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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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2
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Nienhaus K, Nienhaus GU. Fluorescent proteins of the EosFP clade: intriguing marker tools with multiple photoactivation modes for advanced microscopy. RSC Chem Biol 2021; 2:796-814. [PMID: 34458811 PMCID: PMC8341165 DOI: 10.1039/d1cb00014d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/27/2021] [Indexed: 02/04/2023] Open
Abstract
Optical fluorescence microscopy has taken center stage in the exploration of biological structure and dynamics, especially on live specimens, and super-resolution imaging methods continue to deliver exciting new insights into the molecular foundations of life. Progress in the field, however, crucially hinges on advances in fluorescent marker technology. Among these, fluorescent proteins (FPs) of the GFP family are advantageous because they are genetically encodable, so that live cells, tissues or organisms can produce these markers all by themselves. A subclass of them, photoactivatable FPs, allow for control of their fluorescence emission by light irradiation, enabling pulse-chase imaging and super-resolution microscopy. In this review, we discuss FP variants of the EosFP clade that have been optimized by amino acid sequence modification to serve as markers for various imaging techniques. In general, two different modes of photoactivation are found, reversible photoswitching between a fluorescent and a nonfluorescent state and irreversible green-to red photoconversion. First, we describe their basic structural and optical properties. We then summarize recent research aimed at elucidating the photochemical processes underlying photoactivation. Finally, we briefly introduce various advanced imaging methods facilitated by specific EosFP variants, and show some exciting sample applications.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology 76049 Karlsruhe Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology 76049 Karlsruhe Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology 76021 Karlsruhe Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology 76021 Karlsruhe Germany
- Department of Physics, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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Gao X, Fischer R, Takeshita N. Application of PALM Superresolution Microscopy to the Analysis of Microtubule-Organizing Centers (MTOCs) in Aspergillus nidulans. Methods Mol Biol 2021; 2329:277-289. [PMID: 34085230 DOI: 10.1007/978-1-0716-1538-6_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Photoactivated localization microscopy (PALM), one of the super resolution microscopy methods improving the resolution limit to 20 nm, allows the detection of single molecules in complex protein structures in living cells. Microtubule-organizing centres (MTOCs) are large, multisubunit protein complexes, required for microtubule polymerization. The prominent MTOC in higher eukaryotes is the centrosome, and its functional ortholog in fungi is the spindle-pole body (SPB). There is ample evidence that besides centrosomes other MTOCs are important in eukaryotic cells. The filamentous ascomycetous fungus Aspergillus nidulans is a model organism, with hyphae consisting of multinucleate compartments separated by septa. In A. nidulans, besides the SPBs, a second type of MTOCs was discovered at septa (called septal MTOCs, sMTOC). All the MTOC components appear as big dots at SPBs and sMTOCs when tagged with a fluorescent protein and observed with conventional fluorescence microscopy due to the diffraction barrier. In this chapter, we describe the application of PALM in quantifying the numbers of individual proteins at both MTOC sites in A. nidulans and provide evidence that the composition of MTOCs is highly dynamic and dramatically changes during the cell cycle.
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Affiliation(s)
- Xiaolei Gao
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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Takeshita N. Control of Actin and Calcium for Chitin Synthase Delivery to the Hyphal Tip of Aspergillus. Curr Top Microbiol Immunol 2019; 425:113-129. [PMID: 31974757 DOI: 10.1007/82_2019_193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Filamentous fungi are covered by a cell wall consisting mainly of chitin and glucan. The synthesis of chitin, a β-1,4-linked homopolymer of N-acetylglucosamine, is essential for hyphal morphogenesis. Fungal chitin synthases are integral membrane proteins that have been classified into seven classes. ChsB, a class III chitin synthase, is known to play a key role in hyphal tip growth and has been used here as a model to understand the cell biology of cell wall biosynthesis in Aspergillus nidulans. Chitin synthases are transported on secretory vesicles to the plasma membrane for new cell wall synthesis. Super-resolution localization imaging as a powerful biophysical approach indicated dynamics of the Spitzenkörper where spatiotemporally regulated exocytosis and cell extension, whereas high-speed pulse-chase imaging has revealed ChsB transport mechanism mediated by kinesin-1 and myosin-5. In addition, live imaging analysis showed correlations among intracellular Ca2+ levels, actin assembly, and exocytosis in growing hyphal tips. This suggests that pulsed Ca2+ influxes coordinate the temporal control of actin assembly and exocytosis, which results in stepwise cell extension. It is getting clear that turgor pressure and cell wall pressure are involved in the activation of Ca2+ channels for Ca2+ oscillation and cell extension. Here the cell wall synthesis and tip growth meet again.
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Affiliation(s)
- Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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Zhou L, Evangelinos M, Wernet V, Eckert AF, Ishitsuka Y, Fischer R, Nienhaus GU, Takeshita N. Superresolution and pulse-chase imaging reveal the role of vesicle transport in polar growth of fungal cells. SCIENCE ADVANCES 2018; 4:e1701798. [PMID: 29387789 PMCID: PMC5787382 DOI: 10.1126/sciadv.1701798] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Polarized growth of filamentous fungi requires continuous transport of biomolecules to the hyphal tip. To this end, construction materials are packaged in vesicles and transported by motor proteins along microtubules and actin filaments. We have studied these processes with quantitative superresolution localization microscopy of live Aspergillus nidulans cells expressing the photoconvertible protein mEosFPthermo fused to the chitin synthase ChsB. ChsB is mainly located at the Spitzenkörper near the hyphal tip and produces chitin, a key component of the cell wall. We have visualized the pulsatory dynamics of the Spitzenkörper, reflecting vesicle accumulation before exocytosis and their subsequent fusion with the apical plasma membrane. Furthermore, high-speed pulse-chase imaging after photoconversion of mEosFPthermo in a tightly focused spot revealed that ChsB is transported with two different speeds from the cell body to the hyphal tip and vice versa. Comparative analysis using motor protein deletion mutants allowed us to assign the fast movements (7 to 10 μm s-1) to transport of secretory vesicles by kinesin-1, and the slower ones (2 to 7 μm s-1) to transport by kinesin-3 on early endosomes. Our results show how motor proteins ensure the supply of vesicles to the hyphal tip, where temporally regulated exocytosis results in stepwise tip extension.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Nanotechnology, KIT, Karlsruhe, Germany
| | - Minoas Evangelinos
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
- Faculty of Biology, University of Athens, Athens, Greece
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Gosselies, Belgium
| | - Valentin Wernet
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
| | - Antonia F. Eckert
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Nanotechnology, KIT, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute of Toxicology and Genetics, KIT, Eggenstein-Leopoldshafen, Germany
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Wachter RM. Photoconvertible Fluorescent Proteins and the Role of Dynamics in Protein Evolution. Int J Mol Sci 2017; 18:ijms18081792. [PMID: 32962314 PMCID: PMC5578180 DOI: 10.3390/ijms18081792] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/11/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022] Open
Abstract
Photoconvertible fluorescent proteins (pcFPs) constitute a large group of fluorescent proteins related to green fluorescent protein (GFP) that, when exposed to blue light, bear the capability of irreversibly switching their emission color from green to red. Not surprisingly, this fascinating class of FPs has found numerous applications, in particular for the visualization of biological processes. A detailed understanding of the photoconversion mechanism appears indispensable in the design of improved variants for applications such as super-resolution imaging. In this article, recent work is reviewed that involves using pcFPs as a model system for studying protein dynamics. Evidence has been provided that the evolution of pcFPs from a green ancestor involved the natural selection for altered dynamical features of the beta-barrel fold. It appears that photoconversion may be the outcome of a long-range positional shift of a fold-anchoring region. A relatively stiff, rigid element appears to have migrated away from the chromophore-bearing section to the opposite edge of the barrel, thereby endowing pcFPs with increased active site flexibility while keeping the fold intact. In this way, the stage was set for the coupling of light absorption with subsequent chemical transformations. The emerging mechanistic model suggests that highly specific dynamic motions are linked to key chemical steps, preparing the system for a concerted deprotonation and β-elimination reaction that enlarges the chromophore's π-conjugation to generate red color.
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Affiliation(s)
- Rebekka M Wachter
- School of Molecular Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ 85287, USA
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Sezgin E. Super-resolution optical microscopy for studying membrane structure and dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:273001. [PMID: 28481213 PMCID: PMC5952331 DOI: 10.1088/1361-648x/aa7185] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, United Kingdom
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Mohr MA, Kobitski AY, Sabater LR, Nienhaus K, Obara CJ, Lippincott-Schwartz J, Nienhaus GU, Pantazis P. Rational Engineering of Photoconvertible Fluorescent Proteins for Dual-Color Fluorescence Nanoscopy Enabled by a Triplet-State Mechanism of Primed Conversion. Angew Chem Int Ed Engl 2017; 56:11628-11633. [DOI: 10.1002/anie.201706121] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Manuel Alexander Mohr
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
- Howard Hughes Medical Institute; Janelia Research Campus; Ashburn VA 20147 USA
| | - Andrei Yu. Kobitski
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
| | - Lluc Rullan Sabater
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
| | - Karin Nienhaus
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
| | | | | | - Gerd Ulrich Nienhaus
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
- Institute of Toxicology and Genetics; Karlsruhe Institute of Technology (KIT); 76344 Eggenstein-Leopoldshafen Germany
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); 76344 Eggenstein-Leopoldshafen Germany
- Department of Physics; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Periklis Pantazis
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
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9
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Mohr MA, Kobitski AY, Sabater LR, Nienhaus K, Obara CJ, Lippincott-Schwartz J, Nienhaus GU, Pantazis P. Rational Engineering of Photoconvertible Fluorescent Proteins for Dual-Color Fluorescence Nanoscopy Enabled by a Triplet-State Mechanism of Primed Conversion. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Manuel Alexander Mohr
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
- Howard Hughes Medical Institute; Janelia Research Campus; Ashburn VA 20147 USA
| | - Andrei Yu. Kobitski
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
| | - Lluc Rullan Sabater
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
| | - Karin Nienhaus
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
| | | | | | - Gerd Ulrich Nienhaus
- Institute of Applied Physics; Karlsruhe Institute of Technology (KIT); 76131 Karlsruhe Germany
- Institute of Toxicology and Genetics; Karlsruhe Institute of Technology (KIT); 76344 Eggenstein-Leopoldshafen Germany
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); 76344 Eggenstein-Leopoldshafen Germany
- Department of Physics; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Periklis Pantazis
- Department for Biosystems Science and Engineering (D-BSSE); Eidgenössische Technische Hochschule (ETH) Zurich; 4058 Basel Switzerland
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10
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Pulses of Ca 2+ coordinate actin assembly and exocytosis for stepwise cell extension. Proc Natl Acad Sci U S A 2017; 114:5701-5706. [PMID: 28507141 DOI: 10.1073/pnas.1700204114] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many eukaryotic cells grow by extending their cell periphery in pulses. The molecular mechanisms underlying this process are not yet fully understood. Here we present a comprehensive model of stepwise cell extension by using the unique tip growth system of filamentous fungi. Live-cell imaging analysis, including superresolution microscopy, revealed that the fungus Aspergillus nidulans extends the hyphal tip in an oscillatory manner. The amount of F-actin and secretory vesicles (SV) accumulating at the hyphal tip oscillated with a positive temporal correlation, whereas vesicle amounts were negatively correlated to the growth rate. The intracellular Ca2+ level also pulsed with a positive temporal correlation to the amount of F-actin and SV at the hyphal tip. Two Ca2+ channels, MidA and CchA, were needed for proper tip growth and the oscillations of actin polymerization, exocytosis, and the growth rate. The data indicate a model in which transient Ca2+ pluses cause depolymerization of F-actin at the cortex and promote SV fusion with the plasma membrane, thereby extending the cell tip. Over time, Ca2+ diffuses away and F-actin and SV accumulate again at the hyphal tip. Our data provide evidence that temporally controlled actin polymerization and exocytosis are coordinated by pulsed Ca2+ influx, resulting in stepwise cell extension.
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Nienhaus K, Nienhaus GU. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:443001. [PMID: 27604321 DOI: 10.1088/0953-8984/28/44/443001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Straße 1, 76131 Karlsruhe, Germany
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12
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Nienhaus K, Nienhaus GU. Photoswitchable Fluorescent Proteins: Do Not Always Look on the Bright Side. ACS NANO 2016; 10:9104-9108. [PMID: 27723301 DOI: 10.1021/acsnano.6b06298] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoactivatable fluorescent proteins (FPs) have become essential markers for nanoscopy on live specimens. In this issue of ACS Nano, Wang et al. present a reversibly photoswitching FP, GMars-Q, which they promote as an advanced marker for RESOLFT imaging because of its low residual intensity in the off state and low switching fatigue. Here, we explain the observed peculiar photobleaching behavior of GMars-Q by a mechanism that involves efficient shelving of proteins in dark states, resulting in low switching fatigue and low residual off intensity. There is a continuing demand for novel FP markers with properties optimized for specific imaging techniques. Endeavors to engineer such proteins can greatly benefit from increased efforts to acquire deeper mechanistic understanding of their photophysics and photochemistry.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology , 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Abstract
Super resolution imaging is becoming an increasingly important tool in the arsenal of methods available to cell biologists. In recognition of its potential, the Nobel Prize for chemistry was awarded to three investigators involved in the development of super resolution imaging methods in 2014. The availability of commercial instruments for super resolution imaging has further spurred the development of new methods and reagents designed to take advantage of super resolution techniques. Super resolution offers the advantages traditionally associated with light microscopy, including the use of gentle fixation and specimen preparation methods, the ability to visualize multiple elements within a single specimen, and the potential to visualize dynamic changes in living specimens over time. However, imaging of living cells over time is difficult and super resolution imaging is computationally demanding. In this review, we discuss the advantages/disadvantages of different super resolution systems for imaging fixed live specimens, with particular regard to cytoskeleton structures.
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Affiliation(s)
- Eric A Shelden
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Zachary T Colburn
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jonathan C R Jones
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
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14
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Nienhaus K, Nienhaus GU. Where Do We Stand with Super-Resolution Optical Microscopy? J Mol Biol 2016; 428:308-322. [DOI: 10.1016/j.jmb.2015.12.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
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15
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Ishitsuka Y, Savage N, Li Y, Bergs A, Grün N, Kohler D, Donnelly R, Nienhaus GU, Fischer R, Takeshita N. Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growth. SCIENCE ADVANCES 2015; 1:e1500947. [PMID: 26665168 PMCID: PMC4673053 DOI: 10.1126/sciadv.1500947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/14/2015] [Indexed: 05/02/2023]
Abstract
Polar (directional) cell growth, a key cellular mechanism shared among a wide range of species, relies on targeted insertion of new material at specific locations of the plasma membrane. How these cell polarity sites are stably maintained during massive membrane insertion has remained elusive. Conventional live-cell optical microscopy fails to visualize polarity site formation in the crowded cell membrane environment because of its limited resolution. We have used advanced live-cell imaging techniques to directly observe the localization, assembly, and disassembly processes of cell polarity sites with high spatiotemporal resolution in a rapidly growing filamentous fungus, Aspergillus nidulans. We show that the membrane-associated polarity site marker TeaR is transported on microtubules along with secretory vesicles and forms a protein cluster at that point of the apical membrane where the plus end of the microtubule touches. There, a small patch of membrane is added through exocytosis, and the TeaR cluster gets quickly dispersed over the membrane. There is an incessant disassembly and reassembly of polarity sites at the growth zone, and each new polarity site locus is slightly offset from preceding ones. On the basis of our imaging results and computational modeling, we propose a transient polarity model that explains how cell polarity is stably maintained during highly active directional growth.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Natasha Savage
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yiming Li
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Anna Bergs
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Nathalie Grün
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Daria Kohler
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Rebecca Donnelly
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute of Nanotechnology, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
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Manck R, Ishitsuka Y, Herrero S, Takeshita N, Nienhaus GU, Fischer R. Genetic evidence for a microtubule-capture mechanism during polarised growth of Aspergillus nidulans. J Cell Sci 2015; 128:3569-82. [PMID: 26272919 DOI: 10.1242/jcs.169094] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 08/10/2015] [Indexed: 12/13/2022] Open
Abstract
The cellular switch from symmetry to polarity in eukaryotes depends on the microtubule (MT) and actin cytoskeletons. In fungi such as Schizosaccharomyces pombe or Aspergillus nidulans, the MT cytoskeleton determines the sites of actin polymerization through cortical cell-end marker proteins. Here we describe A. nidulans MT guidance protein A (MigA) as the first ortholog of the karyogamy protein Kar9 from Saccharomyces cerevisiae in filamentous fungi. A. nidulans MigA interacts with the cortical ApsA protein and is involved in spindle positioning during mitosis. MigA is also associated with septal and nuclear MT organizing centers (MTOCs). Super-resolution photoactivated localization microscopy (PALM) analyses revealed that MigA is recruited to assembling and retracting MT plus ends in an EbA-dependent manner. MigA is required for MT convergence in hyphal tips and plays a role in correct localization of the cell-end markers TeaA and TeaR. In addition, MigA interacts with a class-V myosin, suggesting that an active mechanism exists to capture MTs and to pull the ends along actin filaments. Hence, the organization of MTs and actin depend on each other, and positive feedback loops ensure robust polar growth.
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Affiliation(s)
- Raphael Manck
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
| | - Yuji Ishitsuka
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Physics and Center for Functional Nanostructures, Karlsruhe 76131, Germany
| | - Saturnino Herrero
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
| | - Norio Takeshita
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany University of Tsukuba, Faculty of Life and Environmental Sciences, Tsukuba, Ibaraki 305-8572, Japan
| | - G Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Physics and Center for Functional Nanostructures, Karlsruhe 76131, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
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Krenek P, Samajova O, Luptovciak I, Doskocilova A, Komis G, Samaj J. Transient plant transformation mediated by Agrobacterium tumefaciens: Principles, methods and applications. Biotechnol Adv 2015; 33:1024-42. [PMID: 25819757 DOI: 10.1016/j.biotechadv.2015.03.012] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 03/05/2015] [Accepted: 03/19/2015] [Indexed: 12/20/2022]
Abstract
Agrobacterium tumefaciens is widely used as a versatile tool for development of stably transformed model plants and crops. However, the development of Agrobacterium based transient plant transformation methods attracted substantial attention in recent years. Transient transformation methods offer several applications advancing stable transformations such as rapid and scalable recombinant protein production and in planta functional genomics studies. Herein, we highlight Agrobacterium and plant genetics factors affecting transfer of T-DNA from Agrobacterium into the plant cell nucleus and subsequent transient transgene expression. We also review recent methods concerning Agrobacterium mediated transient transformation of model plants and crops and outline key physical, physiological and genetic factors leading to their successful establishment. Of interest are especially Agrobacterium based reverse genetics studies in economically important crops relying on use of RNA interference (RNAi) or virus-induced gene silencing (VIGS) technology. The applications of Agrobacterium based transient plant transformation technology in biotech industry are presented in thorough detail. These involve production of recombinant proteins (plantibodies, vaccines and therapeutics) and effectoromics-assisted breeding of late blight resistance in potato. In addition, we also discuss biotechnological potential of recombinant GFP technology and present own examples of successful Agrobacterium mediated transient plant transformations.
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Affiliation(s)
- Pavel Krenek
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Olga Samajova
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Ivan Luptovciak
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Anna Doskocilova
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Jozef Samaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
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18
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Duwé S, Moeyaert B, Dedecker P. Diffraction-unlimited fluorescence microscopy of living biological samples using pcSOFI. ACTA ACUST UNITED AC 2015; 7:27-41. [PMID: 25727061 DOI: 10.1002/9780470559277.ch140025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction-unlimited fluorescence microscopy to resolve them. Because of the vast range of different processes that can be studied, sub-diffraction imaging should work efficiently under many different conditions. Photochromic stochastic optical fluctuation imaging (pcSOFI) is a recent addition to the field of diffraction-unlimited fluorescence microscopy. This robust and versatile method employs a statistical analysis of random fluctuations in the emission of single labels, in this case reversibly switchable fluorescent proteins (RSFPs), to retrieve super-resolution information. Added to the resolution enhancement, pcSOFI also offers contrast enhancement and background reduction in a practical and convenient way. Here, we describe the necessary steps to obtain diffraction-unlimited images, including multicolor and three-dimensional imaging, and highlight the advantages of pcSOFI together with the circumstances under which pcSOFI can be favorably applied.
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Affiliation(s)
- Sam Duwé
- Department of Chemistry, University of Leuven, Heverlee, Belgium
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19
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Hense A, Nienhaus K, Nienhaus GU. Exploring color tuning strategies in red fluorescent proteins. Photochem Photobiol Sci 2015; 14:200-12. [PMID: 25597270 DOI: 10.1039/c4pp00212a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/31/2014] [Indexed: 01/01/2023]
Abstract
Red-emitting fluorescent proteins (RFPs) with fluorescence emission above 600 nm are advantageous for cell and tissue imaging applications for various reasons. Fluorescence from an RFP is well separated from cellular autofluorescence, which is in the green region of the spectrum, and red light is scattered less, which allows thicker specimens to be imaged. Moreover, the phototoxic response of cells is lower for red than blue or green light exposure. Further red-shifted FP variants can be obtained by genetic modifications causing an extension of the conjugated π-electron system of the chromophore, or by placing amino acids near the chromophore that stabilize its excited state or destabilize its ground state. We have selected the tetrameric RFP eqFP611 from Entacmaea quadricolor as a lead structure and discuss several rational design trials to generate RFP variants with improved photochemical properties.
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Affiliation(s)
- Anika Hense
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany.
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20
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Abstract
Endosomes are multipurpose membranous carriers important for endocytosis and secretion. During membrane trafficking, endosomes transport lipids, proteins, and even RNAs. In highly polarized cells such as fungal hyphae, they shuttle bidirectionally along microtubules mediated by molecular motors like kinesins and dynein. For in vivo studies of these highly dynamic protein/membrane complexes, advanced fluorescence microscopy is instrumental. In this chapter, we describe live cell imaging of endosomes in two distantly related fungal model systems, the basidiomycete Ustilago maydis and the ascomycete Aspergillus nidulans. We provide insights into live cell imaging of dynamic endosomal proteins and RNA, dual-color detection for colocalization studies, as well as fluorescence recovery after photobleaching (FRAP) for quantification and photo-activated localization microscopy (PALM) for super-resolution. These methods described in two well-studied fungal model systems are applicable to a broad range of other organisms.
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21
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Fluorescence-Based Methods for the Study of Protein Localization, Interaction, and Dynamics in Filamentous Fungi. Fungal Biol 2015. [DOI: 10.1007/978-3-319-22437-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Nienhaus K, Nienhaus GU. Fluorescent proteins for live-cell imaging with super-resolution. Chem Soc Rev 2014; 43:1088-106. [PMID: 24056711 DOI: 10.1039/c3cs60171d] [Citation(s) in RCA: 259] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent proteins (FPs) from the GFP family have become indispensable as marker tools for imaging live cells, tissues and entire organisms. A wide variety of these proteins have been isolated from natural sources and engineered to optimize their properties as genetically encoded markers. Here we review recent developments in this field. A special focus is placed on photoactivatable FPs, for which the fluorescence emission can be controlled by light irradiation at specific wavelengths. They enable regional optical marking in pulse-chase experiments on live cells and tissues, and they are essential marker tools for live-cell optical imaging with super-resolution. Photoconvertible FPs, which can be activated irreversibly via a photo-induced chemical reaction that either turns on their emission or changes their emission wavelength, are excellent markers for localization-based super-resolution microscopy (e.g., PALM). Patterned illumination microscopy (e.g., RESOLFT), however, requires markers that can be reversibly photoactivated many times. Photoswitchable FPs can be toggled repeatedly between a fluorescent and a non-fluorescent state by means of a light-induced chromophore isomerization coupled to a protonation reaction. We discuss the mechanistic origins of the effect and illustrate how photoswitchable FPs are employed in RESOLFT imaging. For this purpose, special FP variants with low switching fatigue have been introduced in recent years. Despite nearly two decades of FP engineering by many laboratories, there is still room for further improvement of these important markers for live cell imaging.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straβe 1, 76131 Karlsruhe, Germany
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23
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Wisniewski J, Hajj B, Chen J, Mizuguchi G, Xiao H, Wei D, Dahan M, Wu C. Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres. eLife 2014; 3:e02203. [PMID: 24844245 PMCID: PMC4067749 DOI: 10.7554/elife.02203] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.
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Affiliation(s)
- Jan Wisniewski
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Bassam Hajj
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jiji Chen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Gaku Mizuguchi
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Maxime Dahan
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Carl Wu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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24
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Hedde PN, Nienhaus GU. Super-resolution localization microscopy with photoactivatable fluorescent marker proteins. PROTOPLASMA 2014; 251:349-62. [PMID: 24162869 DOI: 10.1007/s00709-013-0566-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 05/02/2023]
Abstract
Fluorescent proteins (FPs) have become popular imaging tools because of their high specificity, minimal invasive labeling and allowing visualization of proteins and structures inside living organisms. FPs are genetically encoded and expressed in living cells, therefore, labeling involves minimal effort in comparison to approaches involving synthetic dyes. Photoactivatable FPs (paFPs) comprise a subclass of FPs that can change their absorption/emission properties such as brightness and color upon irradiation. This methodology has found a broad range of applications in the life sciences, especially in localization-based super-resolution microscopy of cells, tissues and even entire organisms. In this review, we discuss recent developments and applications of paFPs in super-resolution localization imaging.
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Affiliation(s)
- Per Niklas Hedde
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
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25
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Abstract
The use of fluorescent proteins (FPs) in modern cell biology and microscopy has had an extraordinary impact on our ability to investigate dynamic processes in living cells. FPs are unique in that fluorescence is encoded solely by the primary amino acid sequence of the FP and does not require enzymatic modification or cofactors. This genetically encoded fluorescence enables the expression of FPs in diverse cells and organisms and the detection of that fluorescence in living systems. This chapter focuses on microscopy-based applications of FP detection to monitor protein localization, dynamics, interaction, and the cellular environment.
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26
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Moeyaert B, Nguyen Bich N, De Zitter E, Rocha S, Clays K, Mizuno H, van Meervelt L, Hofkens J, Dedecker P. Green-to-red photoconvertible Dronpa mutant for multimodal super-resolution fluorescence microscopy. ACS NANO 2014; 8:1664-73. [PMID: 24410188 DOI: 10.1021/nn4060144] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Advanced imaging techniques crucially depend on the labels used. In this work, we present the structure-guided design of a fluorescent protein that displays both reversibly photochromic and green-to-red photoconversion behavior. We first designed ffDronpa, a mutant of the photochromic fluorescent protein Dronpa that matures up to three times faster while retaining its interesting photochromic features. Using a combined evolutionary and structure-driven rational design strategy, we developed a green-to-red photoconvertible ffDronpa mutant, called pcDronpa, and explored different optimization strategies that resulted in its improved version, pcDronpa2. This fluorescent probe combines a high brightness with low photobleaching and photoblinking. We herein show that, despite its tetrameric nature, pcDronpa2 allows for multimodal subdiffraction imaging by sequentially imaging a given sample using both super-resolution fluctuation imaging and localization microscopy.
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Affiliation(s)
- Benjamien Moeyaert
- Department of Chemistry, KU Leuven , Celestijnenlaan 200F, bus 2404, 3001 Heverlee, Belgium
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27
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Adam V. Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol 2014; 142:19-41. [PMID: 24522394 DOI: 10.1007/s00418-014-1190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 01/10/2023]
Abstract
In these last two decades , fluorescent proteins (FPs) have become highly valued imaging tools for cell biology, owing to their compatibility with living samples, their low levels of invasiveness and the possibility to specifically fuse them to a variety of proteins of interest. Remarkably, the recent development of phototransformable fluorescent proteins (PTFPs) has made it possible to conceive optical imaging experiments that were unimaginable only a few years ago. For example, it is nowadays possible to monitor intra- or intercellular trafficking, to optically individualize single cells in tissues or to observe single molecules in live cells. The tagging specificity brought by these genetically encoded highlighters leads to constant progress in the engineering of increasingly powerful, versatile and non-cytotoxic FPs. This review is focused on the recent developments of PTFPs and highlights their contribution to studies within cells, tissues and even living organisms. The aspects of single-molecule localization microscopy, intracellular tracking of photoactivated molecules, applications of PTFPs in biotechnology/optobiology and complementarities between PTFPs and other microscopy techniques are particularly discussed.
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Affiliation(s)
- Virgile Adam
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, F-38000, Grenoble, France,
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28
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Ishitsuka Y, Nienhaus K, Nienhaus GU. Photoactivatable fluorescent proteins for super-resolution microscopy. Methods Mol Biol 2014; 1148:239-60. [PMID: 24718806 DOI: 10.1007/978-1-4939-0470-9_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Super-resolution fluorescence microscopy techniques such as simulated emission depletion (STED) microscopy and photoactivated localization microscopy (PALM) allow substructures, organelles or even proteins within a cell to be imaged with a resolution far below the diffraction limit of ~200 nm. The development of advanced fluorescent proteins, especially photoactivatable fluorescent proteins of the GFP family, has greatly contributed to the successful application of these techniques to live-cell imaging. Here, we will illustrate how two fluorescent proteins with different photoactivation mechanisms can be utilized in high resolution dual color PALM imaging to obtain insights into a cellular process that otherwise would not be accessible. We will explain how to set up and perform the experiment and how to use our latest software "a-livePALM" for fast and efficient data analysis.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, Karlsruhe, 76131, Germany
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29
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Super-resolution microscopy of live cells using single molecule localization. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-6088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Meyer T, Schmitt M, Dietzek B, Popp J. Accumulating advantages, reducing limitations: multimodal nonlinear imaging in biomedical sciences - the synergy of multiple contrast mechanisms. JOURNAL OF BIOPHOTONICS 2013; 6:887-904. [PMID: 24259267 DOI: 10.1002/jbio.201300176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 05/29/2023]
Abstract
Multimodal nonlinear microscopy has matured during the past decades to one of the key imaging modalities in life science and biomedicine due to its unique capabilities of label-free visualization of tissue structure and chemical composition, high depth penetration, intrinsic 3D sectioning, diffraction limited resolution and low phototoxicity. This review briefly summarizes first recent advances in the field regarding the methodology, e.g., contrast mechanisms and signal characteristics used for contrast generation as well as novel image processing approaches. The second part deals with technologic developments emphasizing improvements in penetration depth, imaging speed, spatial resolution and nonlinear labeling strategies. The third part focuses on recent applications in life science fundamental research and biomedical diagnostics as well as future clinical applications.
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Affiliation(s)
- Tobias Meyer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
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31
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Kim H, Grunkemeyer TJ, Modi C, Chen L, Fromme R, Matz MV, Wachter RM. Acid-base catalysis and crystal structures of a least evolved ancestral GFP-like protein undergoing green-to-red photoconversion. Biochemistry 2013; 52:8048-59. [PMID: 24134825 DOI: 10.1021/bi401000e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In green-to-red photoconvertible fluorescent proteins, a three-ring chromophore is generated by the light-activated incorporation of a histidine residue into the conjugated π-system. We have determined the pH-rate profile and high- and low-pH X-ray structures of a least evolved ancestor (LEA) protein constructed in the laboratory based on statistical sequence analysis. LEA incorporates the minimal number of substitutions necessary and sufficient for facile color conversion and exhibits a maximal photoconversion quantum yield of 0.0015 at pH 6.1. The rate measurements provide a bell-shaped curve, indicating that the reaction is controlled by the two apparent pKa values, 4.5 ± 0.2 and 7.5 ± 0.2, flanking the chromophore pKa of 6.3 ± 0.1. These data demonstrate that the photoconversion rate of LEA is not proportional to the A-form of the GFP-like chromophore, as previously reported for Kaede-type proteins. We propose that the observed proton dissociation constants arise from the internal quadrupolar charge network consisting of Glu222, His203, Glu148, and Arg69. Increased active site flexibility may facilitate twisting of the chromophore upon photoexcitation, thereby disrupting the charge network and activating the Glu222 carboxylate for the abstraction of a proton from a carbon acid. Subsequently, the proton may be delivered to the Phe64 carbonyl by a hydrogen-bonded network involving Gln42 or by means of His65 side chain rotations promoted by protein breathing motions. A structural comparison of LEA with the nonphotoconvertible LEA-Q42A variant supports a role for Gln42 either in catalysis or in the coplanar preorganization of the green chromophore with the His65 imidazole ring.
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Affiliation(s)
- Hanseong Kim
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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32
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Müller B, Heilemann M. Shedding new light on viruses: super-resolution microscopy for studying human immunodeficiency virus. Trends Microbiol 2013; 21:522-33. [PMID: 23916730 DOI: 10.1016/j.tim.2013.06.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/20/2013] [Accepted: 06/27/2013] [Indexed: 01/09/2023]
Abstract
For more than 70 years electron microscopy (EM) techniques have played an important role in investigating structures of enveloped viruses. By contrast, use of fluorescence microscopy (FM) methods for this purpose was limited by the fact that the size of virus particles is generally around or below the diffraction limit of light microscopy. Various super-resolution (SR) fluorescence imaging techniques developed over the past two decades bypass the diffraction limit of light microscopy, allowing visualization of subviral details and bridging the gap between conventional FM and EM methods. We summarize here findings on human immunodeficiency virus (HIV-1) obtained using SR-FM techniques. Although the number of published studies is currently limited and some of the pioneering analyses also covered methodological or descriptive aspects, recent publications clearly indicate the potential to approach open questions in HIV-1 replication from a new angle.
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Affiliation(s)
- Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, Germany.
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33
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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35
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Raymo FM. Photoactivatable Synthetic Dyes for Fluorescence Imaging at the Nanoscale. J Phys Chem Lett 2012; 3:2379-2385. [PMID: 26292118 DOI: 10.1021/jz301021e] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The transition from conventional to photoactivatable fluorophores can bring the resolution of fluorescence images from the micrometer to the nanometer level. Indeed, fluorescence photoactivation can overcome the limitations that diffraction imposes on the resolution of optical microscopes. Specifically, distinct fluorophores positioned within the same subdiffraction volume can be resolved only if their emissions are activated independently at different intervals of time. Under these conditions, the sequential localization of multiple probes permits the reconstruction of images with a spatial resolution that is otherwise impossible to achieve with conventional fluorophores. The irreversible photolysis of protecting groups or the reversible transformations of photochromic compounds can be employed to control the emission of appropriate fluorescent chromophores and allow the implementation of these ingenious operating principles for superresolution imaging. Such molecular constructs enable the spatiotemporal control that is required to avoid diffraction and can become invaluable analytical tools for the optical visualization of biological specimens and nanostructured materials with unprecedented resolution.
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Affiliation(s)
- Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
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Zhang M, Chang H, Zhang Y, Yu J, Wu L, Ji W, Chen J, Liu B, Lu J, Liu Y, Zhang J, Xu P, Xu T. Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat Methods 2012; 9:727-9. [PMID: 22581370 DOI: 10.1038/nmeth.2021] [Citation(s) in RCA: 333] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 04/18/2012] [Indexed: 12/12/2022]
Abstract
Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameric mEos2 and rationally designed improved versions, mEos3.1 and mEos3.2, that are truly monomeric, are brighter, mature faster and exhibit higher photon budget and label density.
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Affiliation(s)
- Mingshu Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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Brodehl A, Hedde PN, Dieding M, Fatima A, Walhorn V, Gayda S, Šarić T, Klauke B, Gummert J, Anselmetti D, Heilemann M, Nienhaus GU, Milting H. Dual color photoactivation localization microscopy of cardiomyopathy-associated desmin mutants. J Biol Chem 2012; 287:16047-57. [PMID: 22403400 PMCID: PMC3346104 DOI: 10.1074/jbc.m111.313841] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/27/2012] [Indexed: 11/06/2022] Open
Abstract
Mutations in the DES gene coding for the intermediate filament protein desmin may cause skeletal and cardiac myopathies, which are frequently characterized by cytoplasmic aggregates of desmin and associated proteins at the cellular level. By atomic force microscopy, we demonstrated filament formation defects of desmin mutants, associated with arrhythmogenic right ventricular cardiomyopathy. To understand the pathogenesis of this disease, it is essential to analyze desmin filament structures under conditions in which both healthy and mutant desmin are expressed at equimolar levels mimicking an in vivo situation. Here, we applied dual color photoactivation localization microscopy using photoactivatable fluorescent proteins genetically fused to desmin and characterized the heterozygous status in living cells lacking endogenous desmin. In addition, we applied fluorescence resonance energy transfer to unravel short distance structural patterns of desmin mutants in filaments. For the first time, we present consistent high resolution data on the structural effects of five heterozygous desmin mutations on filament formation in vitro and in living cells. Our results may contribute to the molecular understanding of the pathological filament formation defects of heterozygous DES mutations in cardiomyopathies.
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Affiliation(s)
- Andreas Brodehl
- From the E. & H. Klessmann Institute for Cardiovascular Research & Development and
| | - Per Niklas Hedde
- the Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Mareike Dieding
- the Experimental Biophysics and Applied Nanoscience, Faculty of Physics and Bielefeld Institute for Biophysics and Nanoscience (BINAS), Bielefeld University, 33615 Bielefeld, Germany
| | - Azra Fatima
- the Institute for Neurophysiology, Medical Center, University of Cologne, 50931 Cologne, Germany
| | - Volker Walhorn
- the Experimental Biophysics and Applied Nanoscience, Faculty of Physics and Bielefeld Institute for Biophysics and Nanoscience (BINAS), Bielefeld University, 33615 Bielefeld, Germany
| | - Susan Gayda
- the Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Tomo Šarić
- the Institute for Neurophysiology, Medical Center, University of Cologne, 50931 Cologne, Germany
| | - Bärbel Klauke
- From the E. & H. Klessmann Institute for Cardiovascular Research & Development and
| | - Jan Gummert
- the Clinic of Cardio-Thoracic Surgery, Heart and Diabetes Center NRW, Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Dario Anselmetti
- the Experimental Biophysics and Applied Nanoscience, Faculty of Physics and Bielefeld Institute for Biophysics and Nanoscience (BINAS), Bielefeld University, 33615 Bielefeld, Germany
| | - Mike Heilemann
- the Department of Biotechnology & Biophysics, Julius-Maximilians-University Würzburg, 97074 Würzburg, Germany, and
| | - Gerd Ulrich Nienhaus
- the Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
- the Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Hendrik Milting
- From the E. & H. Klessmann Institute for Cardiovascular Research & Development and
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A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications. Proc Natl Acad Sci U S A 2012; 109:4455-60. [PMID: 22375034 DOI: 10.1073/pnas.1113770109] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reversibly switchable fluorescent proteins (RSFPs) have attracted widespread interest for emerging techniques including repeated tracking of protein behavior and superresolution microscopy. Among the limited number of RSFPs available, only Dronpa is widely employed for most cell biology applications due to its monomeric and other favorable photochemical properties. Here we developed a series of monomeric green RSFPs with beneficial optical characteristics such as high photon output per switch, high photostability, a broad range of switching rate, and pH-dependence, which make them potentially useful for various applications. One member of this series, mGeos-M, exhibits the highest photon budget and localization precision potential among all green RSFPs. We propose mGeos-M as a candidate to replace Dronpa for applications such as dynamic tracking, dual-color superresolution imaging, and optical lock-in detection.
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Impellizzeri S, McCaughan B, Callan JF, Raymo FM. Photoinduced enhancement in the luminescence of hydrophilic quantum dots coated with photocleavable ligands. J Am Chem Soc 2012; 134:2276-83. [PMID: 22217330 DOI: 10.1021/ja209873g] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In search of strategies to photoactivate the luminescence of semiconductor quantum dots, we devised a synthetic approach to attach photocleavable 2-nitrobenzyl groups to CdSe-ZnS core-shell quantum dots coated with hydrophilic polymeric ligands. The emission intensity of the resulting nanostructured constructs increases by more than 60% with the photolysis of the 2-nitrobenzyl appendages. Indeed, the photoinduced separation of the organic chromophores from the inorganic nanoparticles suppresses an electron-transfer pathway from the latter to the former and is mostly responsible for the luminescence enhancement. However, the thiol groups anchoring the polymeric envelope to the ZnS shell also contribute to the photoinduced emission increase. Presumably, their photooxidation eliminates defects on the nanoparticle surface and promotes the radiative deactivation of the excited quantum dots. This effect is fully reversible but its magnitude is only a fraction of the change caused by the photocleavage of the 2-nitrobenzyl groups. In addition, these particular quantum dots can cross the membrane of model cells and their luminescence increases by ~80% after the intracellular photocleavage of the 2-nitrobenzyl quenchers. Thus, photoswitchable luminescent constructs with biocompatible character can be assembled combining the established photochemistry of the 2-nitrobenzyl photocage with the outstanding photophysical properties of semiconductor quantum dots and the hydrophilic character of appropriate polymeric ligands.
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Affiliation(s)
- Stefania Impellizzeri
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, USA
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Abstract
The replication cycle of HIV proceeds within an infected cell and imaging techniques allow us to focus on the pathogen in this cellular environment. During recent years, both electron microscopy and fluorescence microscopy have evolved from methods providing two-dimensional still images to techniques that can resolve native, three-dimensional structures at resolutions down to approximately 20 Å, or allow direct real-time observation of dynamic intracellular events, respectively, thereby yielding numerous novel insights into HIV biology. Future technological developments are expected to narrow the gap between electron microscopy (high spatial and structural resolution, but no information about dynamics) and fluorescence microscopy (high temporal resolution and high throughput, but low spatial resolution), providing detailed views that will deepen our understanding of HIV–cell interactions.
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Affiliation(s)
- Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
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