51
|
Brumbaugh K, Liao WC, Houchins JP, Cooper J, Stoesz S. Phosphosite-Specific Antibodies: A Brief Update on Generation and Applications. Methods Mol Biol 2017; 1554:1-40. [PMID: 28185181 DOI: 10.1007/978-1-4939-6759-9_1] [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] [Indexed: 01/01/2023]
Abstract
Phosphate addition is a posttranslational modification of proteins, and this modification can affect the activity and other properties of intracellular proteins. Different animal species can be used to generate phosphosite-specific antibodies as either polyclonals or monoclonals, and each approach offers its own benefits and disadvantages. The validation of phosphosite-specific antibodies requires multiple techniques and tactics to demonstrate their specificity. These antibodies can be used in arrays, flow cytometry, and imaging platforms. The specificity of phosphosite-specific antibodies is vital for their use in proteomics and profiling of disease.
Collapse
Affiliation(s)
- Kathy Brumbaugh
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA.
| | - Wen-Chie Liao
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - J P Houchins
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Jeff Cooper
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Steve Stoesz
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| |
Collapse
|
52
|
Lucarelli S, Delos Santos RC, Antonescu CN. Measurement of Epidermal Growth Factor Receptor-Derived Signals Within Plasma Membrane Clathrin Structures. Methods Mol Biol 2017; 1652:191-225. [PMID: 28791645 DOI: 10.1007/978-1-4939-7219-7_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The epidermal growth factor (EGF) receptor (EGFR) is an important regulator of cell growth, proliferation, survival, migration, and metabolism. EGF binding to EGFR triggers the activation of the receptor's intrinsic kinase activity, in turn eliciting the recruitment of many secondary signaling proteins and activation of downstream signals, such as the activation of phosphatidylinositol-3-kinase (PI3K) and Akt, a process requiring the phosphorylation of Gab1. While the identity of many signals that can be activated by EGFR has been revealed, how the spatiotemporal organization of EGFR signaling within cells controls receptor outcome remains poorly understood. Upon EGF binding at the plasma membrane, EGFR is internalized by clathrin-mediated endocytosis following recruitment to clathrin-coated pits (CCPs). Further, plasma membrane CCPs, but not EGFR internalization, are required for EGF-stimulated Akt phosphorylation. Signaling intermediates such as phosphorylated Gab1, which lead to Akt phosphorylation, are enriched within CCPs upon EGF stimulation. These findings indicate that some plasma membrane CCPs also serve as signaling microdomains required for certain facets of EGFR signaling and are enriched in key EGFR signaling intermediates. Understanding how the spatiotemporal organization of EGFR signals within CCP microdomains controls receptor signaling outcome requires imaging methods that can systematically resolve and analyze the properties of CCPs, EGFR and key signaling intermediates. Here, we describe methods using total internal reflection fluorescence microscopy imaging and analysis to systematically study the enrichment of EGFR and key EGFR-derived signals within CCPs.
Collapse
Affiliation(s)
- Stefanie Lucarelli
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3.,Graduate Program in Molecular Science, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3
| | - Ralph Christian Delos Santos
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3.,Graduate Program in Molecular Science, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3
| | - Costin N Antonescu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3. .,Graduate Program in Molecular Science, Ryerson University, 350 Victoria Street, Toronto, ON, Canada, M5B 2K3. .,Keenan Research Centre for Biomedical Science of St. Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8.
| |
Collapse
|
53
|
Nierode G, Kwon PS, Dordick JS, Kwon SJ. Cell-Based Assay Design for High-Content Screening of Drug Candidates. J Microbiol Biotechnol 2016; 26:213-25. [PMID: 26428732 DOI: 10.4014/jmb.1508.08007] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To reduce attrition in drug development, it is crucial to consider the development and implementation of translational phenotypic assays as well as decipher diverse molecular mechanisms of action for new molecular entities. High-throughput fluorescence and confocal microscopes with advanced analysis software have simplified the simultaneous identification and quantification of various cellular processes through what is now referred to as highcontent screening (HCS). HCS permits automated identification of modifiers of accessible and biologically relevant targets and can thus be used to detect gene interactions or identify toxic pathways of drug candidates to improve drug discovery and development processes. In this review, we summarize several HCS-compatible, biochemical, and molecular biology-driven assays, including immunohistochemistry, RNAi, reporter gene assay, CRISPR-Cas9 system, and protein-protein interactions to assess a variety of cellular processes, including proliferation, morphological changes, protein expression, localization, post-translational modifications, and protein-protein interactions. These cell-based assay methods can be applied to not only 2D cell culture but also 3D cell culture systems in a high-throughput manner.
Collapse
Affiliation(s)
- Gregory Nierode
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul S Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| |
Collapse
|
54
|
Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
Collapse
Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| |
Collapse
|
55
|
Handly LN, Yao J, Wollman R. Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks. J Mol Biol 2016; 428:3669-82. [PMID: 27430597 PMCID: PMC5023475 DOI: 10.1016/j.jmb.2016.07.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 12/16/2022]
Abstract
Signal transduction, or how cells interpret and react to external events, is a fundamental aspect of cellular function. Traditional study of signal transduction pathways involves mapping cellular signaling pathways at the population level. However, population-averaged readouts do not adequately illuminate the complex dynamics and heterogeneous responses found at the single-cell level. Recent technological advances that observe cellular response, computationally model signaling pathways, and experimentally manipulate cells now enable studying signal transduction at the single-cell level. These studies will enable deeper insights into the dynamic nature of signaling networks.
Collapse
Affiliation(s)
- L Naomi Handly
- Departments of Chemistry and Biochemistry, Integrative Biology and Physiology, and Institute for Quantitative and Computational Biosciences (QCB), UCLA, Los Angeles, CA 90095, USA
| | - Jason Yao
- Departments of Chemistry and Biochemistry, Integrative Biology and Physiology, and Institute for Quantitative and Computational Biosciences (QCB), UCLA, Los Angeles, CA 90095, USA
| | - Roy Wollman
- Departments of Chemistry and Biochemistry, Integrative Biology and Physiology, and Institute for Quantitative and Computational Biosciences (QCB), UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
56
|
Huynh Nhat KP, Watanabe T, Yoshikoshi K, Hohsaka T. Antibody-based fluorescent and fluorescent ratiometric indicators for detection of phosphotyrosine. J Biosci Bioeng 2016; 122:146-54. [DOI: 10.1016/j.jbiosc.2016.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
|
57
|
Li K, Xiang X, Sun J, He HT, Wu J, Wang Y, Zhu C. Imaging Spatiotemporal Activities of ZAP-70 in Live T Cells Using a FRET-Based Biosensor. Ann Biomed Eng 2016; 44:3510-3521. [PMID: 27384937 DOI: 10.1007/s10439-016-1683-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/21/2016] [Indexed: 01/20/2023]
Abstract
The zeta-chain-associated protein kinase 70 kDa (ZAP-70), a member of the spleen tyrosine kinase (Syk) family, plays an essential role in early T cell receptor (TCR) signaling. Defects in ZAP-70 lead to impaired thymocyte development and peripheral T cell activation. To better understand its activation dynamics and regulation, we visualized ZAP-70 activities in single live T cells with a Förster resonance energy transfer (FRET)-based biosensor, which was designed for probing kinase activities of the Syk family. We observed in Jurkat E6.1 T cells rapid and specific FRET changes following anti-CD3 stimulation and subsequent piceatannol inhibition. The initiation of ZAP-70 activation was prompt (within 10 s) and correlates with the accompanied intracellular calcium elevation, as revealed by simultaneous imaging of the biosensor and calcium. Different from the previously reported ZAP-70 activation in the immunological synapse and the opposite pole (anti-synapse), we have observed rapid and sustained ZAP-70 activation only at the synapse with superantigen-pulsed Raji B cells. Furthermore, ZAP-70 signaling was impaired by cholesterol depletion, further supporting the importance of membrane organization in TCR signaling. Together our results provide a direct characterization of the spatiotemporal features of ZAP-70 activity in real time at subcellular levels.
Collapse
Affiliation(s)
- Kaitao Li
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xue Xiang
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,School of Life Sciences, SUN YAT-SEN University, Guangzhou, China.,UnionPay Smart Co., Ltd, Shanghai, China
| | - Jie Sun
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hai-Tao He
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
| | - Jianhua Wu
- School of Life Sciences, SUN YAT-SEN University, Guangzhou, China.,School of Bioscience, South China University of Technology, Guangzhou, China
| | - Yingxiao Wang
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Cheng Zhu
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
58
|
Yu G, Zhou J, Shen J, Tang G, Huang F. Cationic pillar[6]arene/ATP host-guest recognition: selectivity, inhibition of ATP hydrolysis, and application in multidrug resistance treatment. Chem Sci 2016; 7:4073-4078. [PMID: 30155051 PMCID: PMC6013913 DOI: 10.1039/c6sc00531d] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/02/2016] [Indexed: 12/23/2022] Open
Abstract
Due to the differences in the cavity size of the hosts and the charge and length of the guests, a cationic water-soluble pillar[6]arene (WP6) selectively complexes with ATP to form a stable 1 : 1 inclusion complex WP6⊃ATP. This host-guest complexation was utilized to efficiently inhibit the hydrolysis of ATP, arising from the existence of the hydrophobic cavity of WP6. A folic acid functionalized diblock copolymer (FA-PEG-b-PAA) was employed to PEGylate WP6 to endow the polyion complex (PIC) micelles with specific targeting ability, preferentially delivering WP6 to folate receptor over-expressing KB cell. This host-guest complexation was further used to block the efflux pump to transport anticancer drugs out of cells by cutting off the energy source, which enhanced the efficacy of the cancer chemotherapy of DOX·HCl towards drug resistant MCF-7/ADR cell. This supramolecular method provides an extremely distinct strategy to potentially overcome multidrug resistance (MDR).
Collapse
Affiliation(s)
- Guocan Yu
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
| | - Jiong Zhou
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
| | - Jie Shen
- Department of Chemistry , Institute of Chemical Biology and Pharmaceutical Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Guping Tang
- Department of Chemistry , Institute of Chemical Biology and Pharmaceutical Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
| |
Collapse
|
59
|
Berns EJ, Cabezas MD, Mrksich M. Cellular Assays with a Molecular Endpoint Measured by SAMDI Mass Spectrometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3811-8. [PMID: 27240220 PMCID: PMC4981186 DOI: 10.1002/smll.201502940] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/12/2016] [Indexed: 05/07/2023]
Abstract
Cell-based, high-throughput screening (HTS) assays are increasingly important tools used in drug discovery, but frequently rely on readouts of gene expression or phenotypic changes and require development of specialized, labeled reporters. Here a cell-based, label-free assay compatible with HTS is introduced that can report quantitatively on enzyme activities by measuring mass changes of substrates with matrix-assisted laser desorption/ionization mass spectrometry. The assay uses self-assembled monolayers to culture cells on arrays presenting substrates, which serve as reporters for a desired enzyme activity. Each spot of cells is treated with a compound, cultured and lysed, enabling endogenous enzymes to act on the immobilized peptide substrate. It is demonstrated that the assay can measure protein tyrosine phosphatase (PTP) activity from as few as five cells and a screen is described that identifies a compound that reduces PTP activity in cell lysates. This approach offers a valuable addition to the methods available for cell-based screening.
Collapse
Affiliation(s)
- Eric J. Berns
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Maria D. Cabezas
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| |
Collapse
|
60
|
Copper-catalysed CN/CO coupling in water: a facile access to N-coumaryl amino acids and fluorescent tyrosine & lysine labels. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
61
|
Cyclophilin A promotes cell migration via the Abl-Crk signaling pathway. Nat Chem Biol 2015; 12:117-23. [PMID: 26656091 PMCID: PMC4718742 DOI: 10.1038/nchembio.1981] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 11/03/2015] [Indexed: 12/13/2022]
Abstract
Cyclophilin A (CypA) is overexpressed in a number of human cancer types, but the mechanisms by which the protein promotes oncogenic properties of cells are not understood. Here we demonstrate that CypA binds the CrkII adaptor protein and prevents it from switching to the inhibited state. CrkII influences cell motility and invasion by mediating signaling through its SH2 and SH3 domains. CrkII Tyr221 phosphorylation by the Abl or EGFR kinases induces an inhibited state of CrkII by means of an intramolecular SH2-pTyr221 interaction, causing signaling interruption. We show that the CrkII phosphorylation site constitutes a binding site for CypA. Recruitment of CypA sterically restricts the accessibility of Tyr221 to kinases, thereby suppressing CrkII phosphorylation and promoting the active state. Structural, biophysical and in vivo data show that CypA augments CrkII-mediated signaling. A strong stimulation of cell migration is observed in cancer cells wherein both CypA and CrkII are greatly upregulated.
Collapse
|
62
|
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
|
63
|
González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
Collapse
Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| |
Collapse
|
64
|
Hochreiter B, Garcia AP, Schmid JA. Fluorescent proteins as genetically encoded FRET biosensors in life sciences. SENSORS 2015; 15:26281-314. [PMID: 26501285 PMCID: PMC4634415 DOI: 10.3390/s151026281] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
Abstract
Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.
Collapse
Affiliation(s)
- Bernhard Hochreiter
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Alan Pardo Garcia
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Johannes A Schmid
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| |
Collapse
|
65
|
Dushek O, Lellouch AC, Vaux DJ, Shahrezaei V. Biosensor architectures for high-fidelity reporting of cellular signaling. Biophys J 2015; 107:773-782. [PMID: 25099816 PMCID: PMC4129486 DOI: 10.1016/j.bpj.2014.06.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/26/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022] Open
Abstract
Understanding mechanisms of information processing in cellular signaling networks requires quantitative measurements of protein activities in living cells. Biosensors are molecular probes that have been developed to directly track the activity of specific signaling proteins and their use is revolutionizing our understanding of signal transduction. The use of biosensors relies on the assumption that their activity is linearly proportional to the activity of the signaling protein they have been engineered to track. We use mechanistic mathematical models of common biosensor architectures (single-chain FRET-based biosensors), which include both intramolecular and intermolecular reactions, to study the validity of the linearity assumption. As a result of the classic mechanism of zero-order ultrasensitivity, we find that biosensor activity can be highly nonlinear so that small changes in signaling protein activity can give rise to large changes in biosensor activity and vice versa. This nonlinearity is abolished in architectures that favor the formation of biosensor oligomers, but oligomeric biosensors produce complicated FRET states. Based on this finding, we show that high-fidelity reporting is possible when a single-chain intermolecular biosensor is used that cannot undergo intramolecular reactions and is restricted to forming dimers. We provide phase diagrams that compare various trade-offs, including observer effects, which further highlight the utility of biosensor architectures that favor intermolecular over intramolecular binding. We discuss challenges in calibrating and constructing biosensors and highlight the utility of mathematical models in designing novel probes for cellular signaling.
Collapse
Affiliation(s)
- Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom; Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, United Kingdom.
| | - Annemarie C Lellouch
- Aix Marseille Université, Laboratoire d'Adhésion et Inflammation, Marseille, France; Institut National de la Santé et de la Recherche Médicale U1067, Marseille, France; Centre National de la Recherche Scientifique UMR 7333, Marseille, France
| | - David J Vaux
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, United Kingdom.
| |
Collapse
|
66
|
Jurchenko C, Salaita KS. Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes. Mol Cell Biol 2015; 35:2570-82. [PMID: 26031334 PMCID: PMC4524122 DOI: 10.1128/mcb.00195-15] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes.
Collapse
Affiliation(s)
- Carol Jurchenko
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - Khalid S Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
67
|
Strumillo M, Beltrao P. Towards the computational design of protein post-translational regulation. Bioorg Med Chem 2015; 23:2877-82. [PMID: 25956846 PMCID: PMC4673319 DOI: 10.1016/j.bmc.2015.04.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a fast and versatility mechanism used by the cell to regulate the function of proteins in response to changing conditions. PTMs can alter the activity of proteins by allosteric regulation or by controlling protein interactions, localization and abundance. Recent advances in proteomics have revealed the extent of regulation by PTMs and the different mechanisms used in nature to exert control over protein function via PTMs. These developments can serve as the foundation for the rational design of protein regulation. Here we review the advances in methods to determine the function of PTMs, protein allosteric control and examples of rational design of PTM regulation. These advances create an opportunity to move synthetic biology forward by making use of a level of regulation that is of yet unexplored.
Collapse
Affiliation(s)
- Marta Strumillo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK; iBiMED and Department of Health Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
| |
Collapse
|
68
|
Sun C, Ouyang M, Cao Z, Ma S, Alqublan H, Sriranganathan N, Wang Y, Lu C. Electroporation-delivered fluorescent protein biosensors for probing molecular activities in cells without genetic encoding. Chem Commun (Camb) 2015; 50:11536-9. [PMID: 25133322 PMCID: PMC5783554 DOI: 10.1039/c4cc04730c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent protein biosensors are typically implemented via genetic encoding which makes the examination of scarce cell samples impractical. By directly delivering the protein form of the biosensor into cells using electroporation, we detected intracellular molecular activity with the sample size down to ~100 cells with high spatiotemporal resolution.
Collapse
Affiliation(s)
- Chen Sun
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, Virginia 24061, USA
| | | | | | | | | | | | | | | |
Collapse
|
69
|
Cadra S, Gucciardi A, Valignat MP, Theodoly O, Vacaflores A, Houtman JC, Lellouch AC. ROZA-XL, an improved FRET based biosensor with an increased dynamic range for visualizing Zeta Associated Protein 70 kD (ZAP-70) tyrosine kinase activity in live T cells. Biochem Biophys Res Commun 2015; 459:405-10. [DOI: 10.1016/j.bbrc.2015.02.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/21/2015] [Indexed: 11/24/2022]
|
70
|
Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
| |
Collapse
|
71
|
Halls ML, Poole DP, Ellisdon AM, Nowell CJ, Canals M. Detection and Quantification of Intracellular Signaling Using FRET-Based Biosensors and High Content Imaging. Methods Mol Biol 2015; 1335:131-161. [PMID: 26260599 DOI: 10.1007/978-1-4939-2914-6_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Förster resonance energy transfer (FRET) biosensors represent invaluable tools to detect the spatiotemporal context of second messenger production and intracellular signaling that cannot be attained using traditional methods. Here, we describe a detailed protocol for the use of high content imaging in combination with FRET biosensors to assess second messenger production and intracellular signaling in a time-effective manner. We use four different FRET biosensors to measure cAMP levels, kinase (ERK and PKC), and GTPase activity. Importantly, we provide the protocols to express and measure these sensors in a variety of model cell lines and primary dorsal root ganglia neurons.
Collapse
Affiliation(s)
- Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia,
| | | | | | | | | |
Collapse
|
72
|
Sands B, Jenkins P, Peria WJ, Naivar M, Houston JP, Brent R. Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes. PLoS One 2014; 9:e109940. [PMID: 25302964 PMCID: PMC4193854 DOI: 10.1371/journal.pone.0109940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/04/2014] [Indexed: 01/03/2023] Open
Abstract
Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼1.5 ns vs ∼3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a “pseudophasor” that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation.
Collapse
Affiliation(s)
- Bryan Sands
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Patrick Jenkins
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - William J. Peria
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mark Naivar
- Darkling X, LLC, Los Alamos, New Mexico, United States of America
| | - Jessica P. Houston
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
73
|
Lu G, Tan P, Lei C, Nie Z, Huang Y, Yao S. Fluorescent detection of protein kinase based on positively charged gold nanoparticles. Talanta 2014; 128:360-5. [DOI: 10.1016/j.talanta.2014.04.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
|
74
|
Hou JH, Venkatachalam V, Cohen AE. Temporal dynamics of microbial rhodopsin fluorescence reports absolute membrane voltage. Biophys J 2014; 106:639-48. [PMID: 24507604 DOI: 10.1016/j.bpj.2013.11.4493] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 01/07/2023] Open
Abstract
Plasma membrane voltage is a fundamentally important property of a living cell; its value is tightly coupled to membrane transport, the dynamics of transmembrane proteins, and to intercellular communication. Accurate measurement of the membrane voltage could elucidate subtle changes in cellular physiology, but existing genetically encoded fluorescent voltage reporters are better at reporting relative changes than absolute numbers. We developed an Archaerhodopsin-based fluorescent voltage sensor whose time-domain response to a stepwise change in illumination encodes the absolute membrane voltage. We validated this sensor in human embryonic kidney cells. Measurements were robust to variation in imaging parameters and in gene expression levels, and reported voltage with an absolute accuracy of 10 mV. With further improvements in membrane trafficking and signal amplitude, time-domain encoding of absolute voltage could be applied to investigate many important and previously intractable bioelectric phenomena.
Collapse
Affiliation(s)
- Jennifer H Hou
- Department of Physics, Harvard University, Cambridge, Massachusetts
| | | | - Adam E Cohen
- Department of Physics, Harvard University, Cambridge, Massachusetts; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
| |
Collapse
|
75
|
Beck JR, Peterson LB, Imperiali B, Stains CI. Quantification of protein kinase enzymatic activity in unfractionated cell lysates using CSox-based sensors. ACTA ACUST UNITED AC 2014; 6:135-156. [PMID: 25205563 DOI: 10.1002/9780470559277.ch140106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Defining perturbations in protein kinase activity within biological samples can provide insight into disease mechanisms as well as potential targets for drug development. In this article, we present a method that utilizes a phosphorylation-sensitive amino acid, termed CSox, to afford kinase-selective biosensors capable of reporting on enzymatic activity directly in biological samples. These sensors produce an increase in fluorescence in response to phosphorylation of an amino acid residue adjacent to CSox. Probes can be designed for either serine/threonine or tyrosine kinases, and analysis can be performed using standard fluorescence equipment. The procedures provided herein represent our optimized protocols for the design, validation, and application of CSox-based protein kinase activity sensors.
Collapse
Affiliation(s)
- Jon R Beck
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Laura B Peterson
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| |
Collapse
|
76
|
Pleckstrin homology domain leucine-rich repeat protein phosphatases set the amplitude of receptor tyrosine kinase output. Proc Natl Acad Sci U S A 2014; 111:E3957-65. [PMID: 25201979 DOI: 10.1073/pnas.1404221111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Growth factor receptor levels are aberrantly high in diverse cancers, driving the proliferation and survival of tumor cells. Understanding the molecular basis for this aberrant elevation has profound clinical implications. Here we show that the pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP) suppresses receptor tyrosine kinase (RTK) signaling output by a previously unidentified epigenetic mechanism unrelated to its previously described function as the hydrophobic motif phosphatase for the protein kinase AKT, protein kinase C, and S6 kinase. Specifically, we show that nuclear-localized PHLPP suppresses histone phosphorylation and acetylation, in turn suppressing the transcription of diverse growth factor receptors, including the EGF receptor. These data uncover a much broader role for PHLPP in regulation of growth factor signaling beyond its direct inactivation of AKT: By suppressing RTK levels, PHLPP dampens the downstream signaling output of two major oncogenic pathways, the PI3 kinase/AKT and the Rat sarcoma (RAS)/ERK pathways. Our data are consistent with a model in which PHLPP modifies the histone code to control the transcription of RTKs.
Collapse
|
77
|
Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW. High-sensitivity measurements of multiple kinase activities in live single cells. Cell 2014; 157:1724-34. [PMID: 24949979 DOI: 10.1016/j.cell.2014.04.039] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/19/2014] [Accepted: 04/25/2014] [Indexed: 01/31/2023]
Abstract
Increasing evidence has shown that population dynamics are qualitatively different from single-cell behaviors. Reporters to probe dynamic, single-cell behaviors are desirable yet relatively scarce. Here, we describe an easy-to-implement and generalizable technology to generate reporters of kinase activity for individual cells. Our technology converts phosphorylation into a nucleocytoplasmic shuttling event that can be measured by epifluorescence microscopy. Our reporters reproduce kinase activity for multiple types of kinases and allow for calculation of active kinase concentrations via a mathematical model. Using this technology, we made several experimental observations that had previously been technicallyunfeasible, including stimulus-dependent patterns of c-Jun N-terminal kinase (JNK) and nuclear factor kappa B (NF-κB) activation. We also measured JNK, p38, and ERK activities simultaneously, finding that p38 regulates the peak number, but not the intensity, of ERK fluctuations. Our approach opens the possibility of analyzing a wide range of kinase-mediated processes in individual cells.
Collapse
Affiliation(s)
- Sergi Regot
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Jacob J Hughey
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bryce T Bajar
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Silvia Carrasco
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
78
|
Sinha C, Arora K, Moon CS, Yarlagadda S, Woodrooffe K, Naren AP. Förster resonance energy transfer - an approach to visualize the spatiotemporal regulation of macromolecular complex formation and compartmentalized cell signaling. Biochim Biophys Acta Gen Subj 2014; 1840:3067-72. [PMID: 25086255 DOI: 10.1016/j.bbagen.2014.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND Signaling messengers and effector proteins provide an orchestrated molecular machinery to relay extracellular signals to the inside of cells and thereby facilitate distinct cellular behaviors. Formations of intracellular macromolecular complexes and segregation of signaling cascades dynamically regulate the flow of a biological process. SCOPE OF REVIEW In this review, we provide an overview of the development and application of FRET technology in monitoring cyclic nucleotide-dependent signalings and protein complexes associated with these signalings in real time and space with brief mention of other important signaling messengers and effector proteins involved in compartmentalized signaling. MAJOR CONCLUSIONS The preciseness, rapidity and specificity of cellular responses indicate restricted alterations of signaling messengers, particularly in subcellular compartments rather than globally. Not only the physical confinement and selective depletion, but also the intra- and inter-molecular interactions of signaling effectors modulate the direction of signal transduction in a compartmentalized fashion. To understand the finer details of various intracellular signaling cascades and crosstalk between proteins and other effectors, it is important to visualize these processes in live cells. Förster Resonance Energy Transfer (FRET) has been established as a useful tool to do this, even with its inherent limitations. GENERAL SIGNIFICANCE FRET technology remains as an effective tool for unraveling the complex organization and distribution of various endogenous signaling proteins, as well as the spatiotemporal dynamics of second messengers inside a single cell to distinguish the heterogeneity of cell signaling under normal physiological conditions and during pathological events.
Collapse
Affiliation(s)
- Chandrima Sinha
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA
| | - Kavisha Arora
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Chang Suk Moon
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Sunitha Yarlagadda
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Koryse Woodrooffe
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA.
| |
Collapse
|
79
|
Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell 2014; 55:332-41. [PMID: 25002142 DOI: 10.1016/j.molcel.2014.06.003] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/21/2014] [Accepted: 05/20/2014] [Indexed: 12/29/2022]
Abstract
Obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. We recently developed a method to map proteomes in living cells with an engineered peroxidase (APEX) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when applied to unbounded regions that allow APEX-generated radicals to escape. Here, we combine APEX technology with a SILAC-based ratiometric tagging strategy to substantially reduce unwanted background and achieve nanometer spatial resolution. This is applied to map the proteome of the mitochondrial intermembrane space (IMS), which can freely exchange small molecules with the cytosol. Our IMS proteome of 127 proteins has >94% specificity and includes nine newly discovered mitochondrial proteins. This approach will enable scientists to map proteomes of cellular regions that were previously inaccessible.
Collapse
Affiliation(s)
- Victoria Hung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyun-Woo Rhee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | | | - Valentin Cracan
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
80
|
Tang S, Hu Y, Shen Q, Fang H, Li W, Nie Z, Yao S. Cyclic-AMP-dependent protein kinase (PKA) activity assay based on FRET between cationic conjugated polymer and chromophore-labeled peptide. Analyst 2014; 139:4710-6. [DOI: 10.1039/c4an00814f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
81
|
Wang H, Karadge U, Humphries WH, Fisher AL. Analyzing cell physiology in C. elegans with fluorescent ratiometric reporters. Methods 2014; 68:508-17. [PMID: 24915644 DOI: 10.1016/j.ymeth.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 11/30/2022] Open
Abstract
Ratiometric fluorescent reporters have recently emerged a new technique to non-invasively measure aspects of cell physiology such as redox status, calcium levels, energy production, and NADH levels. These reporters consist of either a single or pair of fluorophores along with specific modifications, such as the addition of a protein domain which binds to a metabolite of interest, thereby producing gradual alterations in fluorescence in response to changes in the measured parameter. Measurement of the changes in fluorescence produces a quantitative read-out of the cellular environment. While these reporters were initially developed to easily visualize and track changes in cultured cells, several groups have adapted these reporters to use in Caenorhabditis elegans which opens a new avenue through which to explore cell physiology during development or aging, in response to changes in external environment, or in response to genetic manipulation. These reporters have the advantage of being easily targeted to any part of the worm, and because C. elegans is transparent both the reporters and changes in their fluorescence can be clearly observed in vivo. Here we discuss the application of ratiometric reporters to C. elegans, and outline a method to quantitatively measure changes in intracellular peroxide levels using the HyPer ratiometric reporter. However, these principles can be applied to alternate ratiometric reporters which are designed to measure either other chemical species or other cellular parameters.
Collapse
Affiliation(s)
- Hongning Wang
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Medicine, UTHSCSA, San Antonio, TX 78229, United States; Center for Healthy Aging, UTHSCSA, San Antonio, TX 78229, United States
| | - Uma Karadge
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | | | - Alfred L Fisher
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Medicine, UTHSCSA, San Antonio, TX 78229, United States; Center for Healthy Aging, UTHSCSA, San Antonio, TX 78229, United States; GRECC, South Texas VA Healthcare System, San Antonio, TX 78229, United States.
| |
Collapse
|
82
|
Liu X, Li Y, Xu X, Li P, Nie Z, Huang Y, Yao S. Nanomaterial-based tools for protein kinase bioanalysis. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
83
|
Liu C, Chang L, Wang H, Bai J, Ren W, Li Z. Upconversion Nanophosphor: An Efficient Phosphopeptides-Recognizing Matrix and Luminescence Resonance Energy Transfer Donor for Robust Detection of Protein Kinase Activity. Anal Chem 2014; 86:6095-102. [DOI: 10.1021/ac501247t] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chenghui Liu
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi Province,
School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, Shaanxi Province P. R. China
- College
of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province P. R. China
| | - Lijuan Chang
- College
of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province P. R. China
| | - Honghong Wang
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi Province,
School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, Shaanxi Province P. R. China
| | - Jie Bai
- College
of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province P. R. China
| | - Wei Ren
- College
of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province P. R. China
| | - Zhengping Li
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi Province,
School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, Shaanxi Province P. R. China
- College
of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province P. R. China
| |
Collapse
|
84
|
Niko Y, Sasaki S, Kawauchi S, Tokumaru K, Konishi GI. Design of Weak-Donor Alkyl-Functionalized Push-Pull Pyrene Dyes Exhibiting Enhanced Fluorescence Quantum Yields and Unique On/Off Switching Properties. Chem Asian J 2014; 9:1797-807. [DOI: 10.1002/asia.201402088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 12/27/2022]
|
85
|
Abstract
Tyrosine phosphorylation of proteins was discovered in 1979, but this posttranslational modification had been "invented" by evolution more than a billion years ago in single-celled eukaryotic organisms that were the antecedents of the first multicellular animals. Because sophisticated cell-cell communication is a sine qua non for the existence of multicellular organisms, the development of cell-surface receptor systems that use tyrosine phosphorylation for transmembrane signal transduction and intracellular signaling seems likely to have been a crucial event in the evolution of metazoans. Like all types of protein phosphorylation, tyrosine phosphorylation serves to regulate proteins in multiple ways, including causing electrostatic repulsion and inducing allosteric transitions, but the most important function of phosphotyrosine (P.Tyr) is to serve as a docking site that promotes a specific interaction between a tyrosine phosphorylated protein and another protein that contains a P.Tyr-binding domain, such as an SH2 or PTB domain. Such docking interactions are essential for signal transduction downstream from receptor tyrosine kinases (RTKs) on the cell surface, which are activated on binding a cognate extracellular ligand, and, as a consequence, elicit specific cellular outcomes.
Collapse
Affiliation(s)
- Tony Hunter
- Salk Institute for Biological Studies, La Jolla, California 92037
| |
Collapse
|
86
|
Conway JRW, Carragher NO, Timpson P. Developments in preclinical cancer imaging: innovating the discovery of therapeutics. Nat Rev Cancer 2014; 14:314-28. [PMID: 24739578 DOI: 10.1038/nrc3724] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Integrating biological imaging into early stages of the drug discovery process can provide invaluable readouts of drug activity within complex disease settings, such as cancer. Iterating this approach from initial lead compound identification in vitro to proof-of-principle in vivo analysis represents a key challenge in the drug discovery field. By embracing more complex and informative models in drug discovery, imaging can improve the fidelity and statistical robustness of preclinical cancer studies. In this Review, we highlight how combining advanced imaging with three-dimensional systems and intravital mouse models can provide more informative and disease-relevant platforms for cancer drug discovery.
Collapse
Affiliation(s)
- James R W Conway
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre Sydney, St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales 2010, Sydney, Australia
| | - Neil O Carragher
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Paul Timpson
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre Sydney, St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales 2010, Sydney, Australia
| |
Collapse
|
87
|
Bale SS, Vernetti L, Senutovitch N, Jindal R, Hegde M, Gough A, McCarty WJ, Bakan A, Bhushan A, Shun TY, Golberg I, DeBiasio R, Usta BO, Taylor DL, Yarmush ML. In vitro platforms for evaluating liver toxicity. Exp Biol Med (Maywood) 2014; 239:1180-1191. [PMID: 24764241 DOI: 10.1177/1535370214531872] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The liver is a heterogeneous organ with many vital functions, including metabolism of pharmaceutical drugs and is highly susceptible to injury from these substances. The etiology of drug-induced liver disease is still debated although generally regarded as a continuum between an activated immune response and hepatocyte metabolic dysfunction, most often resulting from an intermediate reactive metabolite. This debate stems from the fact that current animal and in vitro models provide limited physiologically relevant information, and their shortcomings have resulted in "silent" hepatotoxic drugs being introduced into clinical trials, garnering huge financial losses for drug companies through withdrawals and late stage clinical failures. As we advance our understanding into the molecular processes leading to liver injury, it is increasingly clear that (a) the pathologic lesion is not only due to liver parenchyma but is also due to the interactions between the hepatocytes and the resident liver immune cells, stellate cells, and endothelial cells; and (b) animal models do not reflect the human cell interactions. Therefore, a predictive human, in vitro model must address the interactions between the major human liver cell types and measure key determinants of injury such as the dosage and metabolism of the drug, the stress response, cholestatic effect, and the immune and fibrotic response. In this mini-review, we first discuss the current state of macro-scale in vitro liver culture systems with examples that have been commercialized. We then introduce the paradigm of microfluidic culture systems that aim to mimic the liver with physiologically relevant dimensions, cellular structure, perfusion, and mass transport by taking advantage of micro and nanofabrication technologies. We review the most prominent liver-on-a-chip platforms in terms of their physiological relevance and drug response. We conclude with a commentary on other critical advances such as the deployment of fluorescence-based biosensors to identify relevant toxicity pathways, as well as computational models to create a predictive tool.
Collapse
Affiliation(s)
- Shyam Sundhar Bale
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Lawrence Vernetti
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Nina Senutovitch
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Rohit Jindal
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Manjunath Hegde
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Albert Gough
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - William J McCarty
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Ahmet Bakan
- University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Abhinav Bhushan
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260
| | - Inna Golberg
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Richard DeBiasio
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260
| | - Berk Osman Usta
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Martin L Yarmush
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| |
Collapse
|
88
|
Sample V, Mehta S, Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J Cell Sci 2014; 127:1151-60. [PMID: 24634506 PMCID: PMC3953811 DOI: 10.1242/jcs.099994] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/22/2013] [Indexed: 01/05/2023] Open
Abstract
In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction.
Collapse
Affiliation(s)
- Vedangi Sample
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| |
Collapse
|
89
|
Hertel F, Zhang J. Monitoring of post-translational modification dynamics with genetically encoded fluorescent reporters. Biopolymers 2014; 101:180-7. [PMID: 23576192 PMCID: PMC3883948 DOI: 10.1002/bip.22254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/01/2013] [Indexed: 11/06/2022]
Abstract
Post-translational modifications (PTMs) of proteins are essential mechanisms for virtually all dynamic processes within cellular signaling networks. Genetically encoded reporters based on fluorescent proteins (FPs) are powerful tools for spatiotemporal visualization of cellular parameters. Consequently, commonly used modular biosensor designs have been adapted to generate several protein-based indicators for monitoring various PTMs or the activity of corresponding enzymes in living cells, providing new biological insights into dynamics and regulatory functions of individual PTMs. In this review, we describe the application of general design strategies focusing on PTMs and discuss important considerations for engineering feasible indicators depending on the purpose. Moreover, we present developments and enhancements of PTM biosensors from selected studies and give an outlook on future perspectives of this versatile approach.
Collapse
Affiliation(s)
- Fabian Hertel
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
| | - Jin Zhang
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
| |
Collapse
|
90
|
Oldach L, Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. ACTA ACUST UNITED AC 2014; 21:186-97. [PMID: 24485761 DOI: 10.1016/j.chembiol.2013.12.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
Fluorescence-based, genetically encodable biosensors are widely used tools for real-time analysis of biological processes. Over the last few decades, the number of available genetically encodable biosensors and the types of processes they can monitor have increased rapidly. Here, we aim to introduce the reader to general principles and practices in biosensor development and highlight ways in which biosensors can be used to illuminate outstanding questions of biological function. Specifically, we focus on sensors developed for monitoring kinase activity and use them to illustrate some common considerations for biosensor design. We describe several uses to which kinase and second-messenger biosensors have been put, and conclude with considerations for the use of biosensors once they are developed. Overall, as fluorescence-based biosensors continue to diversify and improve, we expect them to continue to be widely used as reliable and fruitful tools for gaining deeper insights into cellular and organismal function.
Collapse
Affiliation(s)
- Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Department of Oncology, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.
| |
Collapse
|
91
|
Gocek E, Moulas AN, Studzinski GP. Non-receptor protein tyrosine kinases signaling pathways in normal and cancer cells. Crit Rev Clin Lab Sci 2014; 51:125-37. [PMID: 24446827 DOI: 10.3109/10408363.2013.874403] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein tyrosine kinases (PTKs) are enzymes that transfer phosphate groups to tyrosine residues on protein substrates. Phosphorylation of proteins causes changes in their function and/or enzymatic activity resulting in specific biological responses. There are two classes of PTKs: the transmembrane receptor PTKs and the cytoplasmic non-receptor PTKs (NRTKs). NRTKs are involved in transduction of signals originating from extracellular clues, which often interact with transmembrane receptors. Thus, they are important components of signaling pathways which regulate fundamental cellular functions such as cell differentiation, apoptosis, survival, and proliferation. The activity of NRTKs is tightly regulated, and de-regulation and/or overexpression of NRTKs has been implicated in malignant transformation and carcinogenesis. Research on NRTKs has shed light on the mechanisms of a number of cellular processes including those involved in carcinogenesis. Not surprisingly, several tyrosine kinase inhibitors are in use as treatment for a number of malignancies, and more are under investigation. This review deals with the structure, function, and signaling pathways of nine main families of NRTKs in normal and cancer cells.
Collapse
Affiliation(s)
- Elzbieta Gocek
- Department of Protein Biotechnology, Faculty of Biotechnology, University of Wroclaw , Wroclaw , Poland
| | | | | |
Collapse
|
92
|
Gheghiani L, Gavet O. Deciphering the spatio-temporal regulation of entry and progression through mitosis. Biotechnol J 2014; 9:213-23. [DOI: 10.1002/biot.201300194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/19/2013] [Accepted: 12/03/2013] [Indexed: 11/07/2022]
|
93
|
Ouyang M, Lu S, Wang Y. Genetically encoded fluorescent biosensors for live-cell imaging of MT1-MMP protease activity. Methods Mol Biol 2014; 1071:163-174. [PMID: 24052388 PMCID: PMC5550515 DOI: 10.1007/978-1-62703-622-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The proteolytic activity of Membrane-type 1 Matrix Metalloproteinase (MT1-MMP) is crucial for cancer cell invasion and metastasis. To visualize the protease activity of MT1-MMP with high spatiotemporal resolution at the extracellular plasma membrane surface of live cancer cells, a genetically encoded fluorescent biosensor of MT1-MMP has been developed. Here we describe the design principles of the MT1-MMP biosensor, the characterization of the MT1-MMP biosensor in vitro, and the live-cell imaging protocol used to visualize MT1-MMP activity in mammalian cells. We also provide brief guidelines for observing MT1-MMP subcellular activity by fluorescence resonance energy transfer (FRET) in a cell migration assay.
Collapse
Affiliation(s)
- Mingxing Ouyang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | | |
Collapse
|
94
|
Lu S, Wang Y. Single-cell imaging of mechanotransduction in endothelial cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 126:25-51. [PMID: 25081613 DOI: 10.1016/b978-0-12-394624-9.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Endothelial cells (ECs) are constantly exposed to chemical and mechanical microenvironment in vivo. In mechanotransduction, cells can sense and translate the extracellular mechanical cues into intracellular biochemical signals, to regulate cellular processes. This regulation is crucial for many physiological functions, such as cell adhesion, migration, proliferation, and survival, as well as the progression of disease such as atherosclerosis. Here, we overview the current molecular understanding of mechanotransduction in ECs associated with atherosclerosis, especially those in response to physiological shear stress. The enabling technology of live-cell imaging has allowed the study of spatiotemporal molecular events and unprecedented understanding of intracellular signaling responses in mechanotransduction. Hence, we also introduce recent studies on mechanotransduction using single-cell imaging technologies.
Collapse
Affiliation(s)
- Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
95
|
Wang Z, Ding X, Li S, Shi J, Li Y. Engineered fluorescence tags for in vivo protein labelling. RSC Adv 2014. [DOI: 10.1039/c3ra46991c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In vivoprotein labelling with a peptide tag–fluorescent probe system is an important chemical biology strategy for studying protein distribution, interaction and function.
Collapse
Affiliation(s)
- Zhipeng Wang
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
| | - Xiaozhe Ding
- Department of Chemistry
- School of Life Sciences
- Tsinghua University
- Beijing 100084, China
| | - Sijian Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
| | - Jing Shi
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Yiming Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
| |
Collapse
|
96
|
Abstract
Kinase signaling is under tight spatiotemporal control, with signaling hubs within the cell often coordinated by protein scaffolds. Genetically encoded kinase activity reporters afford a unique tool to interrogate the rate, amplitude, and duration of kinase signaling at specific locations throughout the cell. This protocol describes how to assay kinase activity at a protein scaffold in live cells using a fluorescence resonance energy transfer (FRET)-based kinase activity sensor for protein kinase D (PKD) as an example.
Collapse
|
97
|
Genetically encoded fluorescent redox probes. SENSORS 2013; 13:15422-33. [PMID: 24225906 PMCID: PMC3871076 DOI: 10.3390/s131115422] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 11/02/2013] [Accepted: 11/05/2013] [Indexed: 02/02/2023]
Abstract
Redox processes are involved in almost every cell of the body as a consequence of aerobic life. In the past decades, redox biology has been increasingly recognized as one of the key themes in cell signaling. The progress has been accelerated by development of fluorescent probes that can monitor redox conditions and dynamics in cells and cell compartments. This short paper focuses on fluorescent redox probes that are genetically encoded, and discusses their properties, molecular mechanism, advantages and pitfalls. Our recent work on reaction-based encoded probes that are responsive to particular redox signaling molecules is also reviewed. Future challenges and directions are also commented.
Collapse
|
98
|
Ren W, Liu C, Lian S, Li Z. Flow cytometry-assisted mix-and-read assay for ultrasensitive detection of protein kinase activity by use of Zr(4+)-functionalized mesoporous SiO2 microspheres. Anal Chem 2013; 85:10956-61. [PMID: 24138701 DOI: 10.1021/ac4024457] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A flow cytometry-assisted mix-and-read assay is developed for ultrasensitive detection of protein kinase activity by use of Zr(4+)-functionalized mesoporous SiO2 microspheres (ZrMMs). This strategy integrates the distinct advantages of ZrMMs for highly specific recognition as well as high capacity binding of kinase-induced fluorescent phosphopeptides and flow cytometry for powerful and separation-free bead analysis, leading to an ultrahigh sensitivity for kinase analysis in a extremely simple mix-and-read manner. Furthermore, this ultrasensitive design is well suitable for detection of cell kinase activities in complex biological samples and for screening of potential protein kinase inhibitors, which is of great significance for the development of targeted therapy, clinical diagnosis, and studies of cellular signal transduction pathways.
Collapse
Affiliation(s)
- Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University , Xi'an 710062, Shaanxi Province, People's Republic of China
| | | | | | | |
Collapse
|
99
|
Randriamampita C, Lellouch AC. Imaging early signaling events in T lymphocytes with fluorescent biosensors. Biotechnol J 2013; 9:203-12. [PMID: 24166755 DOI: 10.1002/biot.201300195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/09/2013] [Accepted: 10/07/2013] [Indexed: 11/10/2022]
Abstract
Many recent advances in our understanding of T lymphocyte functions in adaptive immunity are derived from sophisticated imaging techniques used to visualize T lymphocyte behavior in vitro and in vivo. A current challenge is to couple such imaging techniques with methods that will allow researchers to visualize signaling phenomenon at the single-cell level. Fluorescent biosensors, either synthetic or genetically encoded, are emerging as important tools for revealing the spatio-temporal regulation of intracellular biochemical events, such as specific enzyme activities or fluctuations in metabolites. In this review, we revisit the development of fluorescent Ca(2+) sensors with which the first experiments visualizing T lymphocyte activation at the single-cell were performed, and which have since become routine tools in immunology. We then examine a number of examples of how fluorescence resonance energy transfer (FRET)-based biosensors have been developed and applied to T lymphocyte migration, adhesion and T-cell receptor (TCR)-mediated signal transduction. These include the study of small GTPases such as RhoA, Rac and Rap1, the tyrosine kinases Lck and ZAP-70, and metabolites such as cAMP and Ca(2+) . Future development and use of biosensors should allow immunologists to reconcile the vast wealth of existing biochemical data concerning T-cell functions with the power of dynamic live-cell imaging.
Collapse
Affiliation(s)
- Clotilde Randriamampita
- CNRS UMR8104, Institut Cochin, Paris, France; INSERM U567, Institut Cochin, Paris, France; Paris Descartes University, Institut Cochin, Paris, France.
| | | |
Collapse
|
100
|
Wright NJD. Evolution of the techniques used in studying associative olfactory learning and memory in adult Drosophila in vivo: a historical and technical perspective. INVERTEBRATE NEUROSCIENCE 2013; 14:1-11. [PMID: 24149895 DOI: 10.1007/s10158-013-0163-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/08/2013] [Indexed: 11/25/2022]
Abstract
Drosophila melanogaster behavioral mutants have been isolated in which the ability to form associative olfactory memories has been disrupted primarily by altering cyclic adenosine monophosphate signal transduction. Unfortunately, the small size of the fruit fly and its neurons has made the application of neurobiological techniques typically used to investigate the physiology underlying these behaviors daunting. However, the realization that adult fruit flies could tolerate a window in the head capsule allowing access to the central structures thought to be involved plus the development of genetically expressed reporters of neuronal function has allowed a meteoric expansion of this field over the last decade. This review attempts to summarize the evolution of the techniques involved from the first use of a window to access these brain areas thought to be involved in associative olfactory learning and memory, the mushroom bodies and antennal lobes, to the current refinements which allow both high-resolution multiphoton imaging and patch clamping of identified neurons while applying the stimuli used in the behavioral protocols. This area of research now appears poised to reveal some very exciting mechanisms underlying behavior.
Collapse
Affiliation(s)
- Nicholas J D Wright
- Levine College of Health Sciences, Wingate University School of Pharmacy, 515 N. Main Street, Wingate, NC, 28174, USA,
| |
Collapse
|