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Aldrete CA, An C, Call CC, Gao XJ, Vlahos AE. Perspectives on Synthetic Protein Circuits in Mammalian Cells. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2024; 32:100555. [PMID: 39372446 PMCID: PMC11448451 DOI: 10.1016/j.cobme.2024.100555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Mammalian synthetic biology aims to engineer cellular behaviors for therapeutic applications, such as enhancing immune cell efficacy against cancers or improving cell transplantation outcomes. Programming complex biological functions necessitates an understanding of molecular mechanisms governing cellular responses to stimuli. Traditionally, synthetic biology has focused on transcriptional circuits, but recent advances have led to the development of synthetic protein circuits, leveraging programmable binding, proteolysis, or phosphorylation to modulate protein interactions and cellular functions. These circuits offer advantages including robust performance, rapid functionality, and compact design, making them suitable for cellular engineering or gene therapies. This review outlines the post-translational toolkit, emphasizing synthetic protein components utilizing proteolysis or phosphorylation to program mammalian cell behaviors. Finally, we focus on key differences between rewiring native signaling pathways and creating orthogonal behaviors, alongside a proposed framework for translating synthetic protein circuits from tool development to pre-clinical applications in biomedicine.
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Affiliation(s)
- Carlos A. Aldrete
- Department of Chemical Engineering, Stanford University, CA, USA, 94305
| | - Connie An
- Department of Chemical Engineering, Stanford University, CA, USA, 94305
| | - Connor C. Call
- Department of Chemical Engineering, Stanford University, CA, USA, 94305
| | - Xiaojing J. Gao
- Department of Chemical Engineering, Stanford University, CA, USA, 94305
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2
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Mu X, Ma C, Mei X, Liao J, Bojar R, Kuang S, Rong Q, Yao J, Zhang YS. On-demand expansion fluorescence and photoacoustic microscopy (ExFLPAM). PHOTOACOUSTICS 2024; 38:100610. [PMID: 38726025 PMCID: PMC11079527 DOI: 10.1016/j.pacs.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 03/04/2024] [Accepted: 04/21/2024] [Indexed: 05/12/2024]
Abstract
Expansion microscopy (ExM) is a promising technology that enables nanoscale imaging on conventional optical microscopes by physically magnifying the specimens. Here, we report the development of a strategy that enables i) on-demand labeling of subcellular organelles in live cells for ExM through transfection of fluorescent proteins that are well-retained during the expansion procedure; and ii) non-fluorescent chromogenic color-development towards efficient bright-field and photoacoustic imaging in both planar and volumetric formats, which is applicable to both cultured cells and biological tissues. Compared to the conventional ExM methods, our strategy provides an expanded toolkit, which we term as expansion fluorescence and photoacoustic microscopy (ExFLPAM), by allowing on-demand fluorescent protein labeling of cultured cells, as well as non-fluorescent absorption contrast-imaging of biological samples.
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Affiliation(s)
- Xuan Mu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Xuan Mei
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Junlong Liao
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Rebecca Bojar
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
- Barnard College, Columbia University, New York, NY 10027, USA
| | - Sizhe Kuang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qiangzhou Rong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
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3
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Kenward C, Vuckovic M, Paetzel M, Strynadka NCJ. Kinetic comparison of all eleven viral polyprotein cleavage site processing events by SARS-CoV-2 main protease using a linked protein FRET platform. J Biol Chem 2024; 300:107367. [PMID: 38750796 PMCID: PMC11209022 DOI: 10.1016/j.jbc.2024.107367] [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] [Received: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
The main protease (Mpro) remains an essential therapeutic target for COVID-19 post infection intervention given its critical role in processing the majority of viral proteins encoded by the genome of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2). Upon viral entry, the +ssRNA genome is translated into two long polyproteins (pp1a or the frameshift-dependent pp1ab) containing all the nonstructural proteins (nsps) required by the virus for immune modulation, replication, and ultimately, virion assembly. Included among these nsps is the cysteine protease Mpro (nsp5) which self-excises from the polyprotein, dimerizes, then sequentially cleaves 11 of the 15 cut-site junctions found between each nsp within the polyprotein. Many structures of Mpro (often bound to various small molecule inhibitors or peptides) have been detailed recently, including structures of Mpro bound to each of the polyprotein cleavage sequences, showing that Mpro can accommodate a wide range of targets within its active site. However, to date, kinetic characterization of the interaction of Mpro with each of its native cleavage sequences remains incomplete. Here, we present a robust and cost-effective FRET based system that benefits from a more consistent presentation of the substrate that is also closer in organization to the native polyprotein environment compared to previously reported FRET systems that use chemically modified peptides. Using this system, we were able to show that while each site maintains a similar Michaelis constant, the catalytic efficiency of Mpro varies greatly between cut-site sequences, suggesting a clear preference for the order of nsp processing.
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Affiliation(s)
- Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Johnson SC, Annamdevula NS, Leavesley SJ, Francis CM, Rich TC. Hyperspectral imaging and dynamic region of interest tracking approaches to quantify localized cAMP signals. Biochem Soc Trans 2024; 52:191-203. [PMID: 38334148 PMCID: PMC11115359 DOI: 10.1042/bst20230352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger known to orchestrate a myriad of cellular functions over a wide range of timescales. In the last 20 years, a variety of single-cell sensors have been developed to measure second messenger signals including cAMP, Ca2+, and the balance of kinase and phosphatase activities. These sensors utilize changes in fluorescence emission of an individual fluorophore or Förster resonance energy transfer (FRET) to detect changes in second messenger concentration. cAMP and kinase activity reporter probes have provided powerful tools for the study of localized signals. Studies relying on these and related probes have the potential to further revolutionize our understanding of G protein-coupled receptor signaling systems. Unfortunately, investigators have not been able to take full advantage of the potential of these probes due to the limited signal-to-noise ratio of the probes and the limited ability of standard epifluorescence and confocal microscope systems to simultaneously measure the distributions of multiple signals (e.g. cAMP, Ca2+, and changes in kinase activities) in real time. In this review, we focus on recently implemented strategies to overcome these limitations: hyperspectral imaging and adaptive thresholding approaches to track dynamic regions of interest (ROI). This combination of approaches increases signal-to-noise ratio and contrast, and allows identification of localized signals throughout cells. These in turn lead to the identification and quantification of intracellular signals with higher effective resolution. Hyperspectral imaging and dynamic ROI tracking approaches offer investigators additional tools with which to visualize and quantify multiplexed intracellular signaling systems.
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Affiliation(s)
- Santina C Johnson
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Naga S Annamdevula
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Department of Physiology and Cell Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Silas J Leavesley
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Chemical and Biomolecular Engineering, University of South Alabama, Mobile, AL, U.S.A
| | - C Michael Francis
- Department of Physiology and Cell Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Thomas C Rich
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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6
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Yang HW. Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches. Methods Mol Biol 2024; 2740:263-273. [PMID: 38393481 DOI: 10.1007/978-1-0716-3557-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Investigating cell-cycle progression has been challenging due to the complex interconnectivity of regulatory processes and inherent cell-to-cell heterogeneity, which often require synchronization procedures. However, recent advancements in cell-cycle sensors and single-cell imaging techniques have turned this heterogeneity into an advantage for investigating the molecular mechanisms underlying diverse responses. This has led to significant progress in our understanding of cell-cycle regulation. In this paper, we present a comprehensive live single-cell imaging workflow that leverages cutting-edge live-cell sensors. These advanced single-cell imaging procedures provide promising opportunities for elucidating the molecular mechanisms underpinnings of heterogeneous responses in cell-cycle progression.
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Affiliation(s)
- Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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7
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Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
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Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
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8
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Biosensors for the detection of protein kinases: Recent progress and challenges. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Kong X, Kapustka A, Sullivan B, Schwarz GJ, Leckband DE. Extracellular matrix regulates force transduction at VE-cadherin junctions. Mol Biol Cell 2022; 33:ar95. [PMID: 35653290 DOI: 10.1091/mbc.e22-03-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Increased tension on VE-cadherin (VE-cad) complexes activates adaptive cell stiffening and local cytoskeletal reinforcement--two key signatures of intercellular mechanotransduction. Here we demonstrate that tugging on VE-cad receptors initiates a cascade that results in downstream integrin activation. The formation of new integrin adhesions potentiates vinculin and actin recruitment to mechanically reinforce stressed cadherin adhesions. This cascade differs from documented antagonistic effects of integrins on intercellular junctions. We identify focal adhesion kinase, Abl kinase, and RhoA GTPase as key components of the positive feedback loop. Results further show that a consequence of integrin involvement is the sensitization of intercellular force transduction to the extracellular matrix (ECM) not by regulating junctional tension but by altering signal cascades that reinforce cell-cell adhesions. On type 1 collagen or fibronectin substrates, integrin subtypes α2β1 and α5β1, respectively, differentially control actin remodeling at VE-cad adhesions. Specifically, ECM-dependent differences in VE-cad force transduction mirror differences in the rigidity sensing mechanisms of α2β1 and α5β1 integrins. The findings verify the role of integrins in VE-cad force transduction and uncover a previously unappreciated mechanism by which the ECM impacts the mechanical reinforcement of interendothelial junctions.
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Affiliation(s)
- Xinyu Kong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Adrian Kapustka
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Brendan Sullivan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gregory J Schwarz
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Deborah E Leckband
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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10
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Reactive oxygen species, the trident of Neptune in the hands of hecate; role in different diseases, signaling pathways, and detection methods. Arch Biochem Biophys 2022; 728:109357. [DOI: 10.1016/j.abb.2022.109357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/29/2022] [Accepted: 07/16/2022] [Indexed: 12/22/2022]
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11
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Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
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Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
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12
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Molecular sensors for detection of tumor-stroma crosstalk. Adv Cancer Res 2022; 154:47-91. [PMID: 35459472 DOI: 10.1016/bs.acr.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In most solid tumors, malignant cells coexist with non-cancerous host tissue comprised of a variety of extracellular matrix components and cell types, notably fibroblasts, immune cells, and endothelial cells. It is becoming increasingly evident that the non-cancerous host tissue, often referred to as the tumor stroma or the tumor microenvironment, wields tremendous influence in the proliferation, survival, and metastatic ability of cancer cells. The tumor stroma has an active biological role in the transmission of signals, such as growth factors and chemokines that activate oncogenic signaling pathways by autocrine and paracrine mechanisms. Moreover, the constituents of the stroma define the mechanical properties and the physical features of solid tumors, which influence cancer progression and response to therapy. Inspired by the emerging importance of tumor-stroma crosstalk and oncogenic physical forces, numerous biosensors, or advanced imaging and analysis techniques have been developed and applied to investigate complex and challenging questions in cancer research. These techniques facilitate measurements and biological readouts at scales ranging from subcellular to tissue-level with unprecedented level of spatial and temporal precision. Here we examine the application of biosensor technology for studying the complex and dynamic multiscale interactions of the tumor-host system.
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Shining Light on Protein Kinase Biomarkers with Fluorescent Peptide Biosensors. Life (Basel) 2022; 12:life12040516. [PMID: 35455007 PMCID: PMC9026840 DOI: 10.3390/life12040516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022] Open
Abstract
Protein kinases (PKs) are established gameplayers in biological signalling pathways, and a large body of evidence points to their dysregulation in diseases, in particular cancer, where rewiring of PK networks occurs frequently. Fluorescent biosensors constitute attractive tools for probing biomolecules and monitoring dynamic processes in complex samples. A wide variety of genetically encoded and synthetic biosensors have been tailored to report on PK activities over the last decade, enabling interrogation of their function and insight into their behaviour in physiopathological settings. These optical tools can further be used to highlight enzymatic alterations associated with the disease, thereby providing precious functional information which cannot be obtained through conventional genetic, transcriptomic or proteomic approaches. This review focuses on fluorescent peptide biosensors, recent developments and strategies that make them attractive tools to profile PK activities for biomedical and diagnostic purposes, as well as insights into the challenges and opportunities brought by this unique toolbox of chemical probes.
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Ovechkina VS, Zakian SM, Medvedev SP, Valetdinova KR. Genetically Encoded Fluorescent Biosensors for Biomedical Applications. Biomedicines 2021; 9:biomedicines9111528. [PMID: 34829757 PMCID: PMC8615007 DOI: 10.3390/biomedicines9111528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Genetically encoded fluorescent biosensors constitute a class of imaging agents that enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically encoded fluorescent biosensors in drug screening. This review summarizes results of the studies that have been conducted in the last years toward the fabrication of genetically encoded fluorescent biosensors for biomedical applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.
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Affiliation(s)
- Vera S. Ovechkina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Suren M. Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sergey P. Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Kamila R. Valetdinova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Correspondence:
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15
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Zhang L, Takahashi Y, Schroeder JI. Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells. PLANT PHYSIOLOGY 2021; 187:527-536. [PMID: 35142856 PMCID: PMC8491035 DOI: 10.1093/plphys/kiab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/16/2021] [Indexed: 05/15/2023]
Abstract
Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor's working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.
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Affiliation(s)
- Li Zhang
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Yohei Takahashi
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
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Zheng F, Meng T, Jiang D, Sun J, Yao H, Zhu J, Min Q. Nanomediator–Effector Cascade Systems for Amplified Protein Kinase Activity Imaging and Phosphorylation‐Induced Drug Release In Vivo. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fenfen Zheng
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Tiantian Meng
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Difei Jiang
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Jiamin Sun
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Haiyang Yao
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Jun‐Jie Zhu
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
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17
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Wang S, Perkins NG, Ji F, Chaudhuri R, Guo Z, Sarkar P, Shao S, Li Z, Xue M. Digitonin-facilitated delivery of imaging probes enables single-cell analysis of AKT signalling activities in suspension cells. Analyst 2021; 146:5307-5315. [PMID: 34351328 DOI: 10.1039/d1an00751c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Analyzing intracellular signalling protein activities in living cells promises a better understanding of the signalling cascade and related biological processes. We have previously developed cyclic peptide-based probes for analyzing intracellular AKT signalling activities, but these peptide probes were not cell-permeable. Implementing fusogenic liposomes as delivery vehicles could circumvent the problem when analyzing adherent cells, but it remained challenging to study suspension cells using similar approaches. Here, we present a method for delivering these imaging probes into suspension cells using digitonin, which could transiently perforate the cell membrane. Using U87, THP-1, and Jurkat cells as model systems representing suspended adherent cells, myeloid cells, and lymphoid cells, we demonstrated that low concentrations of digitonin enabled a sufficient amount of probes to enter the cytosol without affecting cell viability. We further combined this delivery method with a microwell single-cell chip and interrogated the AKT signalling dynamics in THP-1 and Jurkat cells, followed by immunofluorescence-based quantitation of AKT expression levels. We resolved the cellular heterogeneity in AKT signalling activities and showed that the kinetic patterns of AKT signalling and the AKT expression levels were related in THP-1 cells, but decoupled in Jurkat cells. We expect that our approach can be adapted to study other suspension cells.
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Affiliation(s)
- Siwen Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
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18
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Chang TJ, Lai WQ, Chang YF, Wang CL, Yang DM. Development and optimization of heavy metal lead biosensors in biomedical and environmental applications. J Chin Med Assoc 2021; 84:745-753. [PMID: 34225337 DOI: 10.1097/jcma.0000000000000574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The detrimental impact of the heavy metal lead (Pb) on human health has been studied for years. The fact that Pb impairs human body has been established from countless painful and sad historical events. Nowadays, World Health Organization and many developmental countries have established regulations concerning the use of Pb. Measuring the blood lead level (BLL) is so far the only way to officially evaluate the degree of Pb exposure, but the so-called safety value (10 μg/dL in adults and 5 μg/dL in children) seems unreliable to represent the security checkpoint for children through daily intake of drinking water or physical contact with a lower contaminated level of Pb contents. In general, unsolved mysteries about the Pb toxicological mechanisms still remain. In this review article, we report on the methods to prevent Pb poison for further Pb toxicological research. We establish high-sensitivity Pb monitoring, and also report on the use of fluorescent biosensors such as genetically-encoded fluorescence resonance energy transfer-based biosensors built for various large demands such as the detection of severe acute respiratory syndrome coronavirus 2. We also contribute to the development and optimization of the FRET-based Pb biosensors. Our well-performed version of Met-lead 1.44 M1 has achieved a limit of detection of 10 nM (2 ppb; 0.2 μg/dL) and almost 5-fold in dynamic range (DR) supported for the real practical applications-that is, the in-cell Pb sensing device for blood and blood-related samples, and the Pb environmental detections in vitro. The perspective of our powerful Pb biosensor incorporated with a highly sensitive bio-chip of the portable device for quick Pb measurements will be addressed for further manipulation.
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Affiliation(s)
- Tai-Jay Chang
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Wei-Qun Lai
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yu-Fen Chang
- LumiSTAR Biotechnology, Inc., Taipei, Taiwan, ROC
| | - Chia-Lin Wang
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - De-Ming Yang
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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19
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Zheng F, Meng T, Jiang D, Sun J, Yao H, Zhu JJ, Min Q. Nanomediator-Effector Cascade Systems for Amplified Protein Kinase Activity Imaging and Phosphorylation-Induced Drug Release In Vivo. Angew Chem Int Ed Engl 2021; 60:21565-21574. [PMID: 34322988 DOI: 10.1002/anie.202109108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/06/2022]
Abstract
Protein kinases constitute a rich pool of biomarkers and therapeutic targets of tremendous diseases including cancer. However, sensing kinase activity in vivo while implementing treatments according to kinase hyperactivation remains challenging. Herein, we present a nanomediator-effector cascade system that can in situ magnify the subtle events of kinase-catalyzed phosphorylation via DNA amplification machinery to achieve kinase activity imaging and kinase-responsive drug release in vivo. In this cascade, the phosphorylation-mediated disassembly of DNA/peptide complex on the nanomediators initiated the detachment of fluorescent hairpin DNAs from the nanoeffectors via hybridization chain reaction (HCR), leading to fluorescence recovery and therapeutic cargo release. We demonstrated that this nanosystem simultaneously enabled trace protein kinase A (PKA) activity imaging and on-demand drug delivery for inhibition of tumor cell growth both in vitro and in vivo, affording a kinase-specific sense-and-treat paradigm for cancer theranostics.
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Affiliation(s)
- Fenfen Zheng
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.,School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Tiantian Meng
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Difei Jiang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Jiamin Sun
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Haiyang Yao
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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20
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Engler AJ, Wang Y. Editorial: Understanding molecular interactions that underpin vascular mechanobiology. APL Bioeng 2021; 5:030401. [PMID: 34258496 PMCID: PMC8253597 DOI: 10.1063/5.0058611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 02/04/2023] Open
Abstract
Cells are exposed to a variety of mechanical forces in their daily lives, especially endothelial cells that are stretched from vessel distention and are exposed to hemodynamic shear stress from a blood flow. Exposure to excessive forces can induce a disease, but the molecular details on how these cells perceive forces, transduce them into biochemical signals and genetic events, i.e., mechanotransduction, and integrate them into physiological or pathological changes remain unclear. However, seminal studies in endothelial cells over the past several decades have begun to elucidate some of these signals. These studies have been highlighted in APL Bioengineering and elsewhere, describing a complex temporal pattern where forces are sensed immediately by ion channels and force-dependent conformational changes in surface proteins, followed by biochemical cascades, cytoskeletal contraction, and nuclear remodeling that can affect long-term changes in endothelial morphology and fate. Key examples from the endothelial literature that have established these pathways include showing that integrins and Flk-1 or VE-cadherin act as shear stress transducers, activating downstream proteins such as Cbl and Nckβ or Src, respectively. In this Editorial, we summarize a recent literature highlighting these accomplishments, noting the engineering tools and analysis methods used in these discoveries while also highlighting unanswered questions.
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21
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Huang C, Filippone NR, Reiner T, Roberts S. Sensors and Inhibitors for the Detection of Ataxia Telangiectasia Mutated (ATM) Protein Kinase. Mol Pharm 2021; 18:2470-2481. [PMID: 34125542 DOI: 10.1021/acs.molpharmaceut.1c00166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recruitment and activation of the ataxia telangiectasia mutated (ATM) kinase regulate multiple cell-cycle checkpoints relevant to complex biological events like DNA damage repair and apoptosis. Molecularly specific readouts of ATM using protein assays, fluorescence, or radiolabeling have advanced significantly over the past few years. This Review covers the molecular imaging techniques that enable the visualization of ATM-from traditional quantitative protein assays to the potential use of ATM inhibitors to generate new imaging agents to interrogate ATM. We are confident that molecular imaging coupled with advanced technologies will play a pivotal role in visualizing and understanding the biology of ATM and accelerate its applications in the diagnosis and monitoring of disease, including radiation therapy and patient stratification.
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Affiliation(s)
- Cien Huang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States.,City University of New York Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Nina R Filippone
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States.,State University of New York Binghamton University, 4400 Vestal Parkway, East Binghamton, New York 13902, United States
| | - Thomas Reiner
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States.,Department of Radiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Sheryl Roberts
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
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22
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Murphy KJ, Reed DA, Trpceski M, Herrmann D, Timpson P. Quantifying and visualising the nuances of cellular dynamics in vivo using intravital imaging. Curr Opin Cell Biol 2021; 72:41-53. [PMID: 34091131 DOI: 10.1016/j.ceb.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022]
Abstract
Intravital imaging is a powerful technology used to quantify and track dynamic changes in live cells and tissues within an intact environment. The ability to watch cell biology in real-time 'as it happens' has provided novel insight into tissue homeostasis, as well as disease initiation, progression and response to treatment. In this minireview, we highlight recent advances in the field of intravital microscopy, touching upon advances in awake versus anaesthesia-based approaches, as well as the integration of biosensors into intravital imaging. We also discuss current challenges that, in our opinion, need to be overcome to further advance the field of intravital imaging at the single-cell, subcellular and molecular resolution to reveal nuances of cell behaviour that can be targeted in complex disease settings.
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Affiliation(s)
- Kendelle J Murphy
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Daniel A Reed
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Michael Trpceski
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia
| | - David Herrmann
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia.
| | - Paul Timpson
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia.
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23
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Marquilly C, Busto GU, Leger BS, Boulanger A, Giniger E, Walker JA, Fradkin LG, Dura JM. Htt is a repressor of Abl activity required for APP-induced axonal growth. PLoS Genet 2021; 17:e1009287. [PMID: 33465062 PMCID: PMC7845969 DOI: 10.1371/journal.pgen.1009287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 01/29/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
Huntington’s disease is a progressive autosomal dominant neurodegenerative disorder caused by the expansion of a polyglutamine tract at the N-terminus of a large cytoplasmic protein. The Drosophila huntingtin (htt) gene is widely expressed during all developmental stages from embryos to adults. However, Drosophila htt mutant individuals are viable with no obvious developmental defects. We asked if such defects could be detected in htt mutants in a background that had been genetically sensitized to reveal cryptic developmental functions. Amyloid precursor protein (APP) is linked to Alzheimer’s disease. Appl is the Drosophila APP ortholog and Appl signaling modulates axon outgrowth in the mushroom bodies (MBs), the learning and memory center in the fly, in part by recruiting Abl tyrosine kinase. Here, we find that htt mutations suppress axon outgrowth defects of αβ neurons in Appl mutant MB by derepressing the activity of Abl. We show that Abl is required in MB αβ neurons for their axon outgrowth. Importantly, both Abl overexpression and lack of expression produce similar phenotypes in the MBs, indicating the necessity of tightly regulating Abl activity. We find that Htt behaves genetically as a repressor of Abl activity, and consistent with this, in vivo FRET-based measurements reveal a significant increase in Abl kinase activity in the MBs when Htt levels are reduced. Thus, Appl and Htt have essential but opposing roles in MB development, promoting and suppressing Abl kinase activity, respectively, to maintain the appropriate intermediate level necessary for axon growth. Understanding the normal physiological roles of proteins involved in neurodegenerative diseases can provide significant insight into disease mechanisms. Drosophila offers a powerful system in which to ask these fundamental questions. Both Htt, related to Huntington’s disease, and Appl, related to Alzheimer’s disease, have well-conserved single orthologs in the fly genome. Appl has been shown to be a conserved modulator of a Wnt-PCP signaling pathway required for axon outgrowth in the mushroom body (MB) in the Drosophila brain. However, roles for Htt in fly brain development have not been reported. Unexpectedly, we found that htt mutations suppress the axon outgrowth defects of Appl mutants in the MB, indicating a link between these two neurodegenerative proteins and a cryptic role of Htt during development. Abl tyrosine kinase is a downstream effector of the Appl receptor, and we show here that Abl is also required for MB axon outgrowth. Importantly, Abl activity must be tightly regulated as evidenced by our observations that both under and overexpression of Abl result in similar axonal defects. We demonstrate that Htt is an inhibitor of Abl activity and provide evidence that the phenotypic rescue of αβ axons in Appl mutants by reducing htt is mediated by the restoration of proper levels of Abl signaling. These data, therefore, suggest that Appl and Htt act antagonistically to maintain an optimal balance of activation and inhibition of Abl, and thereby promote the growth of MB αβ axons.
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Affiliation(s)
- Claire Marquilly
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Germain U. Busto
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Brittany S. Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ana Boulanger
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Edward Giniger
- Intramural Research Program, NINDS, NIH, Bethesda, Maryland, United States of America
| | - James A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lee G. Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jean-Maurice Dura
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
- * E-mail:
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24
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Soteriou C, Kalli AC, Connell SD, Tyler AII, Thorne JL. Advances in understanding and in multi-disciplinary methodology used to assess lipid regulation of signalling cascades from the cancer cell plasma membrane. Prog Lipid Res 2020; 81:101080. [PMID: 33359620 DOI: 10.1016/j.plipres.2020.101080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022]
Abstract
The lipid bilayer is a functional component of cells, forming a stable platform for the initiation of key biological processes, including cell signalling. There are distinct changes in the lipid composition of cell membranes during oncogenic transformation resulting in aberrant activation and inactivation of signalling transduction pathways. Studying the role of the cell membrane in cell signalling is challenging, since techniques are often limited to by timescale, resolution, sensitivity, and averaging. To overcome these limitations, combining 'computational', 'wet-lab' and 'semi-dry' approaches offers the best opportunity to resolving complex biological processes involved in membrane organisation. In this review, we highlight analytical tools that have been applied for the study of cell signalling initiation from the cancer cell membranes through computational microscopy, biological assays, and membrane biophysics. The cancer therapeutic potential of extracellular membrane-modulating agents, such as cholesterol-reducing agents is also discussed, as is the need for future collaborative inter-disciplinary research for studying the role of the cell membrane and its components in cancer therapy.
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Affiliation(s)
- C Soteriou
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK; Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK; Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - A C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - S D Connell
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - A I I Tyler
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK
| | - J L Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK.
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25
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Ma M, Bordignon P, Dotto GP, Pelet S. Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors. Heliyon 2020; 6:e05574. [PMID: 33319088 PMCID: PMC7723811 DOI: 10.1016/j.heliyon.2020.e05574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements. However, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs (ERK, JNK and p38) that relocates from the nucleus to the cytoplasm when phosphorylated by the kinases. We demonstrate that this reporter displays an improved response compared to other relocation biosensors. This assay allows to monitor the heterogeneity in the MAPK response in a population of isogenic cells, revealing pulses of ERK activity upon a physiological EGFR stimulation. We show applicability of this approach to the analysis of multiple cancer cell lines and primary cells as well as its application in vivo to developing tumors. Using this ERK biosensor, dynamic single cell measurements with high temporal resolution can be obtained. These MAPK reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
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Affiliation(s)
- Min Ma
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Biochemistry, University of Lausanne, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Switzerland
| | | | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
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26
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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.
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Affiliation(s)
| | | | | | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
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27
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Fromm H. GABA signaling in plants: targeting the missing pieces of the puzzle. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6238-6245. [PMID: 32761202 DOI: 10.1093/jxb/eraa358] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/24/2020] [Indexed: 05/25/2023]
Abstract
The adaptation of plants to unstable environments relies on their ability to sense their surroundings and to generate and transmit corresponding signals to different parts of the plant to evoke changes necessary for optimizing growth and defense. Plants, like animals, contain a huge repertoire of intra- and intercellular signals, including organic and inorganic molecules. The occurrence of neurotransmitter-like signaling molecules in plants has been an intriguing field of research. Among these, γ-aminobutyric acid (GABA) was discovered in plants over half a century ago, and studies of its roles as a primary metabolite have been well documented, particularly in the context of stress responses. In contrast, evidence of the potential mechanism by which GABA acts as a signaling molecule in plants has only recently been reported. In spite of this breakthrough, the roles of GABA as a signaling molecule in plants have yet to be established and several aspects of the complexity of the GABA signaling system remain obscure. This review summarizes the uncertainties in GABA signaling in plants and suggests research directions and technologies that would help in answering unsolved questions.
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Affiliation(s)
- Hillel Fromm
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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28
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Huey J, Keutler K, Schultz C. Chemical Biology Toolbox for Studying Pancreatic Islet Function - A Perspective. Cell Chem Biol 2020; 27:1015-1031. [PMID: 32822616 DOI: 10.1016/j.chembiol.2020.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/10/2020] [Accepted: 07/28/2020] [Indexed: 01/14/2023]
Abstract
The islets of Langerhans represent one of the many complex endocrine organs in mammals. Traditionally, islet function is studied by a mixture of physiological, cell biological, and molecular biological methods. Recently, novel techniques stemming from the ever-increasing toolbox provided by chemical laboratories have been added to the repertoire. Many emerging techniques will soon be available to manipulate and monitor islet function at the single-cell level and potentially in intact model animals, as well as in isolated human islets. Here, we review the most current small-molecule-based and genetically encoded molecular tool sets available to study islet function. We provide an outlook regarding future tool developments that will impact islet research, with a special focus on the interplay between different islet cell types.
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Affiliation(s)
- Julia Huey
- Program in Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97210, USA; Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA
| | - Kaya Keutler
- Program in Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97210, USA; Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA
| | - Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA.
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29
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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Szabó Á, Szendi-Szatmári T, Szöllősi J, Nagy P. Quo vadis FRET? Förster's method in the era of superresolution. Methods Appl Fluoresc 2020; 8:032003. [PMID: 32521530 DOI: 10.1088/2050-6120/ab9b72] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although the theoretical foundations of Förster resonance energy transfer (FRET) were laid in the 1940s as part of the quantum physical revolution of the 20th century, it was only in the 1970s that it made its way to biology as a result of the availability of suitable measuring and labeling technologies. Thanks to its ease of application, FRET became widely used for studying molecular associations on the nanometer scale. The development of superresolution techniques at the turn of the millennium promised an unprecedented insight into the structure and function of molecular complexes. Without downplaying the significance of superresolution microscopies this review expresses our view that FRET is still a legitimate tool in the armamentarium of biologists for studying molecular associations since it offers distinct advantages and overcomes certain limitations of superresolution approaches.
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Affiliation(s)
- Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary. MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary
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Zhang L, Takahashi Y, Hsu PK, Kollist H, Merilo E, Krysan PJ, Schroeder JI. FRET kinase sensor development reveals SnRK2/OST1 activation by ABA but not by MeJA and high CO 2 during stomatal closure. eLife 2020; 9:e56351. [PMID: 32463362 PMCID: PMC7289597 DOI: 10.7554/elife.56351] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Sucrose-non-fermenting-1-related protein kinase-2s (SnRK2s) are critical for plant abiotic stress responses, including abscisic acid (ABA) signaling. Here, we develop a genetically encoded reporter for SnRK2 kinase activity. This sensor, named SNACS, shows an increase in the ratio of yellow to cyan fluorescence emission by OST1/SnRK2.6-mediated phosphorylation of a defined serine residue in SNACS. ABA rapidly increases FRET efficiency in N. benthamiana leaf cells and Arabidopsis guard cells. Interestingly, protein kinase inhibition decreases FRET efficiency in guard cells, providing direct experimental evidence that basal SnRK2 activity prevails in guard cells. Moreover, in contrast to ABA, the stomatal closing stimuli, elevated CO2 and MeJA, did not increase SNACS FRET ratios. These findings and gas exchange analyses of quintuple/sextuple ABA receptor mutants show that stomatal CO2 signaling requires basal ABA and SnRK2 signaling, but not SnRK2 activation. A recent model that CO2 signaling is mediated by PYL4/PYL5 ABA-receptors could not be supported here in two independent labs. We report a potent approach for real-time live-cell investigations of stress signaling.
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Affiliation(s)
- Li Zhang
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Yohei Takahashi
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Po-Kai Hsu
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Hannes Kollist
- Institute of Technology, University of TartuTartuEstonia
| | - Ebe Merilo
- Institute of Technology, University of TartuTartuEstonia
| | - Patrick J Krysan
- Horticulture Department, University of Wisconsin-MadisonMadisonUnited States
| | - Julian I Schroeder
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
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QuanTI-FRET: a framework for quantitative FRET measurements in living cells. Sci Rep 2020; 10:6504. [PMID: 32300110 PMCID: PMC7162988 DOI: 10.1038/s41598-020-62924-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
Förster Resonance Energy Transfer (FRET) allows for the visualization of nanometer-scale distances and distance changes. This sensitivity is regularly achieved in single-molecule experiments in vitro but is still challenging in biological materials. Despite many efforts, quantitative FRET in living samples is either restricted to specific instruments or limited by the complexity of the required analysis. With the recent development and expanding utilization of FRET-based biosensors, it becomes essential to allow biologists to produce quantitative results that can directly be compared. Here, we present a new calibration and analysis method allowing for quantitative FRET imaging in living cells with a simple fluorescence microscope. Aside from the spectral crosstalk corrections, two additional correction factors were defined from photophysical equations, describing the relative differences in excitation and detection efficiencies. The calibration is achieved in a single step, which renders the Quantitative Three-Image FRET (QuanTI-FRET) method extremely robust. The only requirement is a sample of known stoichiometry donor:acceptor, which is naturally the case for intramolecular FRET constructs. We show that QuanTI-FRET gives absolute FRET values, independent of the instrument or the expression level. Through the calculation of the stoichiometry, we assess the quality of the data thus making QuanTI-FRET usable confidently by non-specialists.
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Schmitt DL, Mehta S, Zhang J. Illuminating the kinome: Visualizing real-time kinase activity in biological systems using genetically encoded fluorescent protein-based biosensors. Curr Opin Chem Biol 2020; 54:63-69. [PMID: 31911398 PMCID: PMC7131877 DOI: 10.1016/j.cbpa.2019.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/07/2019] [Accepted: 11/16/2019] [Indexed: 02/06/2023]
Abstract
Genetically encoded fluorescent protein-based kinase biosensors are a central tool for illumination of the kinome. The adaptability and versatility of biosensors have allowed for spatiotemporal observation of real-time kinase activity in living cells and organisms. In this review, we highlight various types of kinase biosensors, along with their burgeoning applications in complex biological systems. Specifically, we focus on kinase activity reporters used in neuronal systems and whole animal settings. Genetically encoded kinase biosensors are key for elucidation of the spatiotemporal regulation of protein kinases, with broader applications beyond the Petri dish.
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Affiliation(s)
- Danielle L Schmitt
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA; Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Zheng D, Zhang Y, Liu X, Wang J. Coupling natural systems with synthetic chemistry for light-driven enzymatic biocatalysis. PHOTOSYNTHESIS RESEARCH 2020; 143:221-231. [PMID: 31317382 DOI: 10.1007/s11120-019-00660-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Visible light-driven redox reactions have been widely adopted for the production of chemicals to combat energy shortage and global warming. Key elements of such a reaction system include a photosensitizer, a catalyst, and an electron source. In this review, we introduce the small molecules and nanoparticles that are widely used as photosensitizers, as well as the development of a photosensitizer protein that is based on the expansion of genetic code, with a fluorescent protein that is used as a scaffold. Visible light-driven enzymes using proteins as photosensitizers or as catalysts such as carbon monoxide dehydrogenase (CODH), formic acid dehydrogenase (FDH), hydrogenase, nitrogenase, cytochrome P450 BM3, and alkane synthase are then described. CODH can be coupled with photosensitizing nanoparticles to reduce CO2 to CO, and hydrogenase can produce H2 using high-energy electrons produced from dye-sensitized nanoparticles. When water-soluble zinc porphyrin is coupled with FDH, visible light drives CO2 to produce formic acid. Nitrogenase can reduce N2 to NH3 using CdS nanoparticle as photosensitizer. Cytochrome P450 BM3 can be enhanced by a visible light-driven redox system and thus by hydroxylate lauric acid or fatty acids. CvFAP, an alkane synthase, can decarboxylate palmitic acid to pentadecane under blue light excitation. Moreover, we describe a genetically encoded photosensitive protein, which mimics the function of natural photosynthesis and catalyzes the conversion of CO2 to CO when covalently attached with a Ni-terpyridine complex.
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Affiliation(s)
- Dandan Zheng
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Ying Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Johnson EO, Hung DT. A Point of Inflection and Reflection on Systems Chemical Biology. ACS Chem Biol 2019; 14:2497-2511. [PMID: 31613592 DOI: 10.1021/acschembio.9b00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the past several decades, chemical biologists have been leveraging chemical principles for understanding biology, tackling disease, and biomanufacturing, while systems biologists have holistically applied computation and genome-scale experimental tools to the same problems. About a decade ago, the benefit of combining the philosophies of chemical biology with systems biology into systems chemical biology was advocated, with the potential to systematically understand the way small molecules affect biological systems. Recently, there has been an explosion in new technologies that permit massive expansion in the scale of biological experimentation, increase access to more diverse chemical space, and enable powerful computational interpretation of large datasets. Fueled by these rapidly increasing capabilities, systems chemical biology is now at an inflection point, poised to enter a new era of more holistic and integrated scientific discovery. Systems chemical biology is primed to reveal an integrated understanding of fundamental biology and to discover new chemical probes to comprehensively dissect and systematically understand that biology, thereby providing a path to novel strategies for discovering therapeutics, designing drug combinations, avoiding toxicity, and harnessing beneficial polypharmacology. In this Review, we examine the emergence of new capabilities driving us to this inflection point in systems chemical biology, and highlight holistic approaches and opportunities that are arising from integrating chemical biology with a systems-level understanding of the intersection of biology and chemistry.
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Affiliation(s)
- Eachan O. Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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Roy S, Brasino M, Beirne JM, Harguindey A, Chapnick DA, Liu X, Cha JN, Goodwin AP. Enzymes Photo-Cross-Linked to Live Cell Receptors Retain Activity and EGFR Inhibition after Both Internalization and Recycling. Bioconjug Chem 2019; 31:104-112. [PMID: 31840981 DOI: 10.1021/acs.bioconjchem.9b00781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this work, we show that a prodrug enzyme covalently photoconjugated to live cell receptors survives endosomal proteolysis and retains its catalytic activity over multiple days. Here, a fusion protein was designed with both an antiepidermal growth factor receptor (EGFR) affibody and the prodrug enzyme cytosine deaminase, which can convert prodrug 5-fluorocytosine to the anticancer drug 5-fluorouracil. A benzophenone group was added at a site-specific mutation within the affibody, and the fusion protein was selectively photoconjugated to EGFR receptors expressed on membranes of MDA-MB-468 breast cancer cells. The fusion protein was next labeled with two dyes for tracking uptake: AlexaFluor 488 and pH-sensitive pHAb. Flow cytometry showed that fusion proteins photo-cross-linked to EGFR first underwent receptor-mediated endocytosis within 12 h, followed by recycling back to the cell membrane within 24 h. These findings were also confirmed by confocal microscopy. The unique cross-linking of the affibody-enzyme fusion proteins was utilized for two anticancer treatments. First, the covalent linking of the protein to the EGFR led to inhibition of ERK signaling over a two-day period, whereas conventional antibody therapy only led to 6 h of inhibition. Second, when the affibody-CodA fusion proteins were photo-cross-linked to EGFR overexpressed on MDA-MB-468 breast cancer cells, prodrug conversion was found even 48 h postincubation without any apparent decrease in cell killing, while without photo-cross-linking no cell killing was observed 8 h postincubation. These studies show that affinity-mediated covalent conjugation of the affibody-enzymes to cell receptors allows for prolonged expression on membranes and retained enzymatic activity without genetic engineering.
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Lin W, Mehta S, Zhang J. Genetically encoded fluorescent biosensors illuminate kinase signaling in cancer. J Biol Chem 2019; 294:14814-14822. [PMID: 31434714 DOI: 10.1074/jbc.rev119.006177] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein kinase signaling networks stringently regulate cellular processes, such as proliferation, motility, and cell survival. These networks are also central to the evolution and progression of cancer. Accordingly, genetically encoded fluorescent biosensors capable of directly illuminating the spatiotemporal dynamics of kinase signaling in live cells are being increasingly used to investigate kinase signaling in cancer cells and tumor tissue sections. These biosensors enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Herein, we first review common design strategies for kinase activity biosensors, including signaling targets, biosensor components, and fluorescent proteins involved. Subsequently, we discuss applications of biosensors to study the biology and management of cancer. These versatile molecular tools have been deployed to study oncogenic kinase signaling in living cells and image kinase activities in tumors or to decipher the mechanisms of anticancer drugs. We anticipate that the diversity and precision of genetically encoded biosensors will expand their use to further unravel the dysregulation of kinase signaling in cancer and the modes of actions of cancer-targeting drugs.
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Affiliation(s)
- Wei Lin
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0702
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0702
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0702
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Bhuckory S, Kays JC, Dennis AM. In Vivo Biosensing Using Resonance Energy Transfer. BIOSENSORS 2019; 9:E76. [PMID: 31163706 PMCID: PMC6628364 DOI: 10.3390/bios9020076] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 01/05/2023]
Abstract
Solution-phase and intracellular biosensing has substantially enhanced our understanding of molecular processes foundational to biology and pathology. Optical methods are favored because of the low cost of probes and instrumentation. While chromatographic methods are helpful, fluorescent biosensing further increases sensitivity and can be more effective in complex media. Resonance energy transfer (RET)-based sensors have been developed to use fluorescence, bioluminescence, or chemiluminescence (FRET, BRET, or CRET, respectively) as an energy donor, yielding changes in emission spectra, lifetime, or intensity in response to a molecular or environmental change. These methods hold great promise for expanding our understanding of molecular processes not just in solution and in vitro studies, but also in vivo, generating information about complex activities in a natural, organismal setting. In this review, we focus on dyes, fluorescent proteins, and nanoparticles used as energy transfer-based optical transducers in vivo in mice; there are examples of optical sensing using FRET, BRET, and in this mammalian model system. After a description of the energy transfer mechanisms and their contribution to in vivo imaging, we give a short perspective of RET-based in vivo sensors and the importance of imaging in the infrared for reduced tissue autofluorescence and improved sensitivity.
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Affiliation(s)
- Shashi Bhuckory
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Joshua C Kays
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.
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Koudelková L, Pataki AC, Tolde O, Pavlik V, Nobis M, Gemperle J, Anderson K, Brábek J, Rosel D. Novel FRET-Based Src Biosensor Reveals Mechanisms of Src Activation and Its Dynamics in Focal Adhesions. Cell Chem Biol 2019; 26:255-268.e4. [DOI: 10.1016/j.chembiol.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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Development of novel affinity reagents for detecting protein tyrosine phosphorylation based on superbinder SH2 domain in tumor cells. Anal Chim Acta 2018; 1032:138-146. [DOI: 10.1016/j.aca.2018.05.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 05/07/2018] [Accepted: 05/16/2018] [Indexed: 11/18/2022]
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Liu Y, Lee J, Perez L, Gill AD, Hooley RJ, Zhong W. Selective Sensing of Phosphorylated Peptides and Monitoring Kinase and Phosphatase Activity with a Supramolecular Tandem Assay. J Am Chem Soc 2018; 140:13869-13877. [PMID: 30269482 DOI: 10.1021/jacs.8b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simple tuning of a host:guest pair allows selective sensing of different peptide modifications, exploiting orthogonal recognition mechanisms. Excellent selectivity for either lysine trimethylations or alcohol phosphorylations is possible by simply varying the fluorophore guest. The phosphorylation sensor can be modulated by the presence of small (μM) concentrations of metal ions, allowing array-based sensing. Phosphorylation at serine, threonine, and tyrosine can be selectively sensed via discriminant analysis. The phosphopeptide sensing is effective in the presence of small-molecule phosphates such as ATP, which in turn enables the sensor to be employed in continuous optical assays of both serine kinase and tyrosine phosphatase activity. The activity of multiple different kinases can be monitored, and the sensor is capable of detecting the phosphorylation of peptides containing multiple different modifications, including lysine methylations and acetylation. A single deep cavitand can be used as a "one size fits all" sensor that can selectively detect multiple different modifications to oligopeptides, as well as monitoring the function of their post-translational modification writer and eraser enzymes in complex systems.
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Wang P, Liang J, Shi LZ, Wang Y, Zhang P, Ouyang M, Preece D, Peng Q, Shao L, Fan J, Sun J, Li SS, Berns MW, Zhao H, Wang Y. Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding. ACS PHOTONICS 2018; 5:3565-3574. [PMID: 31069245 PMCID: PMC6502247 DOI: 10.1021/acsphotonics.8b00383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During cell-to-cell communications, the interplay between physical and biochemical cues is essential for informational exchange and functional coordination, especially in multicellular organisms. However, it remains a challenge to visualize intercellular signaling dynamics in single live cells. Here, we report a photonic approach, based on laser microscissors and Förster resonance energy transfer (FRET) microscopy, to study intercellular signaling transmission. First, using our high-throughput screening platform, we developed a highly sensitive FRET-based biosensor (SCAGE) for Src kinase, a key regulator of intercellular interactions and signaling cascades. Notably, SCAGE showed a more than 40-fold sensitivity enhancement than the original biosensor in live mammalian cells. Next, upon local severance of physical intercellular connections by femtosecond laser pulses, SCAGE enabled the visualization of a transient Src activation across neighboring cells. Lastly, we found that this observed transient Src activation following the loss of cell-cell contacts depends on the passive structural support of cytoskeleton but not on the active actomyosin contractility. Hence, by precisely introducing local physical perturbations and directly visualizing spatiotemporal transmission of ensuing signaling events, our integrated approach could be broadly applied to mimic and investigate the wounding process at single-cell resolutions. This integrated approach with highly sensitive FRET-based biosensors provides a unique system to advance our in-depth understanding of molecular mechanisms underlying the physical-biochemical basis of intercellular coupling and wounding processes.
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Affiliation(s)
- Pengzhi Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jing Liang
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology
| | - Linda Z. Shi
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Yi Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ping Zhang
- Institute of Mechanobiology and Biomedical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingxing Ouyang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Daryl Preece
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Qin Peng
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Lunan Shao
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jason Fan
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jie Sun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shawn S. Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario Canada N6A 5C1
- Children’s Health Research Institute, 800 Commissioners Road East, London, Ontario Canada N6C 2 V5
| | - Michael W. Berns
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92612, United States
- Department of Developmental and Cell Biology, School of Biological Sciences, and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92617, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
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Lossi L, Merighi A. The Use of ex Vivo Rodent Platforms in Neuroscience Translational Research With Attention to the 3Rs Philosophy. Front Vet Sci 2018; 5:164. [PMID: 30073174 PMCID: PMC6060265 DOI: 10.3389/fvets.2018.00164] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/29/2018] [Indexed: 01/08/2023] Open
Abstract
The principles of the 3Rs—Replacement, Reduction, and Refinement—are at the basis of most advanced national and supranational (EU) regulations on animal experimentation and welfare. In the perspective to reduce and refine the use of these animals in translational research, we here discuss the use of rodent acute and organotypically cultured central nervous system slices. We describe novel applications of these ex vivo platforms in medium-throughput screening of neuroactive molecules of potential pharmacological interest, with particular attention to more recent developments that permit to fully exploit the potential of direct genetic engineering of organotypic cultures using transfection techniques. We then describe the perspectives for expanding the use ex vivo platforms in neuroscience studies under the 3Rs philosophy using the following approaches: (1) Use of co-cultures of two brain regions physiologically connected to each other (source-target) to analyze axon regeneration and reconstruction of circuitries; (2) Microinjection or co-cultures of primary cells and/or cell lines releasing one or more neuroactive molecules to screen their physiological and/or pharmacological effects onto neuronal survival and slice circuitry. Microinjected or co-cultured cells are ideally made fluorescent after transfection with a plasmid construct encoding green or red fluorescent protein under the control of a general promoter such as hCMV; (3) Use of “sniffer” cells sensing the release of biologically active molecules from organotypic cultures by means of fluorescent probes. These cells can be prepared with activatable green fluorescent protein, a unique chromophore that remains in a “dark” state because its maturation is inhibited, and can be made fluorescent (de-quenched) if specific cellular enzymes, such as proteases or kinases, are activated.
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Affiliation(s)
- Laura Lossi
- Laboratory of Neurobiology, Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Adalberto Merighi
- Laboratory of Neurobiology, Department of Veterinary Sciences, University of Turin, Turin, Italy
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45
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sehgal P, Kong X, Wu J, Sunyer R, Trepat X, Leckband D. Epidermal growth factor receptor and integrins control force-dependent vinculin recruitment to E-cadherin junctions. J Cell Sci 2018; 131:jcs206656. [PMID: 29487179 PMCID: PMC5897709 DOI: 10.1242/jcs.206656] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
This study reports novel findings that link E-cadherin (also known as CDH1)-mediated force-transduction signaling to vinculin targeting to intercellular junctions via epidermal growth factor receptor (EGFR) and integrins. These results build on previous findings that demonstrated that mechanically perturbed E-cadherin receptors activate phosphoinositide 3-kinase and downstream integrins in an EGFR-dependent manner. Results of this study show that this EGFR-mediated kinase cascade controls the force-dependent recruitment of vinculin to stressed E-cadherin complexes - a key early signature of cadherin-based mechanotransduction. Vinculin targeting requires its phosphorylation at tyrosine 822 by Abl family kinases (hereafter Abl), but the origin of force-dependent Abl activation had not been identified. We now present evidence that integrin activation, which is downstream of EGFR signaling, controls Abl activation, thus linking E-cadherin to Abl through a mechanosensitive signaling network. These findings place EGFR and integrins at the center of a positive-feedback loop, through which force-activated E-cadherin signals regulate vinculin recruitment to cadherin complexes in response to increased intercellular tension.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Poonam Sehgal
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL 61802, USA
| | - Xinyu Kong
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL 61802, USA
| | - Jun Wu
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, IL 61802, USA
| | - Raimon Sunyer
- Institute for Bioengineering of Catalonia, Barcelona, Spain 08028
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain 08028
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona, Spain 08028
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain 08028
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain 08028
| | - Deborah Leckband
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL 61802, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, IL 61802, USA
- Department of Chemistry, University of Illinois, Urbana-Champaign, IL 61802, USA
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de la Cova C, Townley R, Regot S, Greenwald I. A Real-Time Biosensor for ERK Activity Reveals Signaling Dynamics during C. elegans Cell Fate Specification. Dev Cell 2017; 42:542-553.e4. [PMID: 28826819 PMCID: PMC5595649 DOI: 10.1016/j.devcel.2017.07.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/19/2017] [Accepted: 07/20/2017] [Indexed: 01/06/2023]
Abstract
Kinase translocation reporters (KTRs) are genetically encoded fluorescent activity sensors that convert kinase activity into a nucleocytoplasmic shuttling equilibrium for visualizing single-cell signaling dynamics. Here, we adapt the first-generation KTR for extracellular signal-regulated kinase (ERK) to allow easy implementation in vivo. This sensor, "ERK-nKTR," allows quantitative and qualitative assessment of ERK activity by analysis of individual nuclei and faithfully reports ERK activity during development and neural function in diverse cell contexts in Caenorhabditis elegans. Analysis of ERK activity over time in the vulval precursor cells, a well-characterized paradigm of epidermal growth factor receptor (EGFR)-Ras-ERK signaling, has identified dynamic features not evident from analysis of developmental endpoints alone, including pulsatile frequency-modulated signaling associated with proximity to the EGF source. The toolkit described here will facilitate studies of ERK signaling in other C. elegans contexts, and the design features will enable implementation of this technology in other multicellular organisms.
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Affiliation(s)
- Claire de la Cova
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Robert Townley
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sergi Regot
- Department of Molecular Biology & Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.
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Saarbach J, Lindberg E, Folliet S, Georgeon S, Hantschel O, Winssinger N. Kinase-templated abiotic reaction. Chem Sci 2017; 8:5119-5125. [PMID: 28970898 PMCID: PMC5615226 DOI: 10.1039/c7sc01416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/20/2017] [Indexed: 12/16/2022] Open
Abstract
Protein kinases are quintessential regulators of cellular function. Numerous pathologies are intimately linked to the dysregulated activity of a particular protein kinase. Herein we report a technology based on a proximity-induced chemical transformation that enables the detection and imaging of specific kinases. Using two probes that target the nucleotide-binding site and substrate binding site of a target kinase respectively, the reagents appended on the probes are brought within reactive distance thereby enabling the chemical transformation. The reaction used for sensing is a ruthenium-photocatalyzed reduction of a pyridinium immolative linker, which uncages a fluorophore (rhodamine). We demonstrate that this technology can be used to discriminate between closely related kinases with a high signal to noise ratio. We further demonstrate that the technology operates within the complexity of a cellular context with a good correlation between the level of kinase activity and fluorescence output.
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Affiliation(s)
- J Saarbach
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - E Lindberg
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Folliet
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Georgeon
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - O Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - N Winssinger
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
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Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
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Kannan R, Song JK, Karpova T, Clarke A, Shivalkar M, Wang B, Kotlyanskaya L, Kuzina I, Gu Q, Giniger E. The Abl pathway bifurcates to balance Enabled and Rac signaling in axon patterning in Drosophila. Development 2017; 144:487-498. [PMID: 28087633 DOI: 10.1242/dev.143776] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/15/2016] [Indexed: 01/31/2023]
Abstract
The Abl tyrosine kinase signaling network controls cell migration, epithelial organization, axon patterning and other aspects of development. Although individual components are known, the relationships among them remain unresolved. We now use FRET measurements of pathway activity, analysis of protein localization and genetic epistasis to dissect the structure of this network in Drosophila We find that the adaptor protein Disabled stimulates Abl kinase activity. Abl suppresses the actin-regulatory factor Enabled, and we find that Abl also acts through the GEF Trio to stimulate the signaling activity of Rac GTPase: Abl gates the activity of the spectrin repeats of Trio, allowing them to relieve intramolecular repression of Trio GEF activity by the Trio N-terminal domain. Finally, we show that a key target of Abl signaling in axons is the WAVE complex that promotes the formation of branched actin networks. Thus, we show that Abl constitutes a bifurcating network, suppressing Ena activity in parallel with stimulation of WAVE. We suggest that the balancing of linear and branched actin networks by Abl is likely to be central to its regulation of axon patterning.
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Affiliation(s)
- Ramakrishnan Kannan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeong-Kuen Song
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana Karpova
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Akanni Clarke
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhuri Shivalkar
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Wang
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lyudmila Kotlyanskaya
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irina Kuzina
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qun Gu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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