151
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Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R. Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Maximilian T. Strauss
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Alexander Auer
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Vilma Jimenez Sabinina
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jervis V. Thevathasan
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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152
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Mann FA, Lv Z, Großhans J, Opazo F, Kruss S. Nanobody‐Conjugated Nanotubes for Targeted Near‐Infrared In Vivo Imaging and Sensing. Angew Chem Int Ed Engl 2019; 58:11469-11473. [DOI: 10.1002/anie.201904167] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/03/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Florian A. Mann
- Institute of Physical ChemistryGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Germany
| | - Zhiyi Lv
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Germany
| | - Jörg Großhans
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Germany
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Strasse 3a 37075 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Germany
- NanoTag Biotechnologies GmbH Rudolf-Wissell-Straße 28a 37079 Göttingen Germany
| | - Sebastian Kruss
- Institute of Physical ChemistryGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Germany
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153
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Figueiras E, Silvestre OF, Ihalainen TO, Nieder JB. Phasor-assisted nanoscopy reveals differences in the spatial organization of major nuclear lamina proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118530. [PMID: 31415840 DOI: 10.1016/j.bbamcr.2019.118530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM) nanoscopy is introduced as a powerful tool for functional cell biology research. Thin metal substrates can be used to obtain axial super-resolution via nanoscale distance-dependent MIET from fluorescent dyes towards a nearby metal layer, thereby creating fluorescence lifetime contrast between dyes located at different nanoscale distance from the metal. Such data can be used to achieve axially super-resolved microscopy images, a process known as MIET-FLIM nanoscopy. Suitability of the phasor approach in MIET-FLIM nanoscopy is first demonstrated using nanopatterned substrates, and furthermore applied to characterize the distance distribution of the epithelial basal membrane of a biological cell from the gold substrate. The phasor plot of an entire cell can be used to characterize the full Förster resonance energy transfer (FRET) trajectory as a large distance heterogeneity within the sensing range of about 100 nm from the metal surface is present due to the extended shape of cell with curvatures. In contrast, the different proteins of nuclear lamina show strong confinement close to the nuclear envelope in nanoscale. We find the lamin B layer resides in average at shorter distances from the gold surface compared to the lamin A/C layer located in more extended ranges. This and the observed heterogeneity of the protein layer thicknesses suggests that A- and B-type lamins form distinct networks in the nuclear lamina. Our results provide detailed insights for the study of the different roles of lamin proteins in chromatin tethering and nuclear mechanics.
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Affiliation(s)
- Edite Figueiras
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Oscar F Silvestre
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Teemu O Ihalainen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, 33014 Tampere, Finland
| | - Jana B Nieder
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal.
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154
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A quest for coordination among activities at the replisome. Biochem Soc Trans 2019; 47:1067-1075. [PMID: 31395754 DOI: 10.1042/bst20180402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Faithful DNA replication is required for transmission of the genetic material across generations. The basic mechanisms underlying this process are shared among all organisms: progressive unwinding of the long double-stranded DNA; synthesis of RNA primers; and synthesis of a new DNA chain. These activities are invariably performed by a multi-component machine called the replisome. A detailed description of this molecular machine has been achieved in prokaryotes and phages, with the replication processes in eukaryotes being comparatively less known. However, recent breakthroughs in the in vitro reconstitution of eukaryotic replisomes have resulted in valuable insight into their functions and mechanisms. In conjunction with the developments in eukaryotic replication, an emerging overall view of replisomes as dynamic protein ensembles is coming into fruition. The purpose of this review is to provide an overview of the recent insights into the dynamic nature of the bacterial replisome, revealed through single-molecule techniques, and to describe some aspects of the eukaryotic replisome under this framework. We primarily focus on Escherichia coli and Saccharomyces cerevisiae (budding yeast), since a significant amount of literature is available for these two model organisms. We end with a description of the methods of live-cell fluorescence microscopy for the characterization of replisome dynamics.
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155
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Chia HE, Marsh ENG, Biteen JS. Extending fluorescence microscopy into anaerobic environments. Curr Opin Chem Biol 2019; 51:98-104. [DOI: 10.1016/j.cbpa.2019.05.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 04/22/2019] [Accepted: 05/13/2019] [Indexed: 12/01/2022]
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156
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Neguembor MV, Sebastian-Perez R, Aulicino F, Gomez-Garcia PA, Cosma MP, Lakadamyali M. (Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed-cell super-resolution imaging of multiple genes. Nucleic Acids Res 2019; 46:e30. [PMID: 29294098 PMCID: PMC5861460 DOI: 10.1093/nar/gkx1271] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/20/2017] [Indexed: 11/15/2022] Open
Abstract
CRISPR/dCas9-based labeling has allowed direct visualization of genomic regions in living cells. However, poor labeling efficiency and signal-to-background ratio have limited its application to visualize genome organization using super-resolution microscopy. We developed (Po)STAC (Polycistronic SunTAg modified CRISPR) by combining CRISPR/dCas9 with SunTag labeling and polycistronic vectors. (Po)STAC enhances both labeling efficiency and fluorescence signal detected from labeled loci enabling live cell imaging as well as super-resolution fixed-cell imaging of multiple genes with high spatiotemporal resolution.
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Affiliation(s)
- Maria V Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Ruben Sebastian-Perez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Francesco Aulicino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Pablo A Gomez-Garcia
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Maria P Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Melike Lakadamyali
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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157
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Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods 2019; 174:27-41. [PMID: 31344404 DOI: 10.1016/j.ymeth.2019.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/28/2019] [Accepted: 07/17/2019] [Indexed: 12/17/2022] Open
Abstract
Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
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158
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Beliu G, Kurz AJ, Kuhlemann AC, Behringer-Pliess L, Meub M, Wolf N, Seibel J, Shi ZD, Schnermann M, Grimm JB, Lavis LD, Doose S, Sauer M. Bioorthogonal labeling with tetrazine-dyes for super-resolution microscopy. Commun Biol 2019; 2:261. [PMID: 31341960 PMCID: PMC6642216 DOI: 10.1038/s42003-019-0518-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022] Open
Abstract
Genetic code expansion (GCE) technology allows the specific incorporation of functionalized noncanonical amino acids (ncAAs) into proteins. Here, we investigated the Diels-Alder reaction between trans-cyclooct-2-ene (TCO)-modified ncAAs, and 22 known and novel 1,2,4,5-tetrazine-dye conjugates spanning the entire visible wavelength range. A hallmark of this reaction is its fluorogenicity - the tetrazine moiety can elicit substantial quenching of the dye. We discovered that photoinduced electron transfer (PET) from the excited dye to tetrazine is the main quenching mechanism in red-absorbing oxazine and rhodamine derivatives. Upon reaction with dienophiles quenching interactions are reduced resulting in a considerable increase in fluorescence intensity. Efficient and specific labeling of all tetrazine-dyes investigated permits super-resolution microscopy with high signal-to-noise ratio even at the single-molecule level. The different cell permeability of tetrazine-dyes can be used advantageously for specific intra- and extracellular labeling of proteins and highly sensitive fluorescence imaging experiments in fixed and living cells.
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Affiliation(s)
- Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas J. Kurz
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander C. Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lisa Behringer-Pliess
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Natalia Wolf
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Zhen-Dan Shi
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850 USA
| | - Martin Schnermann
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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159
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Huang C, Li D, Ren J, Ji F, Jia L. Generation and Application of Fluorescent Anti-Human β2-Microglobulin VHHs via Amino Modification. Molecules 2019; 24:E2600. [PMID: 31319525 PMCID: PMC6680903 DOI: 10.3390/molecules24142600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/07/2019] [Accepted: 07/14/2019] [Indexed: 01/21/2023] Open
Abstract
The functionalization of VHHs enables their application in almost every aspect of biomedical inquiry. Amino modification remains a common strategy for protein functionalization, though is considered to be inferior to site-specific methods and cause protein property changes. In this paper, four anti-β2M VHHs were selected and modified on the amino group by NHS-Fluo. The impacts of amino modification on these VHHs were drastically different, and among all th examples, the modified NB-1 maintained the original stability, bioactivity and homogeneity of unmodified NB-1. Specific recognition of VHHs targeting β2M detected by fluorescence imaging explored the possible applications of VHHs. Via this study, we successfully functionalized the anti-β2M VHHs through amino modification and the results are able to instruct the simple and fast functionalization of VHHs in biomedical researches.
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Affiliation(s)
- Chundong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China.
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160
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Visualizing the inner life of microbes: practices of multi-color single-molecule localization microscopy in microbiology. Biochem Soc Trans 2019; 47:1041-1065. [PMID: 31296734 DOI: 10.1042/bst20180399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/28/2022]
Abstract
In this review, we discuss multi-color single-molecule imaging and tracking strategies for studying microbial cell biology. We first summarize and compare the methods in a detailed literature review of published studies conducted in bacteria and fungi. We then introduce a guideline on which factors and parameters should be evaluated when designing a new experiment, from fluorophore and labeling choices to imaging routines and data analysis. Finally, we give some insight into some of the recent and promising applications and developments of these techniques and discuss the outlook for this field.
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161
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Cramer K, Bolender AL, Stockmar I, Jungmann R, Kasper R, Shin JY. Visualization of Bacterial Protein Complexes Labeled with Fluorescent Proteins and Nanobody Binders for STED Microscopy. Int J Mol Sci 2019; 20:ijms20143376. [PMID: 31295803 PMCID: PMC6678925 DOI: 10.3390/ijms20143376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
In situ visualization of molecular assemblies near their macromolecular scale is a powerful tool to investigate fundamental cellular processes. Super-resolution light microscopies (SRM) overcome the diffraction limit and allow researchers to investigate molecular arrangements at the nanoscale. However, in bacterial cells, visualization of these assemblies can be challenging because of their small size and the presence of the cell wall. Thus, although conceptually promising, successful application of SRM techniques requires careful optimization in labeling biochemistry, fluorescent dye choice, bacterial biology and microscopy to gain biological insights. Here, we apply Stimulated Emission Depletion (STED) microscopy to visualize cell division proteins in bacterial cells, specifically E. coli and B. subtilis. We applied nanobodies that specifically recognize fluorescent proteins, such as GFP, mCherry2 and PAmCherry, fused to targets for STED imaging and evaluated the effect of various organic fluorescent dyes on the performance of STED in bacterial cells. We expect this research to guide scientists for in situ macromolecular visualization using STED in bacterial systems.
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Affiliation(s)
- Kimberly Cramer
- Max Plank Institute of Biochemistry, 82152 Martinsried, 82152 Munich, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Anna-Lena Bolender
- Max Plank Institute of Neurobiology, 82152 Martinsried, 82152 Munich, Germany
| | - Iris Stockmar
- Max Plank Institute of Biochemistry, 82152 Martinsried, 82152 Munich, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Ralf Jungmann
- Max Plank Institute of Biochemistry, 82152 Martinsried, 82152 Munich, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Robert Kasper
- Max Plank Institute of Neurobiology, 82152 Martinsried, 82152 Munich, Germany.
| | - Jae Yen Shin
- Max Plank Institute of Biochemistry, 82152 Martinsried, 82152 Munich, Germany.
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany.
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162
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Mann FA, Lv Z, Großhans J, Opazo F, Kruss S. Nanoröhren‐Nanobody‐Konjugate als zielgerichtete Sonden und Marker für die In‐vivo‐Nahinfrarot‐Bildgebung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Florian A. Mann
- Institut für Physikalische ChemieGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
| | - Zhiyi Lv
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Deutschland
| | - Jörg Großhans
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Deutschland
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Strasse 3a 37075 Göttingen Deutschland
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Deutschland
- NanoTag Biotechnologies GmbH Rudolf-Wissell-Straße 28a 37079 Göttingen Deutschland
| | - Sebastian Kruss
- Institut für Physikalische ChemieGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Deutschland
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163
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Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, Sato Y, Kimura H, Stasevich TJ. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nat Commun 2019; 10:2947. [PMID: 31270320 PMCID: PMC6610143 DOI: 10.1038/s41467-019-10846-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
To expand the toolbox of imaging in living cells, we have engineered a single-chain variable fragment binding the linear HA epitope with high affinity and specificity in vivo. The resulting probe, called the HA frankenbody, can light up in multiple colors HA-tagged nuclear, cytoplasmic, membrane, and mitochondrial proteins in diverse cell types. The HA frankenbody also enables state-of-the-art single-molecule experiments in living cells, which we demonstrate by tracking single HA-tagged histones in U2OS cells and single mRNA translation dynamics in both U2OS cells and neurons. Together with the SunTag, we also track two mRNA species simultaneously to demonstrate comparative single-molecule studies of translation can now be done with genetically encoded tools alone. Finally, we use the HA frankenbody to precisely quantify the expression of HA-tagged proteins in developing zebrafish embryos. The versatility of the HA frankenbody makes it a powerful tool for imaging protein dynamics in vivo.
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Affiliation(s)
- Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kouta Kamijo
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Philip D Fox
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yuko Sato
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
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164
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Richter KN, Patzelt C, Phan NTN, Rizzoli SO. Antibody-driven capture of synaptic vesicle proteins on the plasma membrane enables the analysis of their interactions with other synaptic proteins. Sci Rep 2019; 9:9231. [PMID: 31239503 PMCID: PMC6592915 DOI: 10.1038/s41598-019-45729-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/13/2019] [Indexed: 01/07/2023] Open
Abstract
Many organelles from the secretory pathway fuse to the plasma membrane, to exocytose different cargoes. Their proteins are then retrieved from the plasma membrane by endocytosis, and the organelles are re-formed. It is generally unclear whether the organelle proteins colocalize when they are on the plasma membrane, or whether they disperse. To address this, we generated here a new approach, which we tested on synaptic vesicles, organelles that are known to exo- and endocytose frequently. We tagged the synaptotagmin molecules of newly exocytosed vesicles using clusters of primary and secondary antibodies targeted against the luminal domains of these molecules. The antibody clusters are too large for endocytosis, and thus sequestered the synaptotagmin molecules on the plasma membrane. Immunostainings for other synaptic molecules then revealed whether they colocalized with the sequestered synaptotagmin molecules. We suggest that such assays may be in the future extended to other cell types and other organelles.
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Affiliation(s)
- Katharina N Richter
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
| | - Christina Patzelt
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Nhu T N Phan
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
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165
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Xu J, Liu Y. A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS J 2019; 286:3095-3109. [PMID: 31127980 DOI: 10.1111/febs.14938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/24/2019] [Accepted: 05/23/2019] [Indexed: 12/28/2022]
Abstract
Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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166
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Li Y, Wu YL, Hoess P, Mund M, Ries J. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. BIOMEDICAL OPTICS EXPRESS 2019; 10:2708-2718. [PMID: 31259045 PMCID: PMC6583355 DOI: 10.1364/boe.10.002708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 05/22/2023]
Abstract
Three-dimensional single molecule localization microscopy relies on the fitting of the individual molecules with a point spread function (PSF) model. The reconstructed images often show local squeezing or expansion in z. A common cause is depth-induced aberrations in conjunction with an imperfect PSF model calibrated from beads on a coverslip, resulting in a mismatch between measured PSF and real PSF. Here, we developed a strategy for accurate z-localization in which we use the imperfect PSF model for fitting, determine the fitting errors and correct for them in a post-processing step. We present an open-source software tool and a simple experimental calibration procedure that allow retrieving accurate z-positions in any PSF engineering approach or fitting modality, even at large imaging depths.
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Affiliation(s)
- Yiming Li
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Yu-Le Wu
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Philipp Hoess
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Markus Mund
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Current affiliation: Department of Biochemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
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167
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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168
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Seitz KJ, Rizzoli SO. GFP nanobodies reveal recently-exocytosed pHluorin molecules. Sci Rep 2019; 9:7773. [PMID: 31123313 PMCID: PMC6533288 DOI: 10.1038/s41598-019-44262-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/13/2019] [Indexed: 11/21/2022] Open
Abstract
Neurotransmitter release requires vesicle recycling, which consists of exocytosis, endocytosis and the reformation of new fusion-competent vesicles. One poorly understood aspect in this cycle is the fate of the vesicle proteins after exocytosis, when they are left on the plasma membrane. Such proteins are often visualized by coupling to pH-sensitive GFP moieties (pHluorins). However, pHluorin imaging is typically limited by diffraction to spots several-fold larger than the vesicles. Here we show that pHuorin-tagged vesicle proteins can be easily detected using single-domain antibodies (nanobodies) raised against GFP. By coupling the nanobodies to chemical fluorophores that were optimal for super-resolution imaging, we could analyze the size and intensity of the groups of pHluorin-tagged proteins under a variety of conditions, in a fashion that would have been impossible based solely on the pHluorin fluorescence. We conclude that nanobody-based pHluorin detection is a promising tool for investigating post-exocytosis events in neurons.
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Affiliation(s)
- Katharina J Seitz
- Institute for Neuro- and Sensory Physiology, University Medical Center, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, University Medical Center, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
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169
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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170
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Affiliation(s)
- Regan P Moore
- Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Chapel Hill and Raleigh, NC, USA
| | - Wesley R Legant
- Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Chapel Hill and Raleigh, NC, USA. .,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
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171
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Abstract
Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60-80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.
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172
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Heukers R, De Groof TW, Smit MJ. Nanobodies detecting and modulating GPCRs outside in and inside out. Curr Opin Cell Biol 2019; 57:115-122. [DOI: 10.1016/j.ceb.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
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173
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Banko M, Mucha-Kruczynska I, Weise C, Heyd F, Ewers H. A homozygous genome-edited Sept2-EGFP fibroblast cell line. Cytoskeleton (Hoboken) 2019; 76:73-82. [PMID: 30924304 PMCID: PMC6593442 DOI: 10.1002/cm.21518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/09/2023]
Abstract
Septins are a conserved, essential family of GTPases that interact with actin, microtubules, and membranes and form scaffolds and diffusion barriers in cells. Several of the 13 known mammalian septins assemble into nonpolar, multimeric complexes that can further polymerize into filamentous structures. While some GFP‐coupled septins have been described, overexpression of GFP‐tagged septins often leads to artifacts in localization and function. To overcome this ubiquitous problem, we have here generated a genome‐edited rat fibroblast cell line expressing Septin 2 (Sept2) coupled to enhanced green fluorescent protein (EGFP) from both chromosomal loci. We characterize these cells by genomic polymerase chain reaction (PCR) for genomic integration, by western blot and reverse transcriptase‐PCR for expression, by immunofluorescence and immunoprecipitation for the colocalization of septins with one another and cellular structures and for complex formation of different septins. By live cell imaging, proliferation and migration assays we investigate proper function of septins in these cells. We find that EGFP is incorporated into both chromosomal loci and only EGFP‐coupled Sept2 is expressed in homozygous cells. We find that endogenous Sept2‐EGFP exhibits expression levels, localization and incorporation into cellular septin complexes similar to the wt in these cells. The expression level of other septins is not perturbed and cell division and cell migration proceed normally. We expect our cell line to be a useful tool for the cell biology of septins, especially for quantitative biology.
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Affiliation(s)
- Monika Banko
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.,Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Iwona Mucha-Kruczynska
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Helge Ewers
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.,Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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174
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Schlichthaerle T, Ganji M, Auer A, Kimbu Wade O, Jungmann R. Bacterially Derived Antibody Binders as Small Adapters for DNA-PAINT Microscopy. Chembiochem 2019; 20:1032-1038. [PMID: 30589198 DOI: 10.1002/cbic.201800743] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/21/2022]
Abstract
Current optical super-resolution implementations are capable of resolving features spaced just a few nanometers apart. However, translating this spatial resolution to cellular targets is limited by the large size of traditionally employed primary and secondary antibody reagents. Recent advancements in small and efficient protein binders for super-resolution microscopy, such as nanobodies or aptamers, provide an exciting avenue for the future; however, their widespread availability is still limited. To address this issue, here we report the combination of bacterial-derived binders commonly used in antibody purification with DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy. The small sizes of these protein binders, relative to secondary antibodies, make them an attractive labeling alternative for emerging superresolution techniques. We present here a labeling protocol for DNA conjugation of bacterially derived proteins A and G for DNA-PAINT, having assayed their intracellular performance by targeting primary antibodies against tubulin, TOM20, and the epidermal growth factor receptor (EGFR) and quantified the increases in obtainable resolution.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mahipal Ganji
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Alexander Auer
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Orsolya Kimbu Wade
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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175
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Padmanabhan P, Bademosi AT, Kasula R, Lauwers E, Verstreken P, Meunier FA. Need for speed: Super-resolving the dynamic nanoclustering of syntaxin-1 at exocytic fusion sites. Neuropharmacology 2019; 169:107554. [PMID: 30826343 DOI: 10.1016/j.neuropharm.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Communication between cells relies on regulated exocytosis, a multi-step process that involves the docking, priming and fusion of vesicles with the plasma membrane, culminating in the release of neurotransmitters and hormones. Key proteins and lipids involved in exocytosis are subjected to Brownian movement and constantly switch between distinct motion states which are governed by short-lived molecular interactions. Critical biochemical reactions between exocytic proteins that occur in the confinement of nanodomains underpin the precise sequence of priming steps which leads to the fusion of vesicles. The advent of super-resolution microscopy techniques has provided the means to visualize individual molecules on the plasma membrane with high spatiotemporal resolution in live cells. These techniques are revealing a highly dynamic nature of the nanoscale organization of the exocytic machinery. In this review, we focus on soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) syntaxin-1, which mediates vesicular fusion. Syntaxin-1 is highly mobile at the plasma membrane, and its inherent speed allows fast assembly and disassembly of syntaxin-1 nanoclusters which are associated with exocytosis. We reflect on recent studies which have revealed the mechanisms regulating syntaxin-1 nanoclustering on the plasma membrane and draw inferences on the effect of synaptic activity, phosphoinositides, N-ethylmaleimide-sensitive factor (NSF), α-soluble NSF attachment protein (α-SNAP) and SNARE complex assembly on the dynamic nanoscale organization of syntaxin-1. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Ravikiran Kasula
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia.
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176
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Huang T, Phelps C, Wang J, Lin LJ, Bittel A, Scott Z, Jacques S, Gibbs SL, Gray JW, Nan X. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J 2019; 114:301-310. [PMID: 29401428 DOI: 10.1016/j.bpj.2017.11.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
Single-molecule tracking (SMT) offers rich information on the dynamics of underlying biological processes, but multicolor SMT has been challenging due to spectral cross talk and a need for multiple laser excitations. Here, we describe a single-molecule spectral imaging approach for live-cell tracking of multiple fluorescent species at once using a single-laser excitation. Fluorescence signals from all the molecules in the field of view are collected using a single objective and split between positional and spectral channels. Images of the same molecule in the two channels are then combined to determine both the location and the identity of the molecule. The single-objective configuration of our approach allows for flexible sample geometry and the use of a live-cell incubation chamber required for live-cell SMT. Despite a lower photon yield, we achieve excellent spatial (20-40 nm) and spectral (10-15 nm) resolutions comparable to those obtained with dual-objective, spectrally resolved Stochastic Optical Reconstruction Microscopy. Furthermore, motions of the fluorescent molecules did not cause loss of spectral resolution owing to the dual-channel spectral calibration. We demonstrate SMT in three (and potentially more) colors using spectrally proximal fluorophores and single-laser excitation, and show that trajectories of each species can be reliably extracted with minimal cross talk.
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Affiliation(s)
- Tao Huang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Carey Phelps
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Jing Wang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Li-Jung Lin
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Amy Bittel
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Zubenelgenubi Scott
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Steven Jacques
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
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177
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Gomes de Castro MA, Wildhagen H, Sograte-Idrissi S, Hitzing C, Binder M, Trepel M, Engels N, Opazo F. Differential organization of tonic and chronic B cell antigen receptors in the plasma membrane. Nat Commun 2019; 10:820. [PMID: 30778055 PMCID: PMC6379438 DOI: 10.1038/s41467-019-08677-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/24/2019] [Indexed: 11/09/2022] Open
Abstract
Stimulation of the B cell antigen receptor (BCR) triggers signaling pathways that promote the differentiation of B cells into plasma cells. Despite the pivotal function of BCR in B cell activation, the organization of the BCR on the surface of resting and antigen-activated B cells remains unclear. Here we show, using STED super-resolution microscopy, that IgM-containing BCRs exist predominantly as monomers and dimers in the plasma membrane of resting B cells, but form higher oligomeric clusters upon stimulation. By contrast, a chronic lymphocytic leukemia-derived BCR forms dimers and oligomers in the absence of a stimulus, but a single amino acid exchange reverts its organization to monomers in unstimulated B cells. Our super-resolution microscopy approach for quantitatively analyzing cell surface proteins may thus help reveal the nanoscale organization of immunoreceptors in various cell types.
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MESH Headings
- B-Lymphocytes/metabolism
- Burkitt Lymphoma/pathology
- Cell Line, Tumor
- Cell Membrane/metabolism
- Humans
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/metabolism
- Immunoglobulin M/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Microscopy, Fluorescence/methods
- Protein Multimerization
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
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Affiliation(s)
- Maria Angela Gomes de Castro
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Hanna Wildhagen
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, von-Siebold-Straße 3a, 37075, Göttingen, Germany
| | - Christoffer Hitzing
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany
| | - Mascha Binder
- Department of Oncology and Hematology, BMT with section Pneumology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Trepel
- Department of Oncology and Hematology, BMT with section Pneumology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
- Department of Hematology and Oncology, Augsburg Medical Center, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Niklas Engels
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany.
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, von-Siebold-Straße 3a, 37075, Göttingen, Germany.
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178
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Abstract
Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein-protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved both temporal and spatial resolution, and the technique has been successfully employed in numerous small-scale (single complex mapping) and large-scale (network mapping) initiatives. When paired with quantitative proteomic approaches, the ability of these assays to provide snapshots of stable and transient interactions over time greatly facilitates the mapping of dynamic interactomes. Furthermore, recent innovations have extended biotin-based proximity labeling techniques such as BioID and APEX beyond classic protein-centric assays (tag a protein to label neighboring proteins) to include RNA-centric (tag an RNA species to label RNA-binding proteins) and DNA-centric (tag a gene locus to label associated protein complexes) assays.
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Affiliation(s)
- Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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179
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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180
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Yan Q, Cai M, Zhou L, Xu H, Shi Y, Sun J, Jiang J, Gao J, Wang H. Using an RNA aptamer probe for super-resolution imaging of native EGFR. NANOSCALE ADVANCES 2019; 1:291-298. [PMID: 36132464 PMCID: PMC9473275 DOI: 10.1039/c8na00143j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/08/2019] [Accepted: 08/16/2018] [Indexed: 05/06/2023]
Abstract
Aptamers, referred to as "chemical antibodies", are short single-stranded oligonucleotides that bind to targets with high affinity and specificity. Compared with antibodies, aptamers can be designed, developed and modified easily. Since their discovery, aptamers have been widely used in in vitro diagnostics and molecular imaging. However, they are relatively less studied and applied in advanced microscopy. Here we used an RNA aptamer in dSTORM imaging and obtained a high-quality image of EGFR nanoscale clusters on live cell membranes. The results showed that the cluster number and size with aptamer labeling were almost the same as those with labeling with the natural ligand EGF, but the morphology of the clusters was smaller and more regular than that with cetuximab labeling. Meanwhile, dual-color imaging demonstrated sufficient fluorophore labeling, highly specific recognition and greatly accurate clustering information provided by aptamers. Furthermore, the aptamer labeling method indicated that active EGFR formed larger clusters containing more molecules than resting EGFR, which was hidden under the antibody labeling. Our work suggested that aptamers can be used as versatile probes in super-resolution imaging with small steric hindrance, opening a new avenue for detailed and precise morphological analysis of membrane proteins.
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Affiliation(s)
- Qiuyan Yan
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Lulu Zhou
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yan Shi
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Jiayin Sun
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology Wenhai Road, Aoshanwei, Jimo, Qingdao Shandong 266237 P. R. China
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181
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Sograte-Idrissi S, Oleksiievets N, Isbaner S, Eggert-Martinez M, Enderlein J, Tsukanov R, Opazo F. Nanobody Detection of Standard Fluorescent Proteins Enables Multi-Target DNA-PAINT with High Resolution and Minimal Displacement Errors. Cells 2019; 8:cells8010048. [PMID: 30646582 PMCID: PMC6357156 DOI: 10.3390/cells8010048] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 01/06/2023] Open
Abstract
DNA point accumulation for imaging in nanoscale topography (PAINT) is a rapidly developing fluorescence super-resolution technique, which allows for reaching spatial resolutions below 10 nm. It also enables the imaging of multiple targets in the same sample. However, using DNA-PAINT to observe cellular structures at such resolution remains challenging. Antibodies, which are commonly used for this purpose, lead to a displacement between the target protein and the reporting fluorophore of 20⁻25 nm, thus limiting the resolving power. Here, we used nanobodies to minimize this linkage error to ~4 nm. We demonstrate multiplexed imaging by using three nanobodies, each able to bind to a different family of fluorescent proteins. We couple the nanobodies with single DNA strands via a straight forward and stoichiometric chemical conjugation. Additionally, we built a versatile computer-controlled microfluidic setup to enable multiplexed DNA-PAINT in an efficient manner. As a proof of principle, we labeled and imaged proteins on mitochondria, the Golgi apparatus, and chromatin. We obtained super-resolved images of the three targets with 20 nm resolution, and within only 35 minutes acquisition time.
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Affiliation(s)
- Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany.
- International Max Planck Research School for Molecular Biology, Göttingen, Germany.
| | - Nazar Oleksiievets
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.
| | - Sebastian Isbaner
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.
| | - Mariana Eggert-Martinez
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany.
- International Max Planck Research School for Molecular Biology, Göttingen, Germany.
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.
| | - Roman Tsukanov
- Third Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany.
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182
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 536] [Impact Index Per Article: 107.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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183
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Maidorn M, Olichon A, Rizzoli SO, Opazo F. Nanobodies reveal an extra-synaptic population of SNAP-25 and Syntaxin 1A in hippocampal neurons. MAbs 2018; 11:305-321. [PMID: 30466346 PMCID: PMC6380399 DOI: 10.1080/19420862.2018.1551675] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synaptic vesicle fusion (exocytosis) is a precisely regulated process that entails the formation of SNARE complexes between the vesicle protein synaptobrevin 2 (VAMP2) and the plasma membrane proteins Syntaxin 1 and SNAP-25. The sub-cellular localization of the latter two molecules remains unclear, although they have been the subject of many recent investigations. To address this, we generated two novel camelid single domain antibodies (nanobodies) specifically binding to SNAP-25 and Syntaxin 1A. These probes penetrated more easily into samples and detected their targets more efficiently than conventional antibodies in crowded regions. When investigated by super-resolution imaging, the nanobodies revealed substantial extra-synaptic populations for both SNAP-25 and Syntaxin 1A, which were poorly detected by antibodies. Moreover, extra-synaptic Syntaxin 1A molecules were recruited to synapses during stimulation, suggesting that these are physiologically-active molecules. We conclude that nanobodies are able to reveal qualitatively and quantitatively different organization patterns, when compared to conventional antibodies.
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Affiliation(s)
- Manuel Maidorn
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
| | - Aurélien Olichon
- c Inserm, UMR 1037-CRCT , Toulouse , France.,d Université Toulouse III-Paul Sabatier , Toulouse , France
| | - Silvio O Rizzoli
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
| | - Felipe Opazo
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
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184
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Saal KA, Richter F, Rehling P, Rizzoli SO. Combined Use of Unnatural Amino Acids Enables Dual-Color Super-Resolution Imaging of Proteins via Click Chemistry. ACS NANO 2018; 12:12247-12254. [PMID: 30525434 DOI: 10.1021/acsnano.8b06047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in optical nanoscopy have brought the imaging resolution to the size of the individual macromolecules, thereby setting stringent requirements for the fluorescent labels. Such requirements are optimally fulfilled by the incorporation of unnatural amino acids (UAAs) in the proteins of interest (POIs), followed by fluorophore conjugation via click chemistry. However, this approach has been limited to single POIs in mammalian cells. Here we solve this problem by incorporating different UAAs in different POIs, which are expressed in independent cell sets. The cells are then fused, thereby combining the different proteins and organelles, and are easily imaged by dual-color super-resolution microscopy. This procedure, which we termed Fuse2Click, is simple, requires only the well-established Amber codon, and allows the use of all previously optimized UAAs and tRNA/RS pairs. This should render it a tool of choice for multicolor click-based imaging.
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Affiliation(s)
- Kim-A Saal
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration , University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain , Göttingen , Germany
| | - Frank Richter
- Institute for Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Peter Rehling
- Institute for Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration , University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain , Göttingen , Germany
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185
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DNA-Based Super-Resolution Microscopy: DNA-PAINT. Genes (Basel) 2018; 9:genes9120621. [PMID: 30544986 PMCID: PMC6315775 DOI: 10.3390/genes9120621] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward.
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186
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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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187
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Vigano MA, Bieli D, Schaefer JV, Jakob RP, Matsuda S, Maier T, Plückthun A, Affolter M. DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations. Biol Open 2018; 7:bio.036749. [PMID: 30237292 PMCID: PMC6262872 DOI: 10.1242/bio.036749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Over the last few years, protein-based affinity reagents have proven very helpful in cell and developmental biology. While many of these versatile small proteins can be expressed both in the intracellular and extracellular milieu in cultured cells and in living organisms, they can also be functionalized by fusing them to different protein domains in order to regulate or modulate their target proteins in diverse manners. For example, protein binders have been employed to degrade, trap, localize or enzymatically modify specific target proteins. Whereas binders to many endogenous proteins or small protein tags have been generated, several affinity reagents against fluorescent proteins have also been created and used to manipulate target proteins tagged with the corresponding fluorescent protein. Both of these approaches have resulted in improved methods for cell biological and developmental studies. While binders against GFP and mCherry have been previously isolated and validated, we now report the generation and utilization of designed ankyrin repeat proteins (DARPins) against the monomeric teal fluorescent protein 1 (mTFP1). Here we use the generated DARPins to delocalize Rab proteins to the nuclear compartment, in which they cannot fulfil their regular functions anymore. In the future, such manipulations might enable the production of acute loss-of-function phenotypes in different cell types or in living organisms based on direct protein manipulation rather than on genetic loss-of-function analyses. Summary: Structural characterization of two novel DARPins (designed ankyrin repeat proteins) recognizing the monomeric teal fluorescent protein 1 (mTFP1) and their functionalization for protein manipulation strategies in cultured cells and potentially in living organisms.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Dimitri Bieli
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - Roman P Jakob
- Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Timm Maier
- Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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188
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Klein A, Hank S, Raulf A, Joest EF, Tissen F, Heilemann M, Wieneke R, Tampé R. Live-cell labeling of endogenous proteins with nanometer precision by transduced nanobodies. Chem Sci 2018; 9:7835-7842. [PMID: 30429993 PMCID: PMC6194584 DOI: 10.1039/c8sc02910e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022] Open
Abstract
Accurate labeling of endogenous proteins for advanced light microscopy in living cells remains challenging. Nanobodies have been widely used for antigen labeling, visualization of subcellular protein localization and interactions. To facilitate an expanded application, we present a scalable and high-throughput strategy to simultaneously target multiple endogenous proteins in living cells with micro- to nanometer resolution. For intracellular protein labeling, we advanced nanobodies by site-specific and stoichiometric attachment of bright organic fluorophores. Their fast and fine-tuned intracellular transfer by microfluidic cell squeezing enabled high-throughput delivery with less than 10% dead cells. This strategy allowed for the dual-color imaging of distinct endogenous cellular structures, and culminated in super-resolution imaging of native protein networks in genetically non-modified living cells. The simultaneous delivery of multiple engineered nanobodies does not only offer exciting prospects for multiplexed imaging of endogenous protein, but also holds potential for visualizing native cellular structures with unprecedented accuracy.
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Affiliation(s)
- A Klein
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - S Hank
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - A Raulf
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - E F Joest
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - F Tissen
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - M Heilemann
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - R Wieneke
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - R Tampé
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
- Cluster of Excellence - Macromolecular Complexes , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
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189
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Jayasinghe I, Clowsley AH, de Langen O, Sali SS, Crossman DJ, Soeller C. Shining New Light on the Structural Determinants of Cardiac Couplon Function: Insights From Ten Years of Nanoscale Microscopy. Front Physiol 2018; 9:1472. [PMID: 30405432 PMCID: PMC6204384 DOI: 10.3389/fphys.2018.01472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
Remodelling of the membranes and protein clustering patterns during the pathogenesis of cardiomyopathies has renewed the interest in spatial visualisation of these structures in cardiomyocytes. Coincidental emergence of single molecule (super-resolution) imaging and tomographic electron microscopy tools in the last decade have led to a number of new observations on the structural features of the couplons, the primary sites of excitation-contraction coupling in the heart. In particular, super-resolution and tomographic electron micrographs have revised and refined the classical views of the nanoscale geometries of couplons, t-tubules and the organisation of the principal calcium handling proteins in both healthy and failing hearts. These methods have also allowed the visualisation of some features which were too small to be detected with conventional microscopy tools. With new analytical capabilities such as single-protein mapping, in situ protein quantification, correlative and live cell imaging we are now observing an unprecedented interest in adapting these research tools across the cardiac biophysical research discipline. In this article, we review the depth of the new insights that have been enabled by these tools toward understanding the structure and function of the cardiac couplon. We outline the major challenges that remain in these experiments and emerging avenues of research which will be enabled by these technologies.
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Affiliation(s)
- Izzy Jayasinghe
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Oscar de Langen
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Sonali S Sali
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - David J Crossman
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Christian Soeller
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
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190
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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191
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Vissa A, Giuliani M, Froese CD, Kim MS, Soroor F, Kim PK, Trimble WS, Yip CM. Single‐molecule localization microscopy of septin bundles in mammalian cells. Cytoskeleton (Hoboken) 2018; 76:63-72. [DOI: 10.1002/cm.21481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/04/2018] [Accepted: 07/16/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Adriano Vissa
- Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto Toronto Ontario Canada
| | - Maximiliano Giuliani
- Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto Toronto Ontario Canada
| | - Carol D. Froese
- Program in Cell BiologyThe Hospital for Sick Children Toronto Ontario Canada
| | - Moshe S. Kim
- Program in Cell BiologyThe Hospital for Sick Children Toronto Ontario Canada
| | - Forooz Soroor
- Program in Cell BiologyThe Hospital for Sick Children Toronto Ontario Canada
- Department of BiochemistryUniversity of Toronto Toronto Ontario Canada
| | - Peter K. Kim
- Program in Cell BiologyThe Hospital for Sick Children Toronto Ontario Canada
- Department of BiochemistryUniversity of Toronto Toronto Ontario Canada
| | - William S. Trimble
- Program in Cell BiologyThe Hospital for Sick Children Toronto Ontario Canada
- Department of BiochemistryUniversity of Toronto Toronto Ontario Canada
- Department of PhysiologyUniversity of Toronto Toronto Ontario Canada
| | - Christopher M. Yip
- Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto Toronto Ontario Canada
- Department of BiochemistryUniversity of Toronto Toronto Ontario Canada
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto Toronto Ontario Canada
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192
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Visualisation and analysis of hepatitis C virus non-structural proteins using super-resolution microscopy. Sci Rep 2018; 8:13604. [PMID: 30206266 PMCID: PMC6134135 DOI: 10.1038/s41598-018-31861-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 08/29/2018] [Indexed: 01/17/2023] Open
Abstract
Hepatitis C virus (HCV) RNA replication occurs in the cytosol of infected cells within a specialised membranous compartment. How the viral non-structural (NS) proteins are associated and organised within these structures remains poorly defined. We employed a super-resolution microscopy approach to visualise NS3 and NS5A in HCV infected cells. Using single molecule localisation microscopy, both NS proteins were resolved as clusters of localisations smaller than the diffraction-limited volume observed by wide-field. Analysis of the protein clusters identified a significant difference in size between the NS proteins. We also observed a reduction in NS5A cluster size following inhibition of RNA replication using daclatasvir, a phenotype which was maintained in the presence of the Y93H resistance associated substitution and not observed for NS3 clusters. These results provide insight into the NS protein organisation within hepatitis C virus RNA replication complexes and the mode of action of NS5A inhibitors.
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193
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Dynamics, nanoscale organization, and function of synaptic adhesion molecules. Mol Cell Neurosci 2018; 91:95-107. [DOI: 10.1016/j.mcn.2018.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
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194
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Strauss S, Nickels PC, Strauss MT, Jimenez Sabinina V, Ellenberg J, Carter JD, Gupta S, Janjic N, Jungmann R. Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging. Nat Methods 2018; 15:685-688. [PMID: 30127504 PMCID: PMC6345375 DOI: 10.1038/s41592-018-0105-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/12/2018] [Indexed: 01/12/2023]
Abstract
Although current implementations of super-resolution microscopy are technically approaching true molecular-scale resolution, this has not translated to imaging of biological specimens, because of the large size of conventional affinity reagents. Here we introduce slow off-rate modified aptamers (SOMAmers) as small and specific labeling reagents for use with DNA points accumulation in nanoscale topography (DNA-PAINT). To demonstrate the achievable resolution, specificity, and multiplexing capability of SOMAmers, we labeled and imaged both transmembrane and intracellular targets in fixed and live cells.
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Affiliation(s)
- Sebastian Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Philipp C Nickels
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Vilma Jimenez Sabinina
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | | | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.
- Max Planck Institute of Biochemistry, Martinsried, Germany.
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195
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Schlichthaerle T, Eklund AS, Schueder F, Strauss MT, Tiede C, Curd A, Ries J, Peckham M, Tomlinson DC, Jungmann R. Ortsspezifische Funktionalisierung von Affimeren für die DNA-PAINT-Mikroskopie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thomas Schlichthaerle
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Alexandra S. Eklund
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Florian Schueder
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Maximilian T. Strauss
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Alistair Curd
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Jonas Ries
- European Molecular Biology Laboratory; Cell Biology and Biophysics Unit; Heidelberg Deutschland
| | - Michelle Peckham
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Darren C. Tomlinson
- Astbury Centre for Structural and Molecular Biology; University of Leeds; Leeds Großbritannien
- School of Molecular and Cellular Biology; University of Leeds; Leeds Großbritannien
| | - Ralf Jungmann
- Fakultät für Physik und Center for Nanoscience; LMU München; München Deutschland
- Max-Planck-Institut für Biochemie; Martinsried Deutschland
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196
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Schlichthaerle T, Eklund AS, Schueder F, Strauss MT, Tiede C, Curd A, Ries J, Peckham M, Tomlinson DC, Jungmann R. Site-Specific Labeling of Affimers for DNA-PAINT Microscopy. Angew Chem Int Ed Engl 2018; 57:11060-11063. [PMID: 29873161 DOI: 10.1002/anie.201804020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/11/2018] [Indexed: 12/17/2022]
Abstract
Optical super-resolution techniques allow fluorescence imaging below the classical diffraction limit of light. From a technology standpoint, recent methods are approaching molecular-scale spatial resolution. However, this remarkable achievement is not easily translated to imaging of cellular components, since current labeling approaches are limited by either large label sizes (antibodies) or the sparse availability of small and efficient binders (nanobodies, aptamers, genetically-encoded tags). In this work, we combined recently developed Affimer reagents with site-specific DNA modification for high-efficiency labeling and imaging using DNA-PAINT. We assayed our approach using an actin Affimer. The small DNA-conjugated affinity binders could provide a solution for efficient multitarget super-resolution imaging in the future.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Alistair Curd
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Michelle Peckham
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
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197
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Truckenbrodt S, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep 2018; 19:embr.201845836. [PMID: 29987134 PMCID: PMC6123658 DOI: 10.15252/embr.201845836] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 01/01/2023] Open
Abstract
Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge.
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Affiliation(s)
- Sven Truckenbrodt
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany .,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Manuel Maidorn
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Dagmar Crzan
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Wildhagen
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Selda Kabatas
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
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198
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199
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Mitchell LS, Colwell LJ. Analysis of nanobody paratopes reveals greater diversity than classical antibodies. Protein Eng Des Sel 2018; 31:267-275. [PMID: 30053276 PMCID: PMC6277174 DOI: 10.1093/protein/gzy017] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 05/10/2018] [Accepted: 06/30/2018] [Indexed: 11/12/2022] Open
Abstract
Nanobodies (Nbs) are a class of antigen-binding protein derived from camelid immune systems, which achieve equivalent binding affinities and specificities to classical antibodies (Abs) despite being comprised of only a single variable domain. Here, we use a data set of 156 unique Nb:antigen complex structures to characterize Nb-antigen binding and draw comparison to a set of 156 unique Ab:antigen structures. We analyse residue composition and interactions at the antigen interface, together with structural features of the paratopes of both data sets. Our analysis finds that the set of Nb structures displays much greater paratope diversity, in terms of the structural segments involved in the paratope, the residues used at these positions to contact the antigen and furthermore the type of contacts made with the antigen. Our findings suggest a different relationship between contact propensity and sequence variability from that observed for Ab VH domains. The distinction between sequence positions that control interaction specificity and those that form the domain scaffold is much less clear-cut for Nbs, and furthermore H3 loop positions play a much more dominant role in determining interaction specificity.
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Affiliation(s)
- Laura S Mitchell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Lucy J Colwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
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200
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Bertier L, Hebbrecht T, Mettepenningen E, De Wit N, Zwaenepoel O, Verhelle A, Gettemans J. Nanobodies targeting cortactin proline rich, helical and actin binding regions downregulate invadopodium formation and matrix degradation in SCC-61 cancer cells. Biomed Pharmacother 2018; 102:230-241. [DOI: 10.1016/j.biopha.2018.03.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 01/19/2023] Open
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