101
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Abstract
Spatio-temporal control of RhoA GTPase is critical for regulation of cell migration, attachment to extracellular matrix, and cell-cell adhesions. Activation of RhoA is mediated by guanine nucleotide exchange factors (GEFs), a diverse family of enzymes that are controlled by multiple signaling pathways regulating actin cytoskeleton and cell migration. GEFs can be regulated by different mechanisms. Growing evidence demonstrates that phosphorylation serves as one of the predominant signals controlling activity, interactions, and localization of RhoGEFs. It acts as a positive and a negative regulator, and allows for regulation of RhoGEFs by multiple signaling cascades. Although there are common trends in phosphorylation-mediated regulation of some RhoGEF homologs, the majority of GEFs utilize distinct mechanisms that are dictated by their unique structure and interaction networks. This diversity enables multiple signaling pathways to use different RhoGEFs for regulation of a single central-RhoA. Here, we review current examples of phosphorylation-mediated regulation of GEFs for RhoA and its role in cell migration, discuss mechanisms, and provide insights into potential future directions.
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Affiliation(s)
- Maulik Patel
- Department of Pharmacology; University of Illinois at Chicago; Chicago, IL USA
| | - Andrei V Karginov
- Department of Pharmacology; University of Illinois at Chicago; Chicago, IL USA
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102
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Wymann MP, Schultz C. The chemical biology of phosphoinositide 3-kinases. Chembiochem 2012; 13:2022-35. [PMID: 22965647 DOI: 10.1002/cbic.201200089] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 07/13/2012] [Indexed: 01/14/2023]
Abstract
Since its discovery in the late 1980s, phosphoinositide 3-kinase (PI3K), and its isoforms have arguably reached the forefront of signal transduction research. Regulation of this lipid kinase, its functions, its effectors, in short its entire signaling network, has been extensively studied. PI3K inhibitors are frequently used in biochemistry and cell biology. In addition, many pharmaceutical companies have launched drug-discovery programs to identify modulators of PI3Ks. Despite these efforts and a fairly good knowledge of the PI3K signaling network, we still have only a rudimentary picture of the signaling dynamics of PI3K and its lipid products in space and time. It is therefore essential to create and use novel biological and chemical tools to manipulate the phosphoinositide signaling network with spatial and temporal resolution. In this review, we discuss the current and potential future tools that are available and necessary to unravel the various functions of PI3K and its isoforms.
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Affiliation(s)
- Matthias P Wymann
- Institute of Biochemistry & Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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103
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
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Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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104
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
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105
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Arbely E, Torres-Kolbus J, Deiters A, Chin JW. Photocontrol of Tyrosine Phosphorylation in Mammalian Cells via Genetic Encoding of Photocaged Tyrosine. J Am Chem Soc 2012; 134:11912-5. [DOI: 10.1021/ja3046958] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eyal Arbely
- Medical Research Council Laboratory of Molecular Biology, Hills Road,
Cambridge CB2 0QH, United Kingdom
| | - Jessica Torres-Kolbus
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695-8204, United States
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695-8204, United States
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology, Hills Road,
Cambridge CB2 0QH, United Kingdom
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106
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Olson EJ, Tabor JJ. Post-translational tools expand the scope of synthetic biology. Curr Opin Chem Biol 2012; 16:300-6. [PMID: 22766485 DOI: 10.1016/j.cbpa.2012.06.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 05/29/2012] [Accepted: 06/04/2012] [Indexed: 12/26/2022]
Abstract
Synthetic biology is improving our understanding of and ability to control living organisms. To date, most progress has been made by engineering gene expression. However, computational and genetically encoded tools that allow protein activity and protein-protein interactions to be controlled on their natural time and length scales are emerging. These technologies provide a basis for the construction of post-translational circuits, which are capable of fast, robust and highly spatially resolved signal processing. When combined with their transcriptional and translational counterparts, synthetic post-translational circuits will allow better analysis and control of otherwise intractable biological processes such as cellular differentiation and the growth of tissues.
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Affiliation(s)
- Evan J Olson
- Graduate Program in Applied Physics, Rice University, Houston, TX 77005, United States
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107
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Rutkowska A, Schultz C. Protein Tango: The Toolbox to Capture Interacting Partners. Angew Chem Int Ed Engl 2012; 51:8166-76. [DOI: 10.1002/anie.201201717] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Indexed: 11/07/2022]
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108
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109
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Gardner L, Deiters A. Light-controlled synthetic gene circuits. Curr Opin Chem Biol 2012; 16:292-9. [PMID: 22633822 DOI: 10.1016/j.cbpa.2012.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 04/10/2012] [Accepted: 04/15/2012] [Indexed: 01/09/2023]
Abstract
Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.
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Affiliation(s)
- Laura Gardner
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, United States
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110
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Putyrski M, Schultz C. Protein translocation as a tool: The current rapamycin story. FEBS Lett 2012; 586:2097-105. [DOI: 10.1016/j.febslet.2012.04.061] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/27/2012] [Accepted: 04/29/2012] [Indexed: 01/08/2023]
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111
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Karginov AV, Hahn KM. Allosteric activation of kinases: design and application of RapR kinases. ACTA ACUST UNITED AC 2012; Chapter 14:14.13.1-14.13.16. [PMID: 22161545 DOI: 10.1002/0471143030.cb1413s53] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here we describe a method for the engineered regulation of protein kinases in living cells, the design and application of RapR (rapamycin regulated) kinases. The RapR kinase method enables activation of kinases with high specificity and precise temporal control. Insertion of an engineered allosteric switch, the iFKBP domain, at a structurally conserved position within the kinase catalytic domain makes the modified kinase inactive. Treatment with rapamycin or its non-immunosuppressive analogs triggers interaction with a small FKBP-rapamycin-binding domain (FRB), restoring the activity of the kinase. The reagents used in this method are genetically encoded or membrane permeable, enabling ready application in many systems. Based on the structural similarity of kinase catalytic domains, this method is likely applicable to a wide variety of kinases. Successful regulation has already been demonstrated for three kinases representing both tyrosine and serine/threonine kinase families (p38, FAK, Src). Procedures for designing and testing RapR kinases are discussed.
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Affiliation(s)
- Andrei V Karginov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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112
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Abstract
Cell migration is required for many physiological processes, including wound repair and embryogenesis, and relies on precisely orchestrated events that are regulated in a spatially and temporally controlled manner. Most traditional approaches for studying migration, such as genetic methods or the use of chemical inhibitors, do not offer insight into these important components of protein function. However, chemical tools, which respond on a more rapid time scale and in localized regions of the cell, are capable of providing more detailed, real-time information. This Review describes these recent approaches to investigate cell migration and focuses on proteins that are activated by light or small molecules, as well as fluorescent sensors of protein activity.
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Affiliation(s)
- Brenda N. Goguen
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Barbara Imperiali
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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113
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Xu Y, Melia TJ, Toomre DK. Using light to see and control membrane traffic. Curr Opin Chem Biol 2011; 15:822-30. [PMID: 22079055 DOI: 10.1016/j.cbpa.2011.10.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/01/2011] [Accepted: 10/17/2011] [Indexed: 01/13/2023]
Abstract
Cellular compartmentalization into discrete organelles is maintained by membrane trafficking including vesiculation and tubulation. Recent advances in superresolution imaging have begun to bring these small and dynamic events into focus. Most nanoscopes exploit, and are limited by, switching dyes ON and OFF. Using ground state depletion to switch dyes into long-lived dark states can exploit specific photophysical properties of dyes, such as redox potential or pK(a), and expand the repertoire of nanoscopy probes for multicolor imaging. Seeing is not enough, and new technologies based on homodimerization, heterodimerization and selective release can manipulate membrane trafficking in pulse-chase and light-controlled ways. Herein we highlight the utility and promise of these strategies and discuss their current limitations.
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Affiliation(s)
- Yingke Xu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8002, USA
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114
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Shining light on Drosophila oogenesis: live imaging of egg development. Curr Opin Genet Dev 2011; 21:612-9. [PMID: 21930372 DOI: 10.1016/j.gde.2011.08.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 12/31/2022]
Abstract
Drosophila oogenesis is a powerful model for the study of numerous questions in cell and developmental biology. In addition to its longstanding value as a genetically tractable model of organogenesis, recently it has emerged as an excellent system in which to combine genetics and live imaging. Rapidly improving ex vivo culture conditions, new fluorescent biosensors and photo-manipulation tools, and advances in microscopy have allowed direct observation in real time of processes such as stem cell self-renewal, collective cell migration, and polarized mRNA and protein transport. In addition, entirely new phenomena have been discovered, including revolution of the follicle within the basement membrane and oscillating assembly and disassembly of myosin on a polarized actin network, both of which contribute to elongating this tissue. This review focuses on recent advances in live-cell imaging techniques and the biological insights gleaned from live imaging of egg chamber development.
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115
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Abstract
The absorption of light by bound or diffusible chromophores causes conformational rearrangements in natural and artificial photoreceptor proteins. These rearrangements are coupled to the opening or closing of ion transport pathways, the association or dissociation of binding partners, the enhancement or suppression of catalytic activity, or the transcription or repression of genetic information. Illumination of cells, tissues, or organisms engineered genetically to express photoreceptor proteins can thus be used to perturb biochemical and electrical signaling with exquisite cellular and molecular specificity. First demonstrated in 2002, this principle of optogenetic control has had a profound impact on neuroscience, where it provides a direct and stringent means of probing the organization of neural circuits and of identifying the neural substrates of behavior. The impact of optogenetic control is also beginning to be felt in other areas of cell and organismal biology.
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Affiliation(s)
- Gero Miesenböck
- Centre for Neural Circuits and Behaviour, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3TA, United Kingdom.
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116
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Lippincott-Schwartz J. Bridging structure and process in developmental biology through new imaging technologies. Dev Cell 2011; 21:5-10. [PMID: 21763598 PMCID: PMC3690953 DOI: 10.1016/j.devcel.2011.06.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many unexpected discoveries in developmental biology have depended on advancement of imaging technologies to visualize developmental processes as they unfold across multiple spatial and temporal scales. This essay surveys the recent advances in imaging, highlighting emerging capabilities with an eye toward those poised to have the greatest impact on developmental biology.
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Affiliation(s)
- Jennifer Lippincott-Schwartz
- Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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117
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Gautier A, Deiters A, Chin JW. Light-activated kinases enable temporal dissection of signaling networks in living cells. J Am Chem Soc 2011; 133:2124-7. [PMID: 21271704 PMCID: PMC3048767 DOI: 10.1021/ja1109979] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report a general strategy for creating protein kinases in mammalian cells that are poised for very rapid activation by light. By photoactivating a caged version of MEK1, we demonstrate the specific, rapid, and receptor independent activation of an artificial subnetwork within the Raf/MEK/ERK pathway. Time-lapse microscopy allowed us to precisely characterize the kinetics of elementary steps in the signaling cascade and provided insight into adaptive feedback and rate-determining processes in the pathway.
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Affiliation(s)
- Arnaud Gautier
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, United Kingdom
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