created a bioorthogonalized platform based on complementary 17-mer DNA oligomers. The cyclooctynylated strands were modified nearly quantitatively with the fluorophores via bioorthogonal chemistry steps, using azide- (Cy1; CBRD1) or tetrazine-modified (Cy3; Cy5) dyes. Reactions were followed by capillary electrophoresis using a method specifically developed for this project. FRET efficiencies of the fluorescent dye pairs were compared both in close proximity (5' and 3' matched) and at larger distance (5' and 5' matched). The specificity of FRET signals was further elaborated by denaturation and competition studies. Cy1A/Cy3T and Cy1A/CBRD1A introduced here as novel FRET pairs are highly recommended for FRET applications based on the significant changes in fluorescence intensities of the donor and acceptor peaks. Application of one of the FRET pairs was demonstrated in live cells, transfected with labeled oligos. Furthermore, the concise installation of the dyes allows for efficient fluorescence modification of any selected DNA strands as was demonstrated in the construction of Cy3T labeled oligomers, which were used in the FISH-based detection of Helicobacter pylori.
Collapse
Affiliation(s)
- Réka Petrovics
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Bianka Söveges
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Alexandra Egyed
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Gergely Knorr
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Attila Kormos
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Tímea Imre
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Instrumentation Center, MS Metabolomics Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - György Török
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Enzymology, Molecular Cell Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - András Zeke
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Enzymology, Protein Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - Éva Kocsmár
- 2nd Department of Pathology, Semmelweis University, Budapest H-1091 Üllői str. 93, Hungary
| | - Gábor Lotz
- 2nd Department of Pathology, Semmelweis University, Budapest H-1091 Üllői str. 93, Hungary
| | - Péter Kele
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Krisztina Németh
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| |
Collapse
|
25
|
Bork NI, Nikolaev VO. cGMP Signaling in the Cardiovascular System-The Role of Compartmentation and Its Live Cell Imaging. Int J Mol Sci 2018. [PMID: 29534460 PMCID: PMC5877662 DOI: 10.3390/ijms19030801] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ubiquitous second messenger 3′,5′-cyclic guanosine monophosphate (cGMP) regulates multiple physiologic processes in the cardiovascular system. Its intracellular effects are mediated by stringently controlled subcellular microdomains. In this review, we will illustrate the current techniques available for real-time cGMP measurements with a specific focus on live cell imaging methods. We will also discuss currently accepted and emerging mechanisms of cGMP compartmentation in the cardiovascular system.
Collapse
Affiliation(s)
- Nadja I Bork
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg 20246, Germany.
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Kiel/Lübeck, Hamburg 20246, Germany.
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg 20246, Germany.
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Kiel/Lübeck, Hamburg 20246, Germany.
| |
Collapse
|
26
|
Synergistic antitumor effects of combination PI3K/mTOR and MEK inhibition (SAR245409 and pimasertib) in mucinous ovarian carcinoma cells by fluorescence resonance energy transfer imaging. Oncotarget 2018; 7:29577-91. [PMID: 27102436 PMCID: PMC5045418 DOI: 10.18632/oncotarget.8807] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/29/2016] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to clarify the synergistic effects of dual inhibition of the PI3K/mTOR and MAPK pathways in ovarian mucinous carcinoma (OMC) cells, using fluorescence resonance energy transfer (FRET) imaging. We exposed 6 OMC cell lines to a PI3K/mTOR inhibitor (voxtalisib, SAR245409) and/or a MEK inhibitor (pimasertib), and evaluated synergistic effects using the Chou-Talalay method. Then, S6K (PI3K pathway) and ERK (MAPK pathway) kinase activities, and their individual proliferative or cytotoxic effects were calculated by time-lapse FRET imaging. In combination with SAR245409, pimasertib (30 nM) synergistically inhibited cell growth (combination indexes: 0.03-0.5) and induced apoptosis in all 6 OMC cell lines. FRET-imaging results demonstrated that ERK inhibition induced both anti-proliferation and apoptosis in a dose-dependent manner in both MCAS and OAW42 cells. However, S6K inhibition suppressed proliferation in a threshold manner in both cell lines, although apoptosis was only induced in OAW42 cells. These results demonstrated that combined PI3K/mTOR and MEK inhibition exhibited synergistic antitumor effects in OMC cells and that FRET imaging is useful for analyzing kinase activities in live cells and elucidating their cytostatic and cytotoxic effects.
Collapse
|
27
|
Conyard J, Heisler IA, Chan Y, Bulman Page PC, Meech SR, Blancafort L. A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple. Chem Sci 2018; 9:1803-1812. [PMID: 29675225 PMCID: PMC5892128 DOI: 10.1039/c7sc04091a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/30/2017] [Indexed: 01/19/2023] Open
Abstract
Dynamics of a nonplanar GFP chromophore are studied experimentally and theoretically. Coupled torsional motion is responsible for the ultrafast decay.
The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples.
Collapse
Affiliation(s)
- Jamie Conyard
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Ismael A Heisler
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Yohan Chan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Philip C Bulman Page
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Stephen R Meech
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi , Departament de Química , Facultat de Ciències , Universitat de Girona , C/ M. A. Capmany 69 , 17003 Girona , Spain .
| |
Collapse
|
28
|
Wong HL, Akamatsu A, Wang Q, Higuchi M, Matsuda T, Okuda J, Kosami KI, Inada N, Kawasaki T, Kaneko-Kawano T, Nagawa S, Tan L, Kawano Y, Shimamoto K. In vivo monitoring of plant small GTPase activation using a Förster resonance energy transfer biosensor. PLANT METHODS 2018; 14:56. [PMID: 30002723 PMCID: PMC6035793 DOI: 10.1186/s13007-018-0325-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/29/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Small GTPases act as molecular switches that regulate various plant responses such as disease resistance, pollen tube growth, root hair development, cell wall patterning and hormone responses. Thus, to monitor their activation status within plant cells is believed to be the key step in understanding their roles. RESULTS We have established a plant version of a Förster resonance energy transfer (FRET) probe called Ras and interacting protein chimeric unit (Raichu) that can successfully monitor activation of the rice small GTPase OsRac1 during various defence responses in cells. Here, we describe the protocol for visualizing spatiotemporal activity of plant Rac/ROP GTPase in living plant cells, transfection of rice protoplasts with Raichu-OsRac1 and acquisition of FRET images. CONCLUSIONS Our protocol should be adaptable for monitoring activation for other plant small GTPases and protein-protein interactions for other FRET sensors in various plant cells.
Collapse
Affiliation(s)
- Hann Ling Wong
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
- Present Address: Department of Biological Science, University Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
| | - Akira Akamatsu
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
- Present Address: Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda, 669-1337 Japan
| | - Qiong Wang
- Present Address: Signal Transduction and Immunity Group, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, No. 3888 Chenhua Road, Shanghai, 201602 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Masayuki Higuchi
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
| | - Tomonori Matsuda
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
| | - Jun Okuda
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
| | - Ken-ichi Kosami
- Present Address: Signal Transduction and Immunity Group, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, No. 3888 Chenhua Road, Shanghai, 201602 China
| | - Noriko Inada
- College of Life, Environment, and Advanced, Osaka Prefecture University Sciences, Sakai, Osaka 599-8531 Japan
| | - Tsutomu Kawasaki
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
- Present Address: Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505 Japan
| | | | - Shingo Nagawa
- Core Facility of Cell Biology, Shanghai Center for Plant Stress Biology, No. 3888 Chenhua Road, Shanghai, 201602 China
- Present Address: FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Li Tan
- Core Facility of Cell Biology, Shanghai Center for Plant Stress Biology, No. 3888 Chenhua Road, Shanghai, 201602 China
| | - Yoji Kawano
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
- Present Address: Signal Transduction and Immunity Group, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, No. 3888 Chenhua Road, Shanghai, 201602 China
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813 Japan
| | - Ko Shimamoto
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192 Japan
| |
Collapse
|
29
|
Jha SK, Malik S, Sharma M, Pandey A, Pandey GK. Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management. Curr Genomics 2017; 18:523-541. [PMID: 29204081 PMCID: PMC5684648 DOI: 10.2174/1389202918666170228142703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/13/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation-dephosphorylation is a well-known regulatory mechanism in biological systems and has become one of the significant means of protein function regulation, modulating most of the biological processes. Protein kinases play vital role in numerous cellular processes. Kinases transduce external signal into responses such as growth, immunity and stress tolerance through phosphorylation of their target proteins. In order to understand these cellular processes at the molecular level, one needs to be aware of the different substrates targeted by protein kinases. Advancement in tools and techniques has bestowed practice of multiple approaches that enable target identification of kinases. However, so far none of the methodologies has been proved to be as good as a panacea for the substrate identification. In this review, the recent advances that have been made in the identifications of putative substrates and the implications of these kinases and their substrates in stress management are discussed.
Collapse
Affiliation(s)
- Saroj K Jha
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Shikha Malik
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Amita Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| |
Collapse
|
30
|
Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 92:668-678. [DOI: 10.1016/j.bios.2016.10.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 11/23/2022]
|
31
|
Castro L, Yapo C, Vincent P. [Physiopathology of cAMP/PKA signaling in neurons]. Biol Aujourdhui 2017; 210:191-203. [PMID: 28327278 DOI: 10.1051/jbio/2017005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 11/15/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) and the cyclic-AMP dependent protein kinase (PKA) regulate a plethora of cellular functions in virtually all eukaryotic cells. In neurons, the cAMP/PKA signaling cascade controls a number of biological properties such as axonal growth, synaptic transmission, regulation of excitability or long term changes in the nucleus. Genetically-encoded optical biosensors for cAMP or PKA considerably improved our understanding of these processes by providing a real-time measurement in living neurons. In this review, we describe the recent progresses made in the creation of biosensors for cAMP or PKA activity. These biosensors revealed profound differences in the amplitude of the cAMP signal evoked by neuromodulators between various neuronal preparations. These responses can be resolved at the level of individual neurons, also revealing differences related to the neuronal type. At the subcellular level, biosensors reported different signal dynamics in domains like dendrites, cell body, nucleus and axon. Combining this imaging approach with pharmacology or genetical models points at phosphodiesterases and phosphatases as critical regulatory proteins. Biosensor imaging will certainly help understand the mechanism of action of current drugs as well as help in devising novel therapeutic strategies for neuropsychiatric diseases.
Collapse
|
32
|
Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmüller U, Schultz C. High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells. Cell Chem Biol 2016; 23:1550-1559. [PMID: 27939899 PMCID: PMC5193178 DOI: 10.1016/j.chembiol.2016.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 01/06/2023]
Abstract
Essential characteristics of cellular signaling networks include a complex interconnected architecture and temporal dynamics of protein activity. The latter can be monitored by Förster resonance energy transfer (FRET) biosensors at a single-live-cell level with high temporal resolution. However, these experiments are typically limited to the use of a couple of FRET biosensors. Here, we describe a FRET-based multi-parameter imaging platform (FMIP) that allows simultaneous high-throughput monitoring of multiple signaling pathways. We apply FMIP to monitor the crosstalk between epidermal growth factor receptor (EGFR) and insulin-like growth factor-1 receptor signaling, signaling perturbations caused by pathophysiologically relevant EGFR mutations, and the effects of a clinically important MEK inhibitor (selumetinib) on the EGFR network. We expect that in the future the platform will be applied to develop comprehensive models of signaling networks and will help to investigate the mechanism of action as well as side effects of therapeutic treatments.
Collapse
Affiliation(s)
- Dmitry Kuchenov
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Vibor Laketa
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Florian Salopiata
- Division of Systems Biology of Signal Transduction, Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany; Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97201, USA.
| |
Collapse
|
33
|
Fluorescence bioimaging of intracellular signaling and its clinical application. J Oral Biosci 2016; 58:113-119. [PMID: 32512679 DOI: 10.1016/j.job.2016.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/18/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Fluorescent proteins have continued to shed light on cell biology since the cDNA of wild type green fluorescent protein was first isolated. Nowadays, these remarkable proteins are useful tools, not only in basic research, but also in clinical medicine. HIGHLIGHT By taking advantage of fluorescent protein-based technologies, we identified a signaling network critical for influenza virus internalization and infection. In addition, we developed a highly sensitive biosensor for monitoring kinase activity that utilizes energy transfer between fluorescent proteins. This has led to a high-performance clinical test that enables the prediction of future therapeutic responses and the risk of acquired drug resistance for each individual patient before beginning molecular target therapy. CONCLUSION Technologies that utilize fluorescent proteins, such as the biosensor presented here, should find increasing applications in clinical medicine.
Collapse
|
34
|
Wang F, Bélanger E, Paquet ME, Côté DC, De Koninck Y. Probing pain pathways with light. Neuroscience 2016; 338:248-271. [PMID: 27702648 DOI: 10.1016/j.neuroscience.2016.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
Abstract
We have witnessed an accelerated growth of photonics technologies in recent years to enable not only monitoring the activity of specific neurons, while animals are performing certain types of behavior, but also testing whether specific cells, circuits, and regions are sufficient or necessary for initiating, maintaining, or altering this or that behavior. Compared to other sensory systems, however, such as the visual or olfactory system, photonics applications in pain research are only beginning to emerge. One reason pain studies have lagged behind is that many of the techniques originally developed cannot be directly implemented to study key relay sites within pain pathways, such as the skin, dorsal root ganglia, spinal cord, and brainstem. This is due, in part, to difficulties in accessing these structures with light. Here we review a number of recent advances in design and delivery of light-sensitive molecular probes (sensors and actuators) into pain relay circuits to help decipher their structural and functional organization. We then discuss several challenges that have hampered hardware access to specific structures including light scattering, tissue movement and geometries. We review a number of strategies to circumvent these challenges, by delivering light into, and collecting it from the different key sites to unravel how nociceptive signals are encoded at each level of the neuraxis. We conclude with an outlook on novel imaging modalities for label-free chemical detection and opportunities for multimodal interrogation in vivo. While many challenges remain, these advances offer unprecedented opportunities to bridge cellular approaches with context-relevant behavioral testing, an essential step toward improving translation of basic research findings into clinical applications.
Collapse
Affiliation(s)
- Feng Wang
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada
| | - Erik Bélanger
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada
| | - Marie-Eve Paquet
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, QC, Canada
| | - Daniel C Côté
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de physique, de génie physique et d'optique, Université Laval, Québec, QC, Canada
| | - Yves De Koninck
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada.
| |
Collapse
|
35
|
Lysosome based toxic detection in Saccharomyces cerevisiae using novel portable fluorometer. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-016-0017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
36
|
Cavnar SP, Xiao A, Gibbons AE, Rickelmann AD, Neely T, Luker KE, Takayama S, Luker GD. Imaging Sensitivity of Quiescent Cancer Cells to Metabolic Perturbations in Bone Marrow Spheroids. Tomography 2016; 2:146-157. [PMID: 27478871 PMCID: PMC4963031 DOI: 10.18383/j.tom.2016.00157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Malignant cells from breast cancer and other common cancers such as prostate and melanoma may persist in bone marrow as quiescent, non-dividing cells that remain viable for years or even decades before resuming proliferation to cause recurrent disease. This phenomenon, referred to clinically as tumor dormancy, poses tremendous challenges to curing patients with breast cancer. Quiescent tumor cells resist chemotherapy drugs that predominantly target proliferating cells, limiting success of neo-adjuvant and adjuvant therapies. We recently developed a 3D spheroid model of quiescent breast cancer cells in bone marrow for mechanistic and drug testing studies. We combined this model with optical imaging methods for label-free detection of cells preferentially utilizing glycolysis versus oxidative metabolism to investigate the metabolic state of co-culture spheroids with different bone marrow stromal and breast cancer cells. Through imaging and biochemical assays, we identified different metabolic states of bone marrow stromal cells that control metabolic status and flexibilities of co-cultured breast cancer cells. We tested metabolic stresses and targeted inhibition of specific metabolic pathways to identify approaches to preferentially eliminate quiescent breast cancer cells from bone marrow environments. These studies establish an integrated imaging approach to analyze metabolism in complex tissue environments to identify new metabolically-targeted cancer therapies.
Collapse
Affiliation(s)
- Stephen P. Cavnar
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Annie Xiao
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anne E. Gibbons
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Andrew D. Rickelmann
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Taylor Neely
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kathryn E. Luker
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shuichi Takayama
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan College of Engineering, Ann Arbor, Michigan
- Department of Macromolecular Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan; and
| | - Gary D. Luker
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Macromolecular Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan; and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| |
Collapse
|
37
|
Yoshikoshi K, Watanabe T, Hohsaka T. Double-Fluorescent-Labeled Single-Chain Antibodies Showing Antigen-Dependent Fluorescence Ratio Change. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kensuke Yoshikoshi
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology
| |
Collapse
|
38
|
Kim J, Song SH, Jin Y, Park HJ, Yoon H, Jeon S, Cho SW. Multiphoton luminescent graphene quantum dots for in vivo tracking of human adipose-derived stem cells. NANOSCALE 2016; 8:8512-9. [PMID: 27067507 DOI: 10.1039/c6nr02143c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The applicability of graphene quantum dots (GQDs) for the in vitro and in vivo live imaging and tracking of different types of human stem cells is investigated. GQDs synthesized by the modified graphite intercalated compound method show efficient cellular uptake with improved biocompatibility and highly sensitive optical properties, indicating their feasibility as a bio-imaging probe for stem cell therapy.
Collapse
Affiliation(s)
- Jin Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea.
| | | | | | | | | | | | | |
Collapse
|
39
|
Florian PE, Rouillé Y, Ruta S, Nichita N, Roseanu A. Recent advances in human viruses imaging studies. J Basic Microbiol 2016; 56:591-607. [DOI: 10.1002/jobm.201500575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Paula Ecaterina Florian
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Yves Rouillé
- Center for Infection and Immunity of Lille (CIIL); Inserm U1019; CNRS UMR8204; Institut Pasteur de Lille; Université Lille Nord de France; Lille France
| | - Simona Ruta
- Department of Emergent Diseases; Stefan S. Nicolau Institute of Virology; Bucharest 030304 Romania
| | - Norica Nichita
- Department of Viral Glycoproteins; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Anca Roseanu
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| |
Collapse
|
40
|
Banerjee S, Garcia LR, Versaw WK. Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:300-310. [PMID: 26879593 DOI: 10.1017/s143192761600012x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein-protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.
Collapse
Affiliation(s)
- Swayoma Banerjee
- Department of Biology,Texas A&M University,College Station,TX 77843,USA
| | - Luis Rene Garcia
- Department of Biology,Texas A&M University,College Station,TX 77843,USA
| | - Wayne K Versaw
- Department of Biology,Texas A&M University,College Station,TX 77843,USA
| |
Collapse
|
41
|
Sasaki K, Yoshida M. The exploitation of FRET probes to track bromodomain/histone interactions in cells for bromodomain inhibitors. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:51-56. [PMID: 27769358 DOI: 10.1016/j.ddtec.2016.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/25/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
Bromodomain-containing proteins are epigenetic readers of histone codes, which recognize acetylated histones and are involved in transcription, nucleosome remodeling and DNA repair. Chromosomal translocations of bromodomain-containing proteins have been implicated in many diseases. In this regard, small molecules that inhibit bromodomains are promising as therapeutic agents. A fluorescence microscopy-based approach provides information on bromodomain inhibitors that abrogate the interaction between acetylated histones and bromodomains in living cells. We have developed genetically encoded fluorescent probes for histone acetylation called Histacs. We review how these recently developed probes can serve as useful tools to evaluate the intracellular activity of bromodomain inhibitors.
Collapse
Affiliation(s)
- Kazuki Sasaki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Japan Agency for Medical Research and Development (AMED), CREST, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
| |
Collapse
|
42
|
Chang L, Hu J, Chen F, Chen Z, Shi J, Yang Z, Li Y, Lee LJ. Nanoscale bio-platforms for living cell interrogation: current status and future perspectives. NANOSCALE 2016; 8:3181-3206. [PMID: 26745513 DOI: 10.1039/c5nr06694h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The living cell is a complex entity that dynamically responds to both intracellular and extracellular environments. Extensive efforts have been devoted to the understanding intracellular functions orchestrated with mRNAs and proteins in investigation of the fate of a single-cell, including proliferation, apoptosis, motility, differentiation and mutations. The rapid development of modern cellular analysis techniques (e.g. PCR, western blotting, immunochemistry, etc.) offers new opportunities in quantitative analysis of RNA/protein expression up to a single cell level. The recent entries of nanoscale platforms that include kinds of methodologies with high spatial and temporal resolution have been widely employed to probe the living cells. In this tutorial review paper, we give insight into background introduction and technical innovation of currently reported nanoscale platforms for living cell interrogation. These highlighted technologies are documented in details within four categories, including nano-biosensors for label-free detection of living cells, nanodevices for living cell probing by intracellular marker delivery, high-throughput platforms towards clinical current, and the progress of microscopic imaging platforms for cell/tissue tracking in vitro and in vivo. Perspectives for system improvement were also discussed to solve the limitations remains in current techniques, for the purpose of clinical use in future.
Collapse
Affiliation(s)
- Lingqian Chang
- NSF Nanoscale Science and Engineering Center (NSEC), The Ohio State University, Columbus, OH 43212, USA.
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Oral biosciences: The annual review 2015. J Oral Biosci 2016. [DOI: 10.1016/j.job.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
44
|
Yan Y, Tian J, Hu F, Wang X, Shen Z. A near IR photosensitizer based on self-assembled CdSe quantum dot-aza-BODIPY conjugate coated with poly(ethylene glycol) and folic acid for concurrent fluorescence imaging and photodynamic therapy. RSC Adv 2016. [DOI: 10.1039/c6ra23113f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nanocomposite comprised of CdSe quantum dot-thiophene-substituted aza-BODIPY conjugate coated with FA and PEG has been developed for simultaneous fluorescence imaging and photodynamic therapy of HeLa cells via Förster resonance energy transfer.
Collapse
Affiliation(s)
- Yu Yan
- State Key Laboratory of Coordination Chemistry
- Collaborative Innovation Center of Advanced Microstructures
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210046
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research
- Department of Complex Prescription of TCM
- China Pharmaceutical University
- Nanjing 211198
| | - Fengrui Hu
- Laboratory of Micro/Nano-photonics and Ultrafast Spectroscopy
- School of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Xiaoyong Wang
- Laboratory of Micro/Nano-photonics and Ultrafast Spectroscopy
- School of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Zhen Shen
- State Key Laboratory of Coordination Chemistry
- Collaborative Innovation Center of Advanced Microstructures
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210046
| |
Collapse
|
45
|
Okamoto A. Thiazole Orange-Tethered Nucleic Acids and ECHO Probes for Fluorometric Detection of Nucleic Acids. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
46
|
Suzuki M, Sakata I, Sakai T, Tomioka H, Nishigaki K, Tramier M, Coppey-Moisan M. A high-throughput direct fluorescence resonance energy transfer-based assay for analyzing apoptotic proteases using flow cytometry and fluorescence lifetime measurements. Anal Biochem 2015; 491:10-7. [DOI: 10.1016/j.ab.2015.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/27/2023]
|
47
|
Depry C, Mehta S, Li R, Zhang J. Visualization of Compartmentalized Kinase Activity Dynamics Using Adaptable BimKARs. ACTA ACUST UNITED AC 2015; 22:1470-1479. [PMID: 26548610 DOI: 10.1016/j.chembiol.2015.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/14/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
The ability to monitor kinase activity dynamics in live cells greatly aids the study of how signaling events are spatiotemporally regulated. Here, we report on the adaptability of bimolecular kinase activity reporters (bimKARs) as molecular tools to enhance the real-time visualization of kinase activity. We demonstrate that the bimKAR design is truly versatile and can be used to monitor a variety of kinases, including JNK, ERK, and AMPK. Furthermore, bimKARs can have significantly enhanced dynamic ranges over their unimolecular counterparts, allowing the elucidation of previously undetectable kinase activity dynamics. Using these newly designed bimKARs, we investigate the regulation of AMPK by protein kinase A (PKA) in the plasma membrane, and demonstrate that PKA can both negatively and positively regulate AMPK activity in the same cell.
Collapse
Affiliation(s)
- Charlene Depry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA
| | - Ruojing Li
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA.
| |
Collapse
|
48
|
Rowland CE, Brown CW, Medintz IL, Delehanty JB. Intracellular FRET-based probes: a review. Methods Appl Fluoresc 2015; 3:042006. [PMID: 29148511 DOI: 10.1088/2050-6120/3/4/042006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.
Collapse
Affiliation(s)
- Clare E Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA. National Research Council, Washington, DC 20036, USA
| | | | | | | |
Collapse
|
49
|
Trinh LA, Fraser SE. Imaging the Cell and Molecular Dynamics of Craniofacial Development: Challenges and New Opportunities in Imaging Developmental Tissue Patterning. Curr Top Dev Biol 2015; 115:599-629. [PMID: 26589939 DOI: 10.1016/bs.ctdb.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of the vertebrate head requires cell-cell and tissue-tissue interactions between derivatives of the three germ layers to coordinate morphogenetic movements in four dimensions (4D: x, y, z, t). The high spatial and temporal resolution offered by optical microscopy has made it the main imaging modularity for capturing the molecular and cellular dynamics of developmental processes. In this chapter, we highlight the challenges and new opportunities provided by emerging technologies that enable dynamic, high-information-content imaging of craniofacial development. We discuss the challenges of varying spatial and temporal scales encountered from the biological and technological perspectives. We identify molecular and fluorescence imaging technology that can provide solutions to some of the challenges. Application of the techniques described within this chapter combined with considerations of the biological and technical challenges will aid in formulating the best image-based studies to extend our understanding of the genetic and environmental influences underlying craniofacial anomalies.
Collapse
Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
| |
Collapse
|
50
|
Komatsubara AT, Matsuda M, Aoki K. Quantitative analysis of recombination between YFP and CFP genes of FRET biosensors introduced by lentiviral or retroviral gene transfer. Sci Rep 2015; 5:13283. [PMID: 26290434 PMCID: PMC4542544 DOI: 10.1038/srep13283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/22/2015] [Indexed: 11/25/2022] Open
Abstract
Biosensors based on the principle of Förster (or fluorescence) resonance energy transfer (FRET) have been developed to visualize spatio-temporal dynamics of signalling molecules in living cells. Many of them adopt a backbone of intramolecular FRET biosensor with a cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) as donor and acceptor, respectively. However, there remains the difficulty of establishing cells stably expressing FRET biosensors with a YFP and CFP pair by lentiviral or retroviral gene transfer, due to the high incidence of recombination between YFP and CFP genes. To address this, we examined the effects of codon-diversification of YFP on the recombination of FRET biosensors introduced by lentivirus or retrovirus. The YFP gene that was fully codon-optimized to E.coli evaded the recombination in lentiviral or retroviral gene transfer, but the partially codon-diversified YFP did not. Further, the length of spacer between YFP and CFP genes clearly affected recombination efficiency, suggesting that the intramolecular template switching occurred in the reverse-transcription process. The simple mathematical model reproduced the experimental data sufficiently, yielding a recombination rate of 0.002–0.005 per base. Together, these results show that the codon-diversified YFP is a useful tool for expressing FRET biosensors by lentiviral or retroviral gene transfer.
Collapse
Affiliation(s)
- Akira T Komatsubara
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhiro Aoki
- Imaging Platform for Spatio-Temporal Information, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|