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Hellmeier J, Strauss S, Xu S, Masullo LA, Unterauer EM, Kowalewski R, Jungmann R. Quantification of absolute labeling efficiency at the single-protein level. Nat Methods 2024:10.1038/s41592-024-02242-5. [PMID: 38658647 DOI: 10.1038/s41592-024-02242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024]
Abstract
State-of-the-art super-resolution microscopy allows researchers to spatially resolve single proteins in dense clusters. However, accurate quantification of protein organization and stoichiometries requires a general method to evaluate absolute binder labeling efficiency, which is currently unavailable. Here we introduce a universally applicable approach that uses a reference tag fused to a target protein of interest. By attaching high-affinity binders, such as antibodies or nanobodies, to both the reference tag and the target protein, and then employing DNA-barcoded sequential super-resolution imaging, we can correlate the location of the reference tag with the target molecule binder. This approach facilitates the precise quantification of labeling efficiency at the single-protein level.
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Affiliation(s)
| | | | - Shuhan Xu
- Max Planck Institute of Biochemistry, Planegg, Germany
| | | | | | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany.
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.
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2
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Unterauer EM, Shetab Boushehri S, Jevdokimenko K, Masullo LA, Ganji M, Sograte-Idrissi S, Kowalewski R, Strauss S, Reinhardt SCM, Perovic A, Marr C, Opazo F, Fornasiero EF, Jungmann R. Spatial proteomics in neurons at single-protein resolution. Cell 2024; 187:1785-1800.e16. [PMID: 38552614 DOI: 10.1016/j.cell.2024.02.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/28/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access to the location and interaction of all biomolecules. Significant advances were achieved by super-resolution microscopy, but such methods are still far from reaching the multiplexing capacity of proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that is capable of achieving virtually unlimited multiplexing at better than 15 nm resolution. Using SUM-PAINT, we generated 30-plex single-molecule resolved datasets in neurons and adapted omics-inspired analysis for data exploration. This allowed us to reveal the complexity of synaptic heterogeneity, leading to the discovery of a distinct synapse type. We not only provide a resource for researchers, but also an integrated acquisition and analysis workflow for comprehensive spatial proteomics at single-protein resolution.
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Affiliation(s)
- Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sayedali Shetab Boushehri
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Data & Analytics, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Kristina Jevdokimenko
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Mahipal Ganji
- Max Planck Institute of Biochemistry, Planegg, Germany; Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ana Perovic
- Max Planck Institute of Biochemistry, Planegg, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Department of Life Sciences, University of Trieste, Trieste, Italy.
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany.
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Reinhardt SCM, Masullo LA, Baudrexel I, Steen PR, Kowalewski R, Eklund AS, Strauss S, Unterauer EM, Schlichthaerle T, Strauss MT, Klein C, Jungmann R. Ångström-resolution fluorescence microscopy. Nature 2023; 617:711-716. [PMID: 37225882 PMCID: PMC10208979 DOI: 10.1038/s41586-023-05925-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 05/26/2023]
Abstract
Fluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches1-6 can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations7-14 have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.
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Affiliation(s)
- Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | | | - Isabelle Baudrexel
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Philipp R Steen
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Alexandra S Eklund
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Maximilian T Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Christian Klein
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development, Schlieren, Switzerland
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany.
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany.
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Unterauer EM, Jungmann R. Quantitative Imaging With DNA-PAINT for Applications in Synaptic Neuroscience. Front Synaptic Neurosci 2022; 13:798267. [PMID: 35197837 PMCID: PMC8860300 DOI: 10.3389/fnsyn.2021.798267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 12/02/2022] Open
Abstract
Super-resolution (SR) microscopy techniques have been advancing the understanding of neuronal protein networks and interactions. Unraveling the arrangement of proteins with molecular resolution provided novel insights into neuron cytoskeleton structure and actin polymerization dynamics in synaptic spines. Recent improvements in quantitative SR imaging have been applied to synaptic protein clusters and with improved multiplexing technology, the interplay of multiple protein partners in synaptic active zones has been elucidated. While all SR techniques come with benefits and drawbacks, true molecular quantification is a major challenge with the most complex requirements for labeling reagents and careful experimental design. In this perspective, we provide an overview of quantitative SR multiplexing and discuss in greater detail the quantification and multiplexing capabilities of the SR technique DNA-PAINT. Using predictable binding kinetics of short oligonucleotides, DNA-PAINT provides two unique approaches to address multiplexed molecular quantification: qPAINT and Exchange-PAINT. With precise and accurate quantification and spectrally unlimited multiplexing, DNA-PAINT offers an attractive route to unravel complex protein interaction networks in neurons. Finally, while the SR community has been pushing technological advances from an imaging technique perspective, the development of universally available, small, efficient, and quantitative labels remains a major challenge in the field.
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Affiliation(s)
- Eduard M. Unterauer
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- *Correspondence: Ralf Jungmann,
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5
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Schueder F, Unterauer EM, Ganji M, Jungmann R. Front Cover: DNA‐Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020. [DOI: 10.1002/pmic.202070161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Schueder F, Unterauer EM, Ganji M, Jungmann R. DNA-Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020; 20:e1900368. [PMID: 33030780 DOI: 10.1002/pmic.201900368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Indexed: 12/18/2022]
Abstract
Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an almost routine basis, coupling this high content to spatial information in a single cell and tissue context is challenging. Here, current implementations of spatial omics are discussed and recent developments in the field of DNA-barcoded fluorescence microscopy are reviewed. Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy.
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Affiliation(s)
- Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Eduard M Unterauer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Mahipal Ganji
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
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7
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Abstract
Staphylococcal pathogens adhere to their human targets with exceptional resilience to mechanical stress, some propagating force to the bacterium via small, Ig-like folds called B domains. We examine the mechanical stability of these folds using atomic force microscopy-based single-molecule force spectroscopy. The force required to unfold a single B domain is larger than 2 nN – the highest mechanostability of a protein to date by a large margin. B domains coordinate three calcium ions, which we identify as crucial for their extreme mechanical strength. When calcium is removed through chelation, unfolding forces drop by a factor of four. Through systematic mutations in the calcium coordination sites we can tune the unfolding forces from over 2 nN to 0.15 nN, and dissect the contribution of each ion to B domain mechanostability. Their extraordinary strength, rapid refolding and calcium-tunable force response make B domains interesting protein design targets. Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.
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Affiliation(s)
- Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
| | - Eduard M Unterauer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Thomas Nicolaus
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
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