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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 1: mechanisms and models. Biochem J 2023; 480:1887-1907. [PMID: 38038974 PMCID: PMC10754288 DOI: 10.1042/bcj20230276] [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: 07/09/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Extracellular signal-regulated kinase (ERK) has long been studied as a key driver of both essential cellular processes and disease. A persistent question has been how this single pathway is able to direct multiple cell behaviors, including growth, proliferation, and death. Modern biosensor studies have revealed that the temporal pattern of ERK activity is highly variable and heterogeneous, and critically, that these dynamic differences modulate cell fate. This two-part review discusses the current understanding of dynamic activity in the ERK pathway, how it regulates cellular decisions, and how these cell fates lead to tissue regulation and pathology. In part 1, we cover the optogenetic and live-cell imaging technologies that first revealed the dynamic nature of ERK, as well as current challenges in biosensor data analysis. We also discuss advances in mathematical models for the mechanisms of ERK dynamics, including receptor-level regulation, negative feedback, cooperativity, and paracrine signaling. While hurdles still remain, it is clear that higher temporal and spatial resolution provide mechanistic insights into pathway circuitry. Exciting new algorithms and advanced computational tools enable quantitative measurements of single-cell ERK activation, which in turn inform better models of pathway behavior. However, the fact that current models still cannot fully recapitulate the diversity of ERK responses calls for a deeper understanding of network structure and signal transduction in general.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
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2
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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 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [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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3
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Mattingly HH, Chen JJ, Arur S, Shvartsman SY. A Transport Model for Estimating the Time Course of ERK Activation in the C. elegans Germline. Biophys J 2016; 109:2436-45. [PMID: 26636953 DOI: 10.1016/j.bpj.2015.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/01/2015] [Accepted: 10/01/2015] [Indexed: 02/02/2023] Open
Abstract
The Caenorhabditis elegans germline is a well-studied model system for investigating the control of cell fate by signaling pathways. Cell signals at the distal tip of the germline promote cell proliferation; just before the loop, signals couple cell maturation to organism-level nutrient status; at the proximal end of the germline, signals coordinate oocyte maturation and fertilization in the presence of sperm. The latter two events require dual phosphorylation and activation of ERK, the effector molecule of the Ras/MAPK cascade. In C. elegans, ERK is known as MPK-1. At this point, none of today's methods for real-time monitoring of dually phosphorylated MPK-1 are working in the germline. Consequently, quantitative understanding of the MPK-1-dependent processes during germline development is limited. Here, we make a step toward advancing this understanding using a model-based framework that reconstructs the time course of MPK-1 activation from a snapshot of a fixed germline. Our approach builds on a number of recent studies for estimating temporal dynamics from fixed organisms, but takes advantage of the anatomy of the germline to simplify the analysis. Our model predicts that the MPK-1 signal turns on ∼30 h into germ cell progression and peaks ∼7 h later.
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Affiliation(s)
- Henry H Mattingly
- Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Jessica J Chen
- The University of Texas Graduate School of Biomedical Sciences and Department of Genetics, University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Swathi Arur
- The University of Texas Graduate School of Biomedical Sciences and Department of Genetics, University of Texas M. D. Anderson Cancer Center, Houston, Texas.
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey.
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4
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Kummer L, Hsu CW, Dagliyan O, MacNevin C, Kaufholz M, Zimmermann B, Dokholyan NV, Hahn KM, Plückthun A. Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. ACTA ACUST UNITED AC 2014; 20:847-56. [PMID: 23790495 DOI: 10.1016/j.chembiol.2013.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/11/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
Investigation of protein activation in living cells is fundamental to understanding how proteins are influenced by the full complement of upstream regulators they experience. Here, we describe the generation of a biosensor based on the DARPin binding scaffold suited for intracellular applications. Combining library selection and knowledge-based design, we created an ERK activity biosensor by derivatizing a DARPin specific for phosphorylated ERK with a solvatochromatic merocyanine dye, whose fluorescence increases upon pERK binding. The biosensor specifically responded to pERK2, recognized by its conformation, but not to ERK2 or other closely related mitogen-activated kinases tested. Activated endogenous ERK was visualized in mouse embryo fibroblasts, revealing greater activation in the nucleus, perinuclear regions, and especially the nucleoli. The DARPin-based biosensor will serve as a useful tool for studying biological functions of ERK in vitro and in vivo.
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Affiliation(s)
- Lutz Kummer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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5
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Xu C, Peter M, Bouquier N, Ollendorff V, Villamil I, Liu J, Fagni L, Perroy J. REV, A BRET-Based Sensor of ERK Activity. Front Endocrinol (Lausanne) 2013; 4:95. [PMID: 23908646 PMCID: PMC3727045 DOI: 10.3389/fendo.2013.00095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/17/2013] [Indexed: 11/13/2022] Open
Abstract
Networks of signaling molecules are activated in response to environmental changes. How are these signaling networks dynamically integrated in space and time to process particular information? To tackle this issue, biosensors of single signaling pathways have been engineered. Bioluminescence resonance energy transfer (BRET)-based biosensors have proven to be particularly efficient in that matter due to the high sensitivity of this technology to monitor protein-protein interactions or conformational changes in living cells. Extracellular signal-regulated kinases (ERK) are ubiquitously expressed and involved in many diverse cellular functions that might be encoded by the strength and spatio-temporal pattern of ERK activation. We developed a BRET-based sensor of ERK activity, called Rluc8-ERKsubstrate-Venus (REV). As expected, BRET changes of REV were correlated with ERK phosphorylation, which is required for its kinase activity. In neurons, the nature of the stimuli determines the strength, the location, or the moment of ERK activation, thus highlighting how acute modulation of ERK may encode the nature of initial stimulus to specify the consequences of this activation. This study provides evidence for suitability of REV as a new biosensor to address biological questions.
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Affiliation(s)
- Chanjuan Xu
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- UMR-5203, Universités de Montpellier 1 & 2, Montpellier, France
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Marion Peter
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier (IGMM), Montpellier, France
| | - Nathalie Bouquier
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- UMR-5203, Universités de Montpellier 1 & 2, Montpellier, France
| | - Vincent Ollendorff
- UMR866 Dynamique Musculaire et Métabolisme, INRA, Université Montpellier 1, Université Montpellier 2, Montpellier, France
| | - Ignacio Villamil
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- UMR-5203, Universités de Montpellier 1 & 2, Montpellier, France
| | - Jianfeng Liu
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Laurent Fagni
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- UMR-5203, Universités de Montpellier 1 & 2, Montpellier, France
| | - Julie Perroy
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- UMR-5203, Universités de Montpellier 1 & 2, Montpellier, France
- *Correspondence: Julie Perroy, Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France e-mail:
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Martić S, Gabriel M, Turowec JP, Litchfield DW, Kraatz HB. Versatile Strategy for Biochemical, Electrochemical and Immunoarray Detection of Protein Phosphorylations. J Am Chem Soc 2012; 134:17036-45. [DOI: 10.1021/ja302586q] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sanela Martić
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michelle Gabriel
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Jacob P. Turowec
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - David W. Litchfield
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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7
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Kovarik ML, Allbritton NL. Measuring enzyme activity in single cells. Trends Biotechnol 2011; 29:222-30. [PMID: 21316781 PMCID: PMC3080453 DOI: 10.1016/j.tibtech.2011.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/04/2011] [Accepted: 01/10/2011] [Indexed: 01/09/2023]
Abstract
Seemingly identical cells can differ in their biochemical state, function and fate, and this variability plays an increasingly recognized role in organism-level outcomes. Cellular heterogeneity arises in part from variation in enzyme activity, which results from interplay between biological noise and multiple cellular processes. As a result, single-cell assays of enzyme activity, particularly those that measure product formation directly, are crucial. Recent innovations have yielded a range of techniques to obtain these data, including image-, flow- and separation-based assays. Research to date has focused on easy-to-measure glycosylases and clinically-relevant kinases. Expansion of these techniques to a wider range and larger number of enzymes will answer contemporary questions in proteomics and glycomics, specifically with respect to biological noise and cellular heterogeneity.
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Affiliation(s)
- Michelle L Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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8
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Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 2010; 90:1103-63. [PMID: 20664080 DOI: 10.1152/physrev.00038.2009] [Citation(s) in RCA: 915] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.
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9
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Friedrich MW, Aramuni G, Mank M, Mackinnon JAG, Griesbeck O. Imaging CREB activation in living cells. J Biol Chem 2010; 285:23285-95. [PMID: 20484048 DOI: 10.1074/jbc.m110.124545] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Ca(2+)- and cAMP-responsive element-binding protein (CREB) and the related ATF-1 and CREM are stimulus-inducible transcription factors that link certain forms of cellular activity to changes in gene expression. They are attributed to complex integrative activation characteristics, but current biochemical technology does not allow dynamic imaging of CREB activation in single cells. Using fluorescence resonance energy transfer between mutants of green fluorescent protein we here develop a signal-optimized genetically encoded indicator that enables imaging activation of CREB due to phosphorylation of the critical serine 133. The indicator of CREB activation due to phosphorylation (ICAP) was used to investigate the role of the scaffold and anchoring protein AKAP79/150 in regulating signal pathways converging on CREB. We show that disruption of AKAP79/150-mediated protein kinase A anchoring or knock-down of AKAP150 dramatically reduces the ability of protein kinase A to activate CREB. In contrast, AKAP79/150 regulation of CREB via L-type channels may only have minor importance. ICAP allows dynamic and reversible imaging in living cells and may become useful in studying molecular components and cell-type specificity of activity-dependent gene expression.
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Affiliation(s)
- Michael W Friedrich
- Max-Planck-Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
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10
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Carlin LM, Makrogianneli K, Keppler M, Fruhwirth GO, Ng T. Visualisation of signalling in immune cells. Methods Mol Biol 2010; 616:97-113. [PMID: 20379871 DOI: 10.1007/978-1-60761-461-6_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Currently, a great number of approaches are employed in investigation of the immune system. These range from experiments in live animals and biochemical techniques to investigate whole organs or cell populations down to single cell and molecular techniques to look at dynamics in specific cell-cell interactions. It is the latter approach that this chapter focusses on. The use of Förster resonance energy transfer (FRET) techniques to probe protein-protein interactions that are involved in receptor signalling to the cytoskeleton in intact cells is now well established. Various FRET biosensors are available to visualise several critical cell processes, giving information about activity and the location of key signalling molecules. As a specific set of examples in this chapter, we have generated variants of the original Rho, Rac and Cdc42 "Raichu" probes and improved their fluorophore combination to make them suitable for FLIM. These were employed in a number of assays to determine signal dynamics in T and NK cells. Specific protocols of how to use these probes and technical notes are described.
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Affiliation(s)
- Leo M Carlin
- Cancer Studies Division/Randall Division of Cellular and Molecular Biophysics, Richard Dimbleby Department of Cancer Research, Guy's Medical School Campus, King's College London, London, UK
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11
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Luković E, Vogel Taylor E, Imperiali B. Monitoring protein kinases in cellular media with highly selective chimeric reporters. Angew Chem Int Ed Engl 2009; 48:6828-31. [PMID: 19681083 DOI: 10.1002/anie.200902374] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Elvedin Luković
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, USA
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12
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Luković E, Vogel Taylor E, Imperiali B. Monitoring Protein Kinases in Cellular Media with Highly Selective Chimeric Reporters. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902374] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Abstract
The explosion of scientific interest in protein kinase-mediated signaling networks has led to the infusion of new chemical methods and their applications related to the analysis of phosphorylation pathways. We highlight some of these chemical biology approaches across three areas. First, we discuss the development of chemical tools to modulate the activity of protein kinases to explore kinase mechanisms and their contributions to phosphorylation events and cellular processes. Second, we describe chemical techniques developed in the past few years to dissect the structural and functional effects of phosphate modifications at specific sites in proteins. Third, we cover newly developed molecular imaging approaches to elucidate the spatiotemporal aspects of phosphorylation cascades in live cells. Exciting advances in our understanding of protein phosphorylation have been obtained with these chemical biology approaches, but continuing opportunities for technological innovation remain.
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Affiliation(s)
- Mary Katherine Tarrant
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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14
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Abstract
The activity of the ERK has complex spatial and temporal dynamics that are important for the specificity of downstream effects. However, current biochemical techniques do not allow for the measurement of ERK signaling with fine spatiotemporal resolution. We developed a genetically encoded, FRET-based sensor of ERK activity (the extracellular signal-regulated kinase activity reporter, EKAR), optimized for signal-to-noise ratio and fluorescence lifetime imaging. EKAR selectively and reversibly reported ERK activation in HEK293 cells after epidermal growth factor stimulation. EKAR signals were correlated with ERK phosphorylation, required ERK activity, and did not report the activities of JNK or p38. EKAR reported ERK activation in the dendrites and nucleus of hippocampal pyramidal neurons in brain slices after theta-burst stimuli or trains of back-propagating action potentials. EKAR therefore permits the measurement of spatiotemporal ERK signaling dynamics in living cells, including in neuronal compartments in intact tissues.
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15
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Vlad F, Turk BE, Peynot P, Leung J, Merlot S. A versatile strategy to define the phosphorylation preferences of plant protein kinases and screen for putative substrates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:104-17. [PMID: 18363786 DOI: 10.1111/j.1365-313x.2008.03488.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Most signaling networks are regulated by reversible protein phosphorylation. The specificity of this regulation depends in part on the capacity of protein kinases to recognize and efficiently phosphorylate particular sequence motifs in their substrates. Sequenced plant genomes potentially encode over than 1000 protein kinases, representing 4% of the proteins, twice the proportion found in humans. This plethora of plant kinases requires the development of high-throughput strategies to identify their substrates. In this study, we have implemented a semi-degenerate peptide array screen to define the phosphorylation preferences of four kinases from Arabidopsis thaliana that are representative of the plant calcium-dependent protein kinase and Snf1-related kinase superfamily. We converted these quantitative data into position-specific scoring matrices to identify putative substrates of these kinases in silico in protein sequence databases. Our data show that these kinases display related but nevertheless distinct phosphorylation motif preferences, suggesting that they might share common targets but are likely to have specific substrates. Our analysis also reveals that a conserved motif found in the stress-related dehydrin protein family may be targeted by the SnRK2-10 kinase. Our results indicate that semi-degenerate peptide array screening is a versatile strategy that can be used on numerous plant kinases to facilitate identification of their substrates, and therefore represents a valuable tool to decipher phosphorylation-regulated signaling networks in plants.
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Affiliation(s)
- Florina Vlad
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 1 avenue de la Terrasse, Bât. 23, 91198 Gif-sur-Yvette Cedex, France
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16
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Sheridan DL, Kong Y, Parker SA, Dalby KN, Turk BE. Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs. J Biol Chem 2008; 283:19511-20. [PMID: 18482985 DOI: 10.1074/jbc.m801074200] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) mediate cellular responses to a wide variety of extracellular stimuli. MAPK signal transduction cascades are tightly regulated, and individual MAPKs display exquisite specificity in recognition of their target substrates. All MAPK family members share a common phosphorylation site motif, raising questions as to how substrate specificity is achieved. Here we describe a peptide library screen to identify sequence requirements of the DEF site (docking site for ERK FXF), a docking motif separate from the phosphorylation site. We show that MAPK isoforms recognize DEF sites with unique sequences and identify two key residues on the MAPK that largely dictate sequence specificity. Based on these observations and computational docking studies, we propose a revised model for MAPK interaction with substrates containing DEF sites. Variations in DEF site sequence requirements provide one possible mechanism for encoding complex target specificity among MAPK isoforms.
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Affiliation(s)
- Douglas L Sheridan
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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17
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Paar C, Paster W, Stockinger H, Schütz GJ, Sonnleitner M, Sonnleitner A. High throughput FRET screening of the plasma membrane based on TIRFM. Cytometry A 2008; 73:442-50. [DOI: 10.1002/cyto.a.20551] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Souslova EA, Chudakov DM. Genetically encoded intracellular sensors based on fluorescent proteins. BIOCHEMISTRY (MOSCOW) 2007; 72:683-97. [PMID: 17680759 DOI: 10.1134/s0006297907070012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Green fluorescent protein from Aequorea victoria and its many homologs are now widely used in basic and applied research. These genetically encoded fluorescent markers can detect localization of cell proteins and organelles in living cells and also cells and tissues in living organisms. Unique instruments and methods for studies of molecular biology of a cell and high throughput drug screenings are based on fluorescent proteins. This review deals with the most intensively evolving directions in this field, the development of genetically encoded sensors. Changes in their spectral properties are used for monitoring of cell enzyme activities or changes in concentrations of particular molecules.
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Affiliation(s)
- E A Souslova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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19
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Zhang J, Allen MD. FRET-based biosensors for protein kinases: illuminating the kinome. MOLECULAR BIOSYSTEMS 2007; 3:759-65. [DOI: 10.1039/b706628g] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
Fluorescence microscopy has become a principle methodology in the field of developmental biology. Recent technological advances have led to the design of high-speed and high-resolution confocal and multiphoton microscopes that enable researchers to obtain three- and four-dimensional information in living cells and whole embryos. Paralleling this progress, the development of stable and bright vital fluorescent probes has revolutionized the ability to track individual cells in vitro and in vivo and to visualize intercellular and subcellular molecular interactions in real time. Combining imaging modalities and labeling techniques that are increasingly unobtrusive to cell and whole animal function, our understanding of how proteins interact, tissues take form, and organs synchronize to create a functioning animal is reaching a whole new level.
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Affiliation(s)
| | - MARY E. DICKINSON
- Correspondence: Mary E. Dickinson, Ph.D., Baylor College of Medicine, Department of Molecular Physiology and Biophysics, One Baylor Plaza, Houston, TX 77071; e-mail:
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