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Mukherjee A, Weyant KB, Agrawal U, Walker J, Cann IKO, Schroeder CM. Engineering and characterization of new LOV-based fluorescent proteins from Chlamydomonas reinhardtii and Vaucheria frigida. ACS Synth Biol 2015; 4:371-7. [PMID: 25881501 DOI: 10.1021/sb500237x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flavin-based fluorescent proteins (FbFPs) are a new class of fluorescent reporters that exhibit oxygen-independent fluorescence, which is a key advantage over the green fluorescent protein. Broad application of FbFPs, however, has been generally hindered by low brightness. To maximize the utility of FbFPs, there is a pressing need to expand and diversify the limited FbFP library through the inclusion of bright and robust variants. In this work, we use genome mining to identify and engineer two new FbFPs (CreiLOV and VafLOV) from Chlamydomonas reinhardtii and Vaucheria frigida. We show that CreiLOV is a thermostable, photostable, and fast-maturing monomeric reporter that outperforms existing FbFPs in brightness and operational pH range. Furthermore, we show that CreiLOV can be used to monitor dynamic gene expression in Escherichia coli. Overall, our work introduces CreiLOV as a robust addition to the FbFP repertoire and highlights genome mining as a powerful approach to engineer improved FbFPs.
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Affiliation(s)
- Arnab Mukherjee
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kevin B. Weyant
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Utsav Agrawal
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joshua Walker
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Isaac K. O. Cann
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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102
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Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. Decoding a neural circuit controlling global animal state in C. elegans. eLife 2015; 4. [PMID: 25760081 PMCID: PMC4440410 DOI: 10.7554/elife.04241] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 03/10/2015] [Indexed: 02/05/2023] Open
Abstract
Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed. DOI:http://dx.doi.org/10.7554/eLife.04241.001 From humans to worms, animals must respond appropriately to environmental challenges to survive. Starving animals must conserve energy while they seek food; animals that encounter a predator must fight or flee. These responses involve the animals re-programming their bodies and behavior, and, in humans, are thought to coincide with feelings or emotions such as ‘hunger’ and ‘fear’. Understanding these states in humans is difficult, but studies of simpler animals may provide some insights. The microscopic worm Caenorhabditis elegans offers a unique advantage to these studies because it has the most precisely described nervous system of any animal. The worm lives in rotting fruit, but it avoids the fruit's surface, perhaps because there is an increased risk of it drying out or being eaten by predators. Microbes that grow within the rotting fruit reduce the oxygen level below the 21% oxygen found in the surrounding air, and so one strategy that C. elegans uses to avoid surface exposure is to continuously monitor the oxygen concentration. If the worm senses that the oxygen level is approaching 21%, which suggests it is nearing the surface, it reverses and turns around. If it cannot find a lower-oxygen environment, the worm switches to continuous rapid movement until it locates such an environment, and adapts its body for surface exposure. Laurent, Soltesz et al. sought to understand the circuit of neurons that controls this switch. Monitoring gene expression in the worms revealed that specific oxygen-sensing neurons help generate the widespread changes that occur in the worm's body. These neurons also control the switch in the worm's behavior. Sensory neurons relay signals to downstream neurons that act on muscles to alter behavior. Neurons typically communicate with other neurons via specific connections; but neurons can also release signaling molecules, which act like ‘wireless’ signals and can affect many other cells. Laurent, Soltesz et al. showed that both kinds of signaling are needed to change the worm's behavior, and suggest that the release of signaling molecules may explain the widespread effects of 21% oxygen on the worm. Laurent, Soltesz et al. then monitored the activity of neurons in freely moving worms, and found that some neurons appear to encode and relay specific sensory information. Other neurons encode the behavior the animal is performing, and yet others can encode both kinds of information. To confirm which neurons control particular behavioral responses, Laurent, Soltesz et al. measured changes in the worm’s behavior after destroying or altering specific cells, or while they used light-based techniques to artificially excite or inhibit specific neurons. At a simple level the worm's response to 21% oxygen resembles the response of a mammal to a dangerous environment: both become more aroused, change how they respond to other sensory cues, and adapt both their bodies and behavior. As such, C. elegans provides a great model to explore at a small and accessible scale how changes in animals' states are generated. DOI:http://dx.doi.org/10.7554/eLife.04241.002
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Affiliation(s)
| | - Zoltan Soltesz
- Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Geoffrey M Nelson
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Changchun Chen
- Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Emmanuel Levy
- Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mario de Bono
- Laboratory of Molecular Biology, Cambridge, United Kingdom
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103
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Shcherbakova DM, Shemetov AA, Kaberniuk AA, Verkhusha VV. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu Rev Biochem 2015; 84:519-50. [PMID: 25706899 DOI: 10.1146/annurev-biochem-060614-034411] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. Natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. Here, we give a brief overview of natural photoreceptors and their mechanisms of action. We then discuss fluorescent proteins and biosensors developed from light-oxygen-voltage-sensing (LOV) domains and phytochromes, as well as their properties and applications. These fluorescent tools possess unique characteristics not achievable with green fluorescent protein-like probes, including near-infrared fluorescence, independence of oxygen, small size, and photosensitizer activity. We next provide an overview of available optogenetic tools of various origins, such as LOV and BLUF (blue-light-utilizing flavin adenine dinucleotide) domains, cryptochromes, and phytochromes, enabling control of versatile cellular processes. We analyze the principles of their function and practical requirements for use. We focus mainly on optical tools with demonstrated use beyond bacteria, with a specific emphasis on their applications in mammalian cells.
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Affiliation(s)
- Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;
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104
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Mukherjee A, Schroeder CM. Flavin-based fluorescent proteins: emerging paradigms in biological imaging. Curr Opin Biotechnol 2015; 31:16-23. [DOI: 10.1016/j.copbio.2014.07.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 02/07/2023]
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105
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Valle L, Abatedaga I, Vieyra FEM, Bortolotti A, Cortez N, Borsarelli CD. Enhancement of photophysical and photosensitizing properties of flavin adenine dinucleotide by mutagenesis of the C-terminal extension of a bacterial flavodoxin reductase. Chemphyschem 2015; 16:872-83. [PMID: 25641205 DOI: 10.1002/cphc.201402774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Indexed: 12/26/2022]
Abstract
The role of the mobile C-terminal extension present in Rhodobacter capsulatus ferredoxin-NADP(H) reductase (RcFPR) was evaluated using steady-state and dynamic spectroscopies for both intrinsic Trp and FAD in a series of mutants in the absence of NADP(H). Deletion of the six C-terminal amino acids beyond Ala266 was combined with the replacement A266Y to emulate the structure of plastidic reductases. Our results show that these modifications of the wild-type RcFPR produce subtle global conformational changes, but strongly reduce the local rigidity of the FAD-binding pocket, exposing the isoalloxazine ring to the solvent. Thus, the ultrafast charge-transfer quenching of (1) FAD* by the conserved Tyr66 residue was absent in the mutant series, producing enhancement of the excited singlet- and triplet-state properties of FAD. This work highlights the delicate balance of the specific interactions between FAD and the surrounding amino acids, and how the functionality and/or photostability of redox flavoproteins can be modified.
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Affiliation(s)
- Lorena Valle
- Centro de Investigaciones y Transferencia de Santiago del Estero (CITSE-CONICET), Universidad Nacional de Santiago del Estero, RN9 Km 1125. 4206, Santiago del Estero (Argentina)
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106
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Williams DC, Bejjani RE, Ramirez PM, Coakley S, Kim SA, Lee H, Wen Q, Samuel A, Lu H, Hilliard MA, Hammarlund M. Rapid and permanent neuronal inactivation in vivo via subcellular generation of reactive oxygen with the use of KillerRed. Cell Rep 2015; 5:553-63. [PMID: 24209746 DOI: 10.1016/j.celrep.2013.09.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/01/2013] [Accepted: 09/13/2013] [Indexed: 12/28/2022] Open
Abstract
Inactivation of selected neurons in vivo can define their contribution to specific developmental outcomes, circuit functions, and behaviors. Here, we show that the optogenetic tool KillerRed selectively, rapidly, and permanently inactivates different classes of neurons in C. elegans in response to a single light stimulus, through the generation of reactive oxygen species (ROS). Ablation scales from individual neurons in single animals to multiple neurons in populations and can be applied to freely behaving animals. Using spatially restricted illumination, we demonstrate that localized KillerRed activation in either the cell body or the axon triggers neuronal degeneration and death of the targeted cell. Finally, targeting KillerRed to mitochondria results in organelle fragmentation without killing the cell, in contrast to the cell death observed when KillerRed is targeted to the plasma membrane. We expect this genetic tool to have wide-ranging applications in studies of circuit function and subcellular responses to ROS.
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107
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Torra J, Burgos-Caminal A, Endres S, Wingen M, Drepper T, Gensch T, Ruiz-González R, Nonell S. Singlet oxygen photosensitisation by the fluorescent protein Pp2FbFP L30M, a novel derivative of Pseudomonas putida flavin-binding Pp2FbFP. Photochem Photobiol Sci 2015; 14:280-7. [DOI: 10.1039/c4pp00338a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The flavin-binding protein Pp2FbFP L30M shows a high singlet oxygen quantum yield.
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Affiliation(s)
- Joaquim Torra
- Institut Químic de Sarrià
- Universitat Ramon Llull
- Barcelona
- Spain
| | | | - Stephan Endres
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Marcus Wingen
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Thomas Gensch
- Institute of Complex Systems 4 (ICS-4
- Cellular Biophysics)
- 52425 Jülich
- Germany
| | | | - Santi Nonell
- Institut Químic de Sarrià
- Universitat Ramon Llull
- Barcelona
- Spain
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108
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Abstract
Neuron manipulation in vivo by ablation, activation, or inactivation, and regulation of gene expression, is essential for dissecting nervous system function. Here we describe genetic means for neuron manipulation in the nematode C. elegans, and provide protocols for generating transgenic animals containing these genetic tools.
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Affiliation(s)
- Menachem Katz
- Laboratory of Developmental Genetics, The Rockefeller University, 810 Weiss Research Building, 1230 York Avenue, New York, NY, 10065, USA.
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109
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Caldwell GA, Caldwell KA. Use of Caenorhabditis elegans to Model Human Movement Disorders. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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110
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Pietra F. Molecular Dynamics Simulation of Dioxygen Pathways through Mini Singlet Oxygen Generator (miniSOG), a Genetically Encoded Marker and Killer Protein. Chem Biodivers 2014; 11:1883-91. [DOI: 10.1002/cbdv.201400125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 11/08/2022]
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111
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Lee H, Kim SA, Coakley S, Mugno P, Hammarlund M, Hilliard MA, Lu H. A multi-channel device for high-density target-selective stimulation and long-term monitoring of cells and subcellular features in C. elegans. LAB ON A CHIP 2014; 14:4513-4522. [PMID: 25257026 PMCID: PMC4213302 DOI: 10.1039/c4lc00789a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selective cell ablation can be used to identify neuronal functions in multicellular model organisms such as Caenorhabditis elegans. The optogenetic tool KillerRed facilitates selective ablation by enabling light-activated damage of cell or subcellular components in a temporally and spatially precise manner. However, the use of KillerRed requires stimulating (5 min-1 h), culturing (~24 h) and imaging (often repeatedly) a large number of individual animals. Current manual manipulation methods are limited by their time-consuming, labor-intensive nature, and their usage of anesthetics. To facilitate large-scale selective ablation, culturing, and repetitive imaging, we developed a densely-packed multi-channel device and used it to perform high-throughput neuronal ablation on KillerRed-expressing animals. The ability to load worms in identical locations with high loading efficiency allows us to ablate selected neurons in multiple worms simultaneously. Our device also enables continuous observation of animals for 24 h following KillerRed activation, and allows the animals to be recovered for behavioural assays. We expect this multi-channel device to facilitate a broad range of long-term imaging and selective illumination experiments in neuroscience.
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Affiliation(s)
- Hyewon Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
| | - Shin Ae Kim
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
| | - Sean Coakley
- Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Paula Mugno
- Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Marc Hammarlund
- Department of Genetics, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University
| | - Massimo A. Hilliard
- Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
- Interdisciplinary Program of Bioengineering, Georgia Institute of Technology
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112
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Sano Y, Watanabe W, Matsunaga S. Chromophore-assisted laser inactivation--towards a spatiotemporal-functional analysis of proteins, and the ablation of chromatin, organelle and cell function. J Cell Sci 2014; 127:1621-9. [PMID: 24737873 DOI: 10.1242/jcs.144527] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromophore-assisted laser or light inactivation (CALI) has been employed as a promising technique to achieve spatiotemporal knockdown or loss-of-function of target molecules in situ. CALI is performed using photosensitizers as generators of reactive oxygen species (ROS). There are two CALI approaches that use either transgenic tags with chemical photosensitizers, or genetically encoded fluorescent protein fusions. Using spatially restricted microscopy illumination, CALI can address questions regarding, for example, protein isoforms, subcellular localization or phase-specific analyses of multifunctional proteins that other knockdown approaches, such as RNA interference or treatment with chemicals, cannot. Furthermore, rescue experiments can clarify the phenotypic capabilities of CALI after the depletion of endogenous targets. CALI can also provide information about individual events that are involved in the function of a target protein and highlight them in multifactorial events. Beyond functional analysis of proteins, CALI of nuclear proteins can be performed to induce cell cycle arrest, chromatin- or locus-specific DNA damage. Even at organelle level - such as in mitochondria, the plasma membrane or lysosomes - CALI can trigger cell death. Moreover, CALI has emerged as an optogenetic tool to switch off signaling pathways, including the optical depletion of individual neurons. In this Commentary, we review recent applications of CALI and discuss the utility and effective use of CALI to address open questions in cell biology.
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Affiliation(s)
- Yukimi Sano
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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113
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Turbay MBE, Rey V, Argañaraz NM, Morán Vieyra FE, Aspée A, Lissi EA, Borsarelli CD. Effect of dye localization and self-interactions on the photosensitized generation of singlet oxygen by rose bengal bound to bovine serum albumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:275-82. [DOI: 10.1016/j.jphotobiol.2014.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
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114
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VAV-1 acts in a single interneuron to inhibit motor circuit activity in Caenorhabditis elegans. Nat Commun 2014; 5:5579. [PMID: 25412913 PMCID: PMC4241504 DOI: 10.1038/ncomms6579] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/15/2014] [Indexed: 11/09/2022] Open
Abstract
The complex molecular and cellular mechanisms underlying neuronal control of animal movement are not well understood. Locomotion of Caenorhabditis elegans is mediated by a neuronal circuit that produces coordinated sinusoidal movement. Here we utilize this simple, yet elegant, behaviour to show that VAV-1, a conserved guanine nucleotide exchange factor for Rho-family GTPases, negatively regulates motor circuit activity and the rate of locomotion. While vav-1 is expressed in a small subset of neurons, we find that VAV-1 function is required in a single interneuron, ALA, to regulate motor neuron circuit activity. Furthermore, we show by genetic and optogenetic manipulation of ALA that VAV-1 is required for the excitation and activation of this neuron. We find that ALA signalling inhibits command interneuron activity by abrogating excitatory signalling in the command interneurons, which is responsible for promoting motor neuron circuit activity. Together, our data describe a novel neuromodulatory role for VAV-1-dependent signalling in the regulation of motor circuit activity and locomotion.
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115
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Jewhurst K, Levin M, McLaughlin KA. Optogenetic Control of Apoptosis in Targeted Tissues of Xenopus laevis Embryos. J Cell Death 2014; 7:25-31. [PMID: 25374461 PMCID: PMC4213186 DOI: 10.4137/jcd.s18368] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 11/05/2022] Open
Abstract
KillerRed (KR) is a recently discovered fluorescent protein that, when activated with green light, releases reactive oxygen species (ROS) into the cytoplasm, triggering apoptosis in a KR-expressing cell. This property allows for the use of KR as a means of killing cells in an organism with great temporal and spatial specificity, while minimizing the nonspecific effects that can result from mechanical or chemical exposure damage techniques. Such optogenetic control of cell death, and the resulting ability to induce the targeted death of specific tissues, is invaluable for regeneration/repair studies-particularly in Xenopus laevis, where apoptosis plays a key role in regeneration and repair. We here describe a method by which membrane-bound KR, introduced to Xenopus embryos by mRNA microinjection, can be activated with green light to induce apoptosis in specific organs and tissues, with a focus on the developing eye and pronephric kidney.
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Affiliation(s)
- Kyle Jewhurst
- Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
| | - Michael Levin
- Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
| | - Kelly A McLaughlin
- Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
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116
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Ambrosone A, Pino PD, Marchesano V, Parak WJ, de la Fuente JM, Tortiglione C. Gold nanoprisms for photothermal cell ablation in vivo. Nanomedicine (Lond) 2014; 9:1913-22. [DOI: 10.2217/nnm.14.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim: To develop new methodologies for selective cell ablation in a temporally and spatially precise fashion in model organisms. Materials & methods: living polyps (Hydra vulgaris) treated with gold nanoprisms were near-infrared (NIR) irradiated and the photothermal effects evaluated at whole-animal, cellular and molecular levels. Results: Nanoprisms showed good efficiency of internalization in living specimens, with no sign of toxicity; under NIR irradiation they induced cell death and the overexpression of the hsp70 gene. Conclusion: gold nanoprisms could be employed as efficient heat mediators in model organisms, and NIR-triggered cell ablation may represent a new advanced tool to study cell function. Solving bioethical and economical issues, invertebrates may provide alternative models bridging the gap between cell research and preclinical studies of photothermal therapy.
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Affiliation(s)
- Alfredo Ambrosone
- Istituto di Cibernetica 'E.Caianiello', Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Pablo del Pino
- Instituto de Nanociencia de Aragon, University of Zaragoza. C/ Mariano Esquillor s/n, Zaragoza, Spain
| | - Valentina Marchesano
- Istituto di Cibernetica 'E.Caianiello', Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Wolfgang J Parak
- Philipps University of Marburg, FB Physics, Biophotonics, Renthof 7, D-35037 Marburg, Germany
| | - Jesus M de la Fuente
- Instituto de Nanociencia de Aragon, University of Zaragoza. C/ Mariano Esquillor s/n, Zaragoza, Spain
| | - Claudia Tortiglione
- Istituto di Cibernetica 'E.Caianiello', Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
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117
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Takemoto K, Matsuda T, Sakai N, Fu D, Noda M, Uchiyama S, Kotera I, Arai Y, Horiuchi M, Fukui K, Ayabe T, Inagaki F, Suzuki H, Nagai T. SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation. Sci Rep 2014; 3:2629. [PMID: 24043132 PMCID: PMC3775092 DOI: 10.1038/srep02629] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/22/2013] [Indexed: 11/20/2022] Open
Abstract
Chromophore-assisted light inactivation (CALI) is a powerful technique for acute perturbation of biomolecules in a spatio-temporally defined manner in living specimen with reactive oxygen species (ROS). Whereas a chemical photosensitizer including fluorescein must be added to specimens exogenously and cannot be restricted to particular cells or sub-cellular compartments, a genetically-encoded photosensitizer, KillerRed, can be controlled in its expression by tissue specific promoters or subcellular localization tags. Despite of this superiority, KillerRed hasn't yet become a versatile tool because its dimerization tendency prevents fusion with proteins of interest. Here, we report the development of monomeric variant of KillerRed (SuperNova) by direct evolution using random mutagenesis. In contrast to KillerRed, SuperNova in fusion with target proteins shows proper localization. Furthermore, unlike KillerRed, SuperNova expression alone doesn't perturb mitotic cell division. Supernova retains the ability to generate ROS, and hence promote CALI-based functional analysis of target proteins overcoming the major drawbacks of KillerRed.
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Affiliation(s)
- Kiwamu Takemoto
- 1] Research Institute for Electronic Sciences, Hokkaido University, Kita-20 Nishi-10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan [2] [3]
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118
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Ichikawa Y, Kamiya M, Obata F, Miura M, Terai T, Komatsu T, Ueno T, Hanaoka K, Nagano T, Urano Y. Selective Ablation of β-Galactosidase-Expressing Cells with a Rationally Designed Activatable Photosensitizer. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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119
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Ichikawa Y, Kamiya M, Obata F, Miura M, Terai T, Komatsu T, Ueno T, Hanaoka K, Nagano T, Urano Y. Selective Ablation of β-Galactosidase-Expressing Cells with a Rationally Designed Activatable Photosensitizer. Angew Chem Int Ed Engl 2014; 53:6772-5. [DOI: 10.1002/anie.201403221] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 11/09/2022]
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Gao W, Su Z, Liu Q, Zhou L. State-dependent and site-directed photodynamic transformation of HCN2 channel by singlet oxygen. ACTA ACUST UNITED AC 2014; 143:633-44. [PMID: 24733837 PMCID: PMC4003188 DOI: 10.1085/jgp.201311112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Singlet oxygen acts through a histidine residue to delay HCN channel deactivation and enhance voltage-insensitive current. Singlet oxygen (1O2), which is generated through metabolic reactions and oxidizes numerous biological molecules, has been a useful tool in basic research and clinical practice. However, its role as a signaling factor, as well as a mechanistic understanding of the oxidation process, remains poorly understood. Here, we show that hyperpolarization-activated, cAMP-gated (HCN) channels–which conduct the hyperpolarization-activated current (Ih) and the voltage-insensitive instantaneous current (Iinst), and contribute to diverse physiological functions including learning and memory, cardiac pacemaking, and the sensation of pain–are subject to modification by 1O2. To increase the site specificity of 1O2 generation, we used fluorescein-conjugated cAMP, which specifically binds to HCN channels, or a chimeric channel in which an in-frame 1O2 generator (SOG) protein was fused to the HCN C terminus. Millisecond laser pulses reduced Ih current amplitude, slowed channel deactivation, and enhanced Iinst current. The modification of HCN channel function is a photodynamic process that involves 1O2, as supported by the dependence on dissolved oxygen in solutions, the inhibitory effect by a 1O2 scavenger, and the results with the HCN2-SOG fusion protein. Intriguingly, 1O2 modification of the HCN2 channel is state dependent: laser pulses applied to open channels mainly slow down deactivation and increase Iinst, whereas for the closed channels, 1O2 modification mainly reduced Ih amplitude. We identified a histidine residue (H434 in S6) near the activation gate in the pore critical for 1O2 modulation of HCN function. Alanine replacement of H434 abolished the delay in channel deactivation and the generation of Iinst induced by photodynamic modification. Our study provides new insights into the instantaneous current conducted by HCN channels, showing that modifications to the region close to the intracellular gate underlie the expression of Iinst, and establishes a well-defined model for studying 1O2 modifications at the molecular level.
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Affiliation(s)
- Weihua Gao
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298
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121
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Inducible and titratable silencing of Caenorhabditis elegans neurons in vivo with histamine-gated chloride channels. Proc Natl Acad Sci U S A 2014; 111:2770-5. [PMID: 24550306 DOI: 10.1073/pnas.1400615111] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent progress in neuroscience has been facilitated by tools for neuronal activation and inactivation that are orthogonal to endogenous signaling systems. We describe here a chemical-genetic approach for inducible silencing of Caenorhabditis elegans neurons in intact animals, using the histamine-gated chloride channel HisCl1 from Drosophila and exogenous histamine. Administering histamine to freely moving C. elegans that express HisCl1 transgenes in neurons leads to rapid and potent inhibition of neural activity within minutes, as assessed by behavior, functional calcium imaging, and electrophysiology of neurons expressing HisCl1. C. elegans does not use histamine as an endogenous neurotransmitter, and exogenous histamine has little apparent effect on wild-type C. elegans behavior. HisCl1-histamine silencing of sensory neurons, interneurons, and motor neurons leads to behavioral effects matching their known functions. In addition, the HisCl1-histamine system can be used to titrate the level of neural activity, revealing quantitative relationships between neural activity and behavioral output. We use these methods to dissect escape circuits, define interneurons that regulate locomotion speed (AVA, AIB) and escape-related omega turns (AIB), and demonstrate graded control of reversal length by AVA interneurons and DA/VA motor neurons. The histamine-HisCl1 system is effective, robust, compatible with standard behavioral assays, and easily combined with optogenetic tools, properties that should make it a useful addition to C. elegans neurotechnology.
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Wojtovich AP, Foster TH. Optogenetic control of ROS production. Redox Biol 2014; 2:368-76. [PMID: 24563855 PMCID: PMC3926119 DOI: 10.1016/j.redox.2014.01.019] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/28/2022] Open
Abstract
Reactive Oxygen Species (ROS) are known to cause oxidative damage to DNA, proteins and lipids. In addition, recent evidence suggests that ROS can also initiate signaling cascades that respond to stress and modify specific redox-sensitive moieties as a regulatory mechanism. This suggests that ROS are physiologically-relevant signaling molecules. However, these sensor/effector molecules are not uniformly distributed throughout the cell. Moreover, localized ROS damage may elicit site-specific compensatory measures. Thus, the impact of ROS can be likened to that of calcium, a ubiquitous second messenger, leading to the prediction that their effects are exquisitely dependent upon their location, quantity and even the timing of generation. Despite this prediction, ROS signaling is most commonly intuited through the global administration of chemicals that produce ROS or by ROS quenching through global application of antioxidants. Optogenetics, which uses light to control the activity of genetically-encoded effector proteins, provides a means of circumventing this limitation. Photo-inducible genetically-encoded ROS-generating proteins (RGPs) were originally employed for their phototoxic effects and cell ablation. However, reducing irradiance and/or fluence can achieve sub-lethal levels of ROS that may mediate subtle signaling effects. Hence, transgenic expression of RGPs as fusions to native proteins gives researchers a new tool to exert spatial and temporal control over ROS production. This review will focus on the new frontier defined by the experimental use of RGPs to study ROS signaling. ROS signaling is implicated in numerous cellular functions. Genetically encoded proteins are capable light-induced ROS production. Cell ablation, protein inactivation, and ROS signaling applications are described.
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Affiliation(s)
- Andrew P Wojtovich
- Department of Medicine, University of Rochester Medical Center, Box 711, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Thomas H Foster
- Department of Imaging Sciences, University of Rochester Medical Center, Rochester, NY, USA
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123
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Drepper T, Gensch T, Pohl M. Advanced in vivo applications of blue light photoreceptors as alternative fluorescent proteins. Photochem Photobiol Sci 2014; 12:1125-34. [PMID: 23660639 DOI: 10.1039/c3pp50040c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultimate ambition in cell biology, microbiology and biomedicine is to unravel complex physiological and pathophysiological processes within living organisms. To conquer this challenge, fluorescent proteins (FPs) are used as versatile in vivo reporters and biosensors to study gene regulation as well as the synthesis, localization and function of proteins in living cells. The most widely used FPs are the green fluorescent protein (GFP) and its derivatives and relatives. Their use as in vivo reporter proteins, however, is sometimes restricted by different environmental and cellular factors. Consequently, a whole range of alternative, cofactor-dependent reporter proteins have been developed recently. In this perspective, we summarize the advantages and limitations of the novel class of cyan-green fluorescent flavoproteins in comparison to members of the GFP family and discuss some correlated consequences for the use of FPs as in vivo reporters.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Jülich, 52425 Juelich, Germany.
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List NH, Pimenta FM, Holmegaard L, Jensen RL, Etzerodt M, Schwabe T, Kongsted J, Ogilby PR, Christiansen O. Effect of chromophore encapsulation on linear and nonlinear optical properties: the case of “miniSOG”, a protein-encased flavin. Phys Chem Chem Phys 2014; 16:9950-9. [DOI: 10.1039/c3cp54470b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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125
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Cram EJ. Mechanotransduction in C. elegans morphogenesis and tissue function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 126:281-316. [PMID: 25081623 DOI: 10.1016/b978-0-12-394624-9.00012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mechanobiology is an emerging field that investigates how living cells sense and respond to their physical surroundings. Recent interest in the field has been sparked by the finding that stem cells differentiate along different lineages based on the stiffness of the cell surroundings (Engler et al., 2006), and that metastatic behavior of cancer cells is strongly influenced by the mechanical properties of the surrounding tissue (Kumar and Weaver, 2009). Many questions remain about how cells convert mechanical information, such as viscosity, stiffness of the substrate, or stretch state of the cells, into the biochemical signals that control tissue function. Caenorhabditis elegans researchers are making significant contributions to the understanding of mechanotransduction in vivo. This review summarizes recent insights into the role of mechanical forces in morphogenesis and tissue function. Examples of mechanical regulation across length scales, from the single-celled zygote, to the intercellular coordination that enables cohesive tissue function, to the mechanical influences between tissues, are considered. The power of the C. elegans system as a gene discovery and in vivo quantitative bioimaging platform is enabling an important discoveries in this exciting field.
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Affiliation(s)
- Erin J Cram
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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126
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Zhou K, Stawicki TM, Goncharov A, Jin Y. Position of UNC-13 in the active zone regulates synaptic vesicle release probability and release kinetics. eLife 2013; 2:e01180. [PMID: 24220508 PMCID: PMC3821175 DOI: 10.7554/elife.01180] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The presynaptic active zone proteins UNC-13/Munc13s are essential for synaptic vesicle (SV) exocytosis by directly interacting with SV fusion apparatus. An open question is how their association with active zones, hence their position to Ca2+ entry sites, regulates SV release. The N-termini of major UNC-13/Munc13 isoforms contain a non-calcium binding C2A domain that mediates protein homo- or hetero-meric interactions. Here, we show that the C2A domain of Caenorhabditis elegans UNC-13 regulates release probability of evoked release and its precise active zone localization. Kinetics analysis of SV release supports that the proximity of UNC-13 to Ca2+ entry sites, mediated by the C2A-domain containing N-terminus, is critical for accelerating neurotransmitter release. Additionally, the C2A domain is specifically required for spontaneous release. These data reveal multiple roles of UNC-13 C2A domain, and suggest that spontaneous release and the fast phase of evoked release may involve a common pool of SVs at the active zone. DOI:http://dx.doi.org/10.7554/eLife.01180.001 Neurons are connected to each other by junctions called synapses. When an electrical signal travelling along a neuron arrives at a synapse, it causes the release of bubble-like structures called synaptic vesicles that contain chemicals called neurotransmitters. When released by the vesicles these neurotransmitters bind to receptors on a second neuron and allow the signal to continue on its way through the nervous system. The release of synaptic vesicles from the neuron depends largely on the number of calcium ions that enter this neuron via structures called ion channels, and also on the rate at which they enter. Vesicles are released in one of three ways: they can be released quickly (within a few milliseconds) in response to the influx of calcium ions; they can be released slowly (over a period of tens or hundreds of milliseconds) in response to the influx; or they can be released at random times that are not related to the influx. It is known that the sensitivity of certain calcium sensors near the synapse influences the release of the vesicles. It had been thought that the distance between the “active zone” where the calcium ions enter the neuron and the region where the vesicles reside might also influence rate of release, but the molecular mechanism underlying this hypothesis is poorly understood. Zhou et al. have now shed new light on this question by performing a series of experiments that involved manipulating a protein called UNC-13 – which is known to be involved in the release of vesicles – in neurons from C. elegans, a nematode worm. First it was shown that the precise position of UNC-13 in the active zone depended on a domain within the protein called the C2A domain. Next it was shown that the distance between the UNC-13 protein and the calcium ion channels strongly influences the quick mode of vesicle release. Finally, Zhou et al. showed that the C2A domain also had a significant influence on the spontaneous release of vesicles, which suggests that a common fleet of vesicles might be used for both the quick and the spontaneous modes of vesicle release. Zhou et al. also generated mutant worms that mimicked a neurological disease, epileptic seizure, and showed that eliminating the C2A domain can relieve some of the symptoms associated with the disease. Many neurological diseases are caused by signals not being transmitted properly at synapses, so in addition to providing insights into the basic mechanism underlying synaptic action, these results could also assist with the development of new strategies for managing neurological diseases. DOI:http://dx.doi.org/10.7554/eLife.01180.002
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Affiliation(s)
- Keming Zhou
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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127
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Abstract
In this issue of Neuron, Lin et al. (2013) describe InSynC, an optogenetic approach that utilizes chromophore-assisted light inactivation (CALI) to inactivate presynaptic neurotransmitter release proteins VAMP2 and synaptophysin. InSynC selectively reduces synaptic transmission in illuminated regions in vitro and in vivo.
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Affiliation(s)
- Andreas Reiner
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, 271 Life Sciences Addition, University of California, Berkeley, Berkeley, CA 94720, USA
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128
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Lin JY, Sann SB, Zhou K, Nabavi S, Proulx CD, Malinow R, Jin Y, Tsien RY. Optogenetic inhibition of synaptic release with chromophore-assisted light inactivation (CALI). Neuron 2013; 79:241-53. [PMID: 23889931 DOI: 10.1016/j.neuron.2013.05.022] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 12/18/2022]
Abstract
Optogenetic techniques provide effective ways of manipulating the functions of selected neurons with light. In the current study, we engineered an optogenetic technique that directly inhibits neurotransmitter release. We used a genetically encoded singlet oxygen generator, miniSOG, to conduct chromophore assisted light inactivation (CALI) of synaptic proteins. Fusions of miniSOG to VAMP2 and synaptophysin enabled disruption of presynaptic vesicular release upon illumination with blue light. In cultured neurons and hippocampal organotypic slices, synaptic release was reduced up to 100%. Such inhibition lasted >1 hr and had minimal effects on membrane electrical properties. When miniSOG-VAMP2 was expressed panneuronally in Caenorhabditis elegans, movement of the worms was reduced after illumination, and paralysis was often observed. The movement of the worms recovered overnight. We name this technique Inhibition of Synapses with CALI (InSynC). InSynC is a powerful way to silence genetically specified synapses with light in a spatially and temporally precise manner.
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Affiliation(s)
- John Y Lin
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0647, USA.
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129
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Mironova KE, Proshkina GM, Ryabova AV, Stremovskiy OA, Lukyanov SA, Petrov RV, Deyev SM. Genetically encoded immunophotosensitizer 4D5scFv-miniSOG is a highly selective agent for targeted photokilling of tumor cells in vitro. Am J Cancer Res 2013; 3:831-40. [PMID: 24312153 PMCID: PMC3841334 DOI: 10.7150/thno.6715] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/09/2013] [Indexed: 01/08/2023] Open
Abstract
Tumor-targeted delivery of cytotoxins presents considerable advantages over their passive transport. Chemical conjugation of cytotoxic module to antibody is limited due to insufficient reproducibility of synthesis, and recombinant immunotoxins are aimed to overcome this disadvantage. We obtained genetically encoded immunophotosensitizer 4D5scFv-miniSOG and evaluated its photocytotoxic effect in vitro. A single-chain variable fragment (scFv) of humanized 4D5 antibody was used as a targeting vehicle for selective recognition of the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu) overexpressed in many human carcinomas. As a phototoxic module we used a recently described photoactivated fluorescent flavoprotein miniSOG. We found that recombinant protein 4D5scFv-miniSOG exerts a highly specific photo-induced cytotoxic effect on HER2/neu-positive human breast adenocarcinoma SK-BR-3 cells (IC50= 160 nM). We demonstrated that the 4D5scFv-miniSOG specifically binds to HER2-positive cells and internalizes via receptor-mediated endocytosis. Co-treatment of breast cancer cells with 4D5scFv-miniSOG and Taxol or junction opener protein JO-1 produced remarkable additive effects.
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130
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Rakowski F, Srinivasan J, Sternberg PW, Karbowski J. Synaptic polarity of the interneuron circuit controlling C. elegans locomotion. Front Comput Neurosci 2013; 7:128. [PMID: 24106473 PMCID: PMC3788333 DOI: 10.3389/fncom.2013.00128] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/07/2013] [Indexed: 11/27/2022] Open
Abstract
Caenorhabditis elegans is the only animal for which a detailed neural connectivity diagram has been constructed. However, synaptic polarities in this diagram, and thus, circuit functions are largely unknown. Here, we deciphered the likely polarities of seven pre-motor neurons implicated in the control of worm's locomotion, using a combination of experimental and computational tools. We performed single and multiple laser ablations in the locomotor interneuron circuit and recorded times the worms spent in forward and backward locomotion. We constructed a theoretical model of the locomotor circuit and searched its all possible synaptic polarity combinations and sensory input patterns in order to find the best match to the timing data. The optimal solution is when either all or most of the interneurons are inhibitory and forward interneurons receive the strongest input, which suggests that inhibition governs the dynamics of the locomotor interneuron circuit. From the five pre-motor interneurons, only AVB and AVD are equally likely to be excitatory, i.e., they have probably similar number of inhibitory and excitatory connections to distant targets. The method used here has a general character and thus can be also applied to other neural systems consisting of small functional networks.
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Affiliation(s)
- Franciszek Rakowski
- Interdisciplinary Center for Mathematical and Computational Modeling, University of Warsaw Warsaw, Poland
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131
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Neuropeptide signaling remodels chemosensory circuit composition in Caenorhabditis elegans. Nat Neurosci 2013; 16:1461-7. [PMID: 24013594 PMCID: PMC3786745 DOI: 10.1038/nn.3511] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/05/2013] [Indexed: 11/15/2022]
Abstract
Neural circuits detect environmental changes and drive behavior. The routes of information flow through dense neural networks are dynamic; however, the mechanisms underlying this circuit flexibility are poorly understood. Here, we define a novel, sensory context-dependent and neuropeptide-regulated switch in the composition of a C. elegans salt sensory circuit. The primary salt detectors, ASE sensory neurons, use BLI-4 endoprotease-dependent cleavage to release the insulin-like peptide INS-6 in response to large but not small changes in external salt stimuli. Insulins, signaling through the insulin receptor DAF-2, functionally switch the AWC olfactory sensory neuron into an interneuron in the salt circuit. Animals with disrupted insulin signaling have deficits in salt attraction, suggesting that peptidergic signaling potentiates responses to high salt stimuli, which may promote ion homeostasis. Our results show that sensory context and neuropeptide signaling modify neural networks and suggest general mechanisms for generating flexible behavioral outputs by modulating neural circuit composition.
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132
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A method for selective ablation of neurons in C. elegans using the phototoxic fluorescent protein, KillerRed. Neurosci Lett 2013; 548:261-4. [DOI: 10.1016/j.neulet.2013.05.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 11/15/2022]
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133
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Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior. PLoS One 2013; 8:e69653. [PMID: 23922769 PMCID: PMC3724933 DOI: 10.1371/journal.pone.0069653] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/11/2013] [Indexed: 12/30/2022] Open
Abstract
A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs.
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134
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Ryumina AP, Serebrovskaya EO, Shirmanova MV, Snopova LB, Kuznetsova MM, Turchin IV, Ignatova NI, Klementieva NV, Fradkov AF, Shakhov BE, Zagaynova EV, Lukyanov KA, Lukyanov SA. Flavoprotein miniSOG as a genetically encoded photosensitizer for cancer cells. Biochim Biophys Acta Gen Subj 2013; 1830:5059-67. [PMID: 23876295 DOI: 10.1016/j.bbagen.2013.07.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/20/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Genetically encoded photosensitizers are a promising optogenetic instrument for light-induced production of reactive oxygen species in desired locations within cells in vitro or whole body in vivo. Only two such photosensitizers are currently known, GFP-like protein KillerRed and FMN-binding protein miniSOG. In this work we studied phototoxic effects of miniSOG in cancer cells. METHODS HeLa Kyoto cell lines stably expressing miniSOG in different localizations, namely, plasma membrane, mitochondria or chromatin (fused with histone H2B) were created. Phototoxicity of miniSOG was tested on the cells in vitro and tumor xenografts in vivo. RESULTS Blue light induced pronounced cell death in all three cell lines in a dose-dependent manner. Caspase 3 activation was characteristic of illuminated cells with mitochondria- and chromatin-localized miniSOG, but not with miniSOG in the plasma membrane. In addition, H2B-miniSOG-expressing cells demonstrated light-induced activation of DNA repair machinery, which indicates massive damage of genomic DNA. In contrast to these in vitro data, no detectable phototoxicity was observed on tumor xenografts with HeLa Kyoto cell lines expressing mitochondria- or chromatin-localized miniSOG. CONCLUSIONS miniSOG is an excellent genetically encoded photosensitizer for mammalian cells in vitro, but it is inferior to KillerRed in the HeLa tumor. GENERAL SIGNIFICANCE This is the first study to assess phototoxicity of miniSOG in cancer cells. The results suggest an effective ontogenetic tool and may be of interest for molecular and cell biology and biomedical applications.
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Affiliation(s)
- Alina P Ryumina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
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135
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Pimenta FM, Jensen RL, Breitenbach T, Etzerodt M, Ogilby PR. Oxygen-dependent photochemistry and photophysics of "miniSOG," a protein-encased flavin. Photochem Photobiol 2013; 89:1116-26. [PMID: 23869989 DOI: 10.1111/php.12111] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/09/2013] [Indexed: 01/03/2023]
Abstract
Selected photochemical and photophysical parameters of flavin mononucleotide (FMN) have been examined under conditions in which FMN is (1) solvated in a buffered aqueous solution, and (2) encased in a protein likewise solvated in a buffered aqueous solution. The latter was achieved using the so-called "mini Singlet Oxygen Generator" (miniSOG), an FMN-containing flavoprotein engineered from Arabidopsis thaliana phototropin 2. Although FMN is a reasonably good singlet oxygen photosensitizer in bulk water (ϕΔ = 0.65 ± 0.04), enclosing FMN in this protein facilitates photoinitiated electron-transfer reactions (Type-I chemistry) at the expense of photosensitized singlet oxygen production (Type-II chemistry) and results in a comparatively poor yield of singlet oxygen (ϕΔ = 0.030 ± 0.002). This observation on the effect of the local environment surrounding FMN is supported by a host of spectroscopic and chemical trapping experiments. The results of this study not only elucidate the behavior of miniSOG but also provide useful information for the further development of well-characterized chromophores suitable for use as intracellular sensitizers in mechanistic studies of reactive oxygen species.
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Affiliation(s)
- Frederico M Pimenta
- Department of Chemistry, Center for Oxygen Microscopy and Imaging, Aarhus University, Aarhus, Denmark
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136
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Very long-term memories may be stored in the pattern of holes in the perineuronal net. Proc Natl Acad Sci U S A 2013; 110:12456-61. [PMID: 23832785 DOI: 10.1073/pnas.1310158110] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A hypothesis and the experiments to test it propose that very long-term memories, such as fear conditioning, are stored as the pattern of holes in the perineuronal net (PNN), a specialized ECM that envelops mature neurons and restricts synapse formation. The 3D intertwining of PNN and synapses would be imaged by serial-section EM. Lifetimes of PNN vs. intrasynaptic components would be compared with pulse-chase (15)N labeling in mice and (14)C content in human cadaver brains. Genetically encoded indicators and antineoepitope antibodies should improve spatial and temporal resolution of the in vivo activity of proteases that locally erode PNN. Further techniques suggested include genetic KOs, better pharmacological inhibitors, and a genetically encoded snapshot reporter, which will capture the pattern of activity throughout a large ensemble of neurons at a time precisely defined by the triggering illumination, drive expression of effector genes to mark those cells, and allow selective excitation, inhibition, or ablation to test their functional importance. The snapshot reporter should enable more precise inhibition or potentiation of PNN erosion to compare with behavioral consequences. Finally, biosynthesis of PNN components and proteases would be imaged.
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137
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Feng Z, Zhang W, Xu J, Gauron C, Ducos B, Vriz S, Volovitch M, Jullien L, Weiss S, Bensimon D. Optical control and study of biological processes at the single-cell level in a live organism. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:072601. [PMID: 23764902 PMCID: PMC3736146 DOI: 10.1088/0034-4885/76/7/072601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Living organisms are made of cells that are capable of responding to external signals by modifying their internal state and subsequently their external environment. Revealing and understanding the spatio-temporal dynamics of these complex interaction networks is the subject of a field known as systems biology. To investigate these interactions (a necessary step before understanding or modelling them) one needs to develop means to control or interfere spatially and temporally with these processes and to monitor their response on a fast timescale (< minute) and with single-cell resolution. In 2012, an EMBO workshop on 'single-cell physiology' (organized by some of us) was held in Paris to discuss those issues in the light of recent developments that allow for precise spatio-temporal perturbations and observations. This review will be largely based on the investigations reported there. We will first present a non-exhaustive list of examples of cellular interactions and developmental pathways that could benefit from these new approaches. We will review some of the novel tools that have been developed for the observation of cellular activity and then discuss the recent breakthroughs in optical super-resolution microscopy that allow for optical observations beyond the diffraction limit. We will review the various means to photo-control the activity of biomolecules, which allow for local perturbations of physiological processes. We will end up this review with a report on the current status of optogenetics: the use of photo-sensitive DNA-encoded proteins as sensitive reporters and efficient actuators to perturb and monitor physiological processes.
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Affiliation(s)
- Zhiping Feng
- Department of Molecular, Cellular and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
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138
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Ruiz-González R, Cortajarena AL, Mejias SH, Agut M, Nonell S, Flors C. Singlet oxygen generation by the genetically encoded tag miniSOG. J Am Chem Soc 2013; 135:9564-7. [PMID: 23781844 DOI: 10.1021/ja4020524] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The genetically encodable fluorescent tag miniSOG is expected to revolutionize correlative light- and electron microscopy due to its ability to produce singlet oxygen upon light irradiation. The quantum yield of this process was reported as ΦΔ = 0.47 ± 0.05, as derived from miniSOG's ability to photooxidize the fluorescent probe anthracene dipropionic acid (ADPA). In this report, a significantly smaller value of ΦΔ = 0.03 ± 0.01 is obtained by two methods: direct measurement of its phosphorescence at 1275 nm and chemical trapping using uric acid as an alternative probe. We present insight into the photochemistry of miniSOG and ascertain the reasons for the discrepancy in ΦΔ values. We find that miniSOG oxidizes ADPA by both singlet oxygen-dependent and -independent processes. We also find that cumulative irradiation of miniSOG increases its ΦΔ value ~10-fold due to a photoinduced transformation of the protein. This may be the reason why miniSOG outperforms other fluorescent proteins reported to date as singlet oxygen generators.
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Affiliation(s)
- Rubén Ruiz-González
- Institut Quimic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017, Barcelona, Spain
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139
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Hyperactivation of B-type motor neurons results in aberrant synchrony of the Caenorhabditis elegans motor circuit. J Neurosci 2013; 33:5319-25. [PMID: 23516296 DOI: 10.1523/jneurosci.4017-12.2013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Excitatory acetylcholine motor neurons drive Caenorhabditis elegans locomotion. Coordinating the activation states of the backward-driving A and forward-driving B class motor neurons is critical for generating sinusoidal and directional locomotion. Here, we show by in vivo calcium imaging that expression of a hyperactive, somatodendritic ionotropic acetylcholine receptor ACR-2(gf) in A and B class motor neurons induces aberrant synchronous activity in both ventral- and dorsal-innervating B and A class motor neurons. Expression of ACR-2(gf) in either ventral- or dorsal-innervating B neurons is sufficient for triggering the aberrant synchrony that results in arrhythmic convulsions. Silencing of AVB, the premotor interneurons that innervate B motor neurons suppresses ACR-2(gf)-dependent convulsion; activating AVB by channelrhodopsin induces the onset of convulsion. These results support that the activity state of B motor neurons plays an instructive role for the coordination of motor circuit.
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140
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Stawicki TM, Takayanagi-Kiya S, Zhou K, Jin Y. Neuropeptides function in a homeostatic manner to modulate excitation-inhibition imbalance in C. elegans. PLoS Genet 2013; 9:e1003472. [PMID: 23658528 PMCID: PMC3642046 DOI: 10.1371/journal.pgen.1003472] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
Neuropeptides play crucial roles in modulating neuronal networks, including changing intrinsic properties of neurons and synaptic efficacy. We previously reported a Caenorhabditis elegans mutant, acr-2(gf), that displays spontaneous convulsions as the result of a gain-of-function mutation in a neuronal nicotinic acetylcholine receptor subunit. The ACR-2 channel is expressed in the cholinergic motor neurons, and acr-2(gf) causes cholinergic overexcitation accompanied by reduced GABAergic inhibition in the locomotor circuit. Here we show that neuropeptides play a homeostatic role that compensates for this excitation-inhibition imbalance in the locomotor circuit. Loss of function in genes required for neuropeptide processing or release of dense core vesicles specifically modulate the convulsion frequency of acr-2(gf). The proprotein convertase EGL-3 is required in the cholinergic motor neurons to restrain convulsions. Electrophysiological recordings of neuromuscular junctions show that loss of egl-3 in acr-2(gf) causes a further reduction of GABAergic inhibition. We identify two neuropeptide encoding genes, flp-1 and flp-18, that together counteract the excitation-inhibition imbalance in acr-2(gf) mutants. We further find that acr-2(gf) causes an increased expression of flp-18 in the ventral cord cholinergic motor neurons and that overexpression of flp-18 reduces the convulsion of acr-2(gf) mutants. The effects of these peptides are in part mediated by two G-protein coupled receptors, NPR-1 and NPR-5. Our data suggest that the chronic overexcitation of the cholinergic motor neurons imposed by acr-2(gf) leads to an increased production of FMRFamide neuropeptides, which act to decrease the activity level of the locomotor circuit, thereby homeostatically modulating the excitation and inhibition imbalance. Imbalanced neuronal circuit activity is considered a major underlying cause in many neurological disorders, such as epilepsy and autism. Neuropeptides are small polypeptides that are released from neurons. They are widely known to provide neuromodulatory functions and have diverse roles in the nervous system. By investigating a C. elegans mutant that exhibits convulsions as the result of an imbalanced excitation and inhibition in the locomotor circuit, we have identified a homeostatic mechanism involving two distinct neuropeptide genes. We find that the expression of the neuropeptides is up-regulated in response to over-excitation and that, in turn, they act to increase inhibitory transmission. While current treatment strategies for epilepsy have focused on targeting fast synaptic transmission, this work supports the general notion that manipulating slow neuropeptide neurotransmission can strongly influence neural excitation and inhibition imbalance.
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Affiliation(s)
- Tamara M. Stawicki
- Division of Biological Sciences, Section of Neurobiology, University of California San Diego, La Jolla, California, United States of America
| | - Seika Takayanagi-Kiya
- Division of Biological Sciences, Section of Neurobiology, University of California San Diego, La Jolla, California, United States of America
| | - Keming Zhou
- Division of Biological Sciences, Section of Neurobiology, University of California San Diego, La Jolla, California, United States of America
| | - Yishi Jin
- Division of Biological Sciences, Section of Neurobiology, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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141
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Wang Z, Wu L, Cheng X, Liu S, Li B, Li H, Kang F, Wang J, Xia H, Ping C, Nassal M, Sun D. Replication-competent infectious hepatitis B virus vectors carrying substantially sized transgenes by redesigned viral polymerase translation. PLoS One 2013; 8:e60306. [PMID: 23589756 PMCID: PMC3615001 DOI: 10.1371/journal.pone.0060306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/25/2013] [Indexed: 12/13/2022] Open
Abstract
Viral vectors are engineered virus variants able to deliver nonviral genetic information into cells, usually by the same routes as the parental viruses. For several virus families, replication-competent vectors carrying reporter genes have become invaluable tools for easy and quantitative monitoring of replication and infection, and thus also for identifying antivirals and virus susceptible cells. For hepatitis B virus (HBV), a small enveloped DNA virus causing B-type hepatitis, such vectors are not available because insertions into its tiny 3.2 kb genome almost inevitably affect essential replication elements. HBV replicates by reverse transcription of the pregenomic (pg) RNA which is also required as bicistronic mRNA for the capsid (core) protein and the reverse transcriptase (Pol); their open reading frames (ORFs) overlap by some 150 basepairs. Translation of the downstream Pol ORF does not involve a conventional internal ribosome entry site (IRES). We reasoned that duplicating the overlap region and providing artificial IRES control for translation of both Pol and an in-between inserted transgene might yield a functional tricistronic pgRNA, without interfering with envelope protein expression. As IRESs we used a 22 nucleotide element termed Rbm3 IRES to minimize genome size increase. Model plasmids confirmed its activity even in tricistronic arrangements. Analogous plasmids for complete HBV genomes carrying 399 bp and 720 bp transgenes for blasticidin resistance (BsdR) and humanized Renilla green fluorescent protein (hrGFP) produced core and envelope proteins like wild-type HBV; while the hrGFP vector replicated poorly, the BsdR vector generated around 40% as much replicative DNA as wild-type HBV. Both vectors, however, formed enveloped virions which were infectious for HBV-susceptible HepaRG cells. Because numerous reporter and effector genes with sizes of around 500 bp or less are available, the new HBV vectors should become highly useful tools to better understand, and combat, this important pathogen.
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Affiliation(s)
- Zihua Wang
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
- The Third Military Medical University, Chongqing, PR China
| | - Li Wu
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Xin Cheng
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Shizhu Liu
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Baosheng Li
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Haijun Li
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Fubiao Kang
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Junping Wang
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Huan Xia
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Caiyan Ping
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Freiburg, Germany
- * E-mail: (DS); (MN)
| | - Dianxing Sun
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, PR China
- * E-mail: (DS); (MN)
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142
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Using C. elegans to Decipher the Cellular and Molecular Mechanisms Underlying Neurodevelopmental Disorders. Mol Neurobiol 2013; 48:465-89. [DOI: 10.1007/s12035-013-8434-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
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143
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Abstract
This protocol describes a method for light-inducible cell ablation in live worms. miniSOG (mini Singlet Oxygen Generator) generates singlet oxygen upon blue light illumination (Shu et al., 2011). Mitochondrially membrane targeted miniSOG (the first 55 a. a. of C. e. tomm-20 fused at the N'-terminus of miniSOG, termed as mito-miniSOG in the following) is transgenically expressed in specific cells/tissues (Qi et al., 2012). Groups of transgenic animals are illuminated under open field fluorescence light on a compound microscope or LED light setup for photo-ablation.
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Affiliation(s)
- Yingchuan Qi
- Division of Biological Sciences, Neurobiology Section, University of California, San Diego, CA, USA
| | - Suhong Xu
- Division of Biological Sciences, Neurobiology Section, University of California, San Diego, CA, USA
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144
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Matsunaga S, Katagiri Y, Nagashima Y, Sugiyama T, Hasegawa J, Hayashi K, Sakamoto T. New insights into the dynamics of plant cell nuclei and chromosomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:253-301. [PMID: 23890384 DOI: 10.1016/b978-0-12-407695-2.00006-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The plant lamin-like protein NMCP/AtLINC and orthologues of the SUN-KASH complex across the nuclear envelope (NE) show the universality of nuclear structure in eukaryotes. However, depletion of components in the connection complex of the NE in plants does not induce severe defects, unlike in animals. Appearance of the Rabl configuration is not dependent on genome size in plant species. Topoisomerase II and condensin II are not essential for plant chromosome condensation. Plant endoreduplication shares several common characteristics with animals, including involvement of cyclin-dependent kinases and E2F transcription factors. Recent finding regarding endomitosis regulator GIG1 shed light on the suppression mechanism of endomitosis in plants. The robustness of plants, compared with animals, is reflected in their genome redundancy. Spatiotemporal functional analyses using chromophore-assisted light inactivation, super-resolution microscopy, and 4D (3D plus time) imaging will reveal new insights into plant nuclear and chromosomal dynamics.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
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145
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Abstract
Chromophore-assisted laser inactivation (CALI) is a technique that uses photochemically-generated reactive oxygen species to acutely inactivate target proteins in living cells. Neural development includes highly dynamic cellular processes such as asymmetric cell division, migration, axon and dendrite outgrowth and synaptogenesis. Although many key molecules of neural development have been identified since the past decades, their spatiotemporal contributions to these cellular events are not well understood. CALI provides an appealing tool for elucidating the precise functions of these molecules during neural development. In this review, we summarize the principles of CALI, a recent microscopic setup to perform CALI experiments, and the application of CALI to the study of growth-cone motility and neuroblast asymmetric division.
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Affiliation(s)
- Wei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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146
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Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol 2012; 30:1143-8. [PMID: 23086203 PMCID: PMC3699407 DOI: 10.1038/nbt.2375] [Citation(s) in RCA: 491] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/29/2012] [Indexed: 11/09/2022]
Abstract
Electron microscopy (EM) is the standard method for imaging cellular structures with nanometer resolution, but existing genetic tags are inactive in most cellular compartments or require light and can be difficult to use. Here we report the development of 'APEX', a genetically encodable EM tag that is active in all cellular compartments and does not require light. APEX is a monomeric 28-kDa peroxidase that withstands strong EM fixation to give excellent ultrastructural preservation. We demonstrate the utility of APEX for high-resolution EM imaging of a variety of mammalian organelles and specific proteins using a simple and robust labeling procedure. We also fused APEX to the N or C terminus of the mitochondrial calcium uniporter (MCU), a recently identified channel whose topology is disputed. These fusions give EM contrast exclusively in the mitochondrial matrix, suggesting that both the N and C termini of MCU face the matrix. Because APEX staining is not dependent on light activation, APEX should make EM imaging of any cellular protein straightforward, regardless of the size or thickness of the specimen.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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147
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Meinertzhagen IA, Lee CH. The genetic analysis of functional connectomics in Drosophila. ADVANCES IN GENETICS 2012; 80:99-151. [PMID: 23084874 DOI: 10.1016/b978-0-12-404742-6.00003-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fly and vertebrate nervous systems share many organizational features, such as layers, columns and glomeruli, and utilize similar synaptic components, such as ion channels and receptors. Both also exhibit similar network features. Recent technological advances, especially in electron microscopy, now allow us to determine synaptic circuits and identify pathways cell-by-cell, as part of the fly's connectome. Genetic tools provide the means to identify synaptic components, as well as to record and manipulate neuronal activity, adding function to the connectome. This review discusses technical advances in these emerging areas of functional connectomics, offering prognoses in each and identifying the challenges in bridging structural connectomics to molecular biology and synaptic physiology, thereby determining fundamental mechanisms of neural computation that underlie behavior.
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Affiliation(s)
- Ian A Meinertzhagen
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2.
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