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Martens KJA, Turkowyd B, Hohlbein J, Endesfelder U. Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking. Nat Methods 2024; 21:1074-1081. [PMID: 38225387 DOI: 10.1038/s41592-023-02149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024]
Abstract
In single-particle tracking, individual particles are localized and tracked over time to probe their diffusion and molecular interactions. Temporal crossing of trajectories, blinking particles, and false-positive localizations present computational challenges that have remained difficult to overcome. Here we introduce a robust, parameter-free alternative to single-particle tracking: temporal analysis of relative distances (TARDIS). In TARDIS, an all-to-all distance analysis between localizations is performed with increasing temporal shifts. These pairwise distances represent either intraparticle distances originating from the same particle, or interparticle distances originating from unrelated particles, and are fitted analytically to obtain quantitative measures on particle dynamics. We showcase that TARDIS outperforms tracking algorithms, benchmarked on simulated and experimental data of varying complexity. We further show that TARDIS performs accurately in complex conditions characterized by high particle density, strong emitter blinking or false-positive localizations, and is in fact limited by the capabilities of localization algorithms. TARDIS' robustness enables fivefold shorter measurements without loss of information.
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Affiliation(s)
- Koen J A Martens
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA.
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, the Netherlands.
| | - Bartosz Turkowyd
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, the Netherlands
- Microspectroscopy Research Facility, Wageningen University and Research, Wageningen, the Netherlands
| | - Ulrike Endesfelder
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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2
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Virant D, Vojnovic I, Winkelmeier J, Endesfelder M, Turkowyd B, Lando D, Endesfelder U. Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging. J Cell Biol 2023; 222:213836. [PMID: 36705602 PMCID: PMC9930162 DOI: 10.1083/jcb.202209096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.
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Affiliation(s)
- David Virant
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Ilijana Vojnovic
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jannik Winkelmeier
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Marc Endesfelder
- https://ror.org/05591te55Institute for Assyriology and Hittitology, Ludwig-Maximilians-Universität München, München, Germany
| | - Bartosz Turkowyd
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Endesfelder
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Correspondence to Ulrike Endesfelder:
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3
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Single molecule imaging simulations with advanced fluorophore photophysics. Commun Biol 2023; 6:53. [PMID: 36646743 PMCID: PMC9842740 DOI: 10.1038/s42003-023-04432-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Advanced fluorescence imaging techniques such as single-molecule localization microscopy (SMLM) fundamentally rely on the photophysical behavior of the employed fluorophores. This behavior is generally complex and impacts data quality in a subtle manner. A simulation software named Single-Molecule Imaging Simulator (SMIS) is introduced that simulates a widefield microscope and incorporates fluorophores with their spectral and photophysical properties. With SMIS, data collection schemes combining 3D, multicolor, single-particle-tracking or quantitative SMLM can be implemented. The influence of advanced fluorophore characteristics, imaging conditions, and environmental parameters can be evaluated, facilitating the design of real experiments and their proper interpretation.
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4
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Abstract
Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sheng Liu
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Philipp Hoess
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Jonas Ries
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
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5
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Martens KJA, Turkowyd B, Endesfelder U. Raw Data to Results: A Hands-On Introduction and Overview of Computational Analysis for Single-Molecule Localization Microscopy. FRONTIERS IN BIOINFORMATICS 2022; 1:817254. [PMID: 36303761 PMCID: PMC9580916 DOI: 10.3389/fbinf.2021.817254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/28/2021] [Indexed: 09/28/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) is an advanced microscopy method that uses the blinking of fluorescent molecules to determine the position of these molecules with a resolution below the diffraction limit (∼5-40 nm). While SMLM imaging itself is becoming more popular, the computational analysis surrounding the technique is still a specialized area and often remains a "black box" for experimental researchers. Here, we provide an introduction to the required computational analysis of SMLM imaging, post-processing and typical data analysis. Importantly, user-friendly, ready-to-use and well-documented code in Python and MATLAB with exemplary data is provided as an interactive experience for the reader, as well as a starting point for further analysis. Our code is supplemented by descriptions of the computational problems and their implementation. We discuss the state of the art in computational methods and software suites used in SMLM imaging and data analysis. Finally, we give an outlook into further computational challenges in the field.
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Affiliation(s)
- Koen J. A. Martens
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Bartosz Turkowyd
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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6
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Turkowyd B, Schreiber S, Wörtz J, Segal ES, Mevarech M, Duggin IG, Marchfelder A, Endesfelder U. Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the Archaeon Haloferax volcanii. Front Microbiol 2020; 11:583010. [PMID: 33329447 PMCID: PMC7714787 DOI: 10.3389/fmicb.2020.583010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/16/2020] [Indexed: 01/30/2023] Open
Abstract
In recent years, fluorescence microscopy techniques for the localization and tracking of single molecules in living cells have become well-established and are indispensable tools for the investigation of cellular biology and in vivo biochemistry of many bacterial and eukaryotic organisms. Nevertheless, these techniques are still not established for imaging archaea. Their establishment as a standard tool for the study of archaea will be a decisive milestone for the exploration of this branch of life and its unique biology. Here, we have developed a reliable protocol for the study of the archaeon Haloferax volcanii. We have generated an autofluorescence-free H. volcanii strain, evaluated several fluorescent proteins for their suitability to serve as single-molecule fluorescence markers and codon-optimized them to work under optimal H. volcanii cultivation conditions. We found that two of them, Dendra2Hfx and PAmCherry1Hfx, provide state-of-the-art single-molecule imaging. Our strategy is quantitative and allows dual-color imaging of two targets in the same field of view (FOV) as well as DNA co-staining. We present the first single-molecule localization microscopy (SMLM) images of the subcellular organization and dynamics of two crucial intracellular proteins in living H. volcanii cells, FtsZ1, which shows complex structures in the cell division ring, and RNA polymerase, which localizes around the periphery of the cellular DNA. This work should provide incentive to develop SMLM strategies for other archaeal organisms in the near future.
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Affiliation(s)
- Bartosz Turkowyd
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Julia Wörtz
- Department of Biology II, Ulm University, Ulm, Germany
| | - Ella Shtifman Segal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Mevarech
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iain G. Duggin
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Mellon College of Science, Carnegie-Mellon University, Pittsburgh, PA, United States
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7
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De Zitter E, Ridard J, Thédié D, Adam V, Lévy B, Byrdin M, Gotthard G, Van Meervelt L, Dedecker P, Demachy I, Bourgeois D. Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State. J Am Chem Soc 2020; 142:10978-10988. [PMID: 32463688 DOI: 10.1021/jacs.0c01880] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis-trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.
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Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Jacqueline Ridard
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Daniel Thédié
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Bernard Lévy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | | | - Peter Dedecker
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Isabelle Demachy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
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8
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Abstract
The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article, we review what we have learned during the past decade about the Z-ring's structure, function, and dynamics, with a particular focus on insights generated by recent high-resolution imaging and single-molecule analyses. We suggest that the major function of the Z-ring is to govern nascent cell pole morphogenesis by directing the spatiotemporal distribution of septal cell wall remodeling enzymes through the Z-ring's GTP hydrolysis-dependent treadmilling dynamics. In this role, FtsZ functions in cell division as the counterpart of the cell shape-determining actin homolog MreB in cell elongation.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
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9
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Dietz MS, Heilemann M. Optical super-resolution microscopy unravels the molecular composition of functional protein complexes. NANOSCALE 2019; 11:17981-17991. [PMID: 31573593 DOI: 10.1039/c9nr06364a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Optical super-resolution microscopy has revolutionized our understanding of cell biology. Next to visualizing cellular structures with near-molecular spatial resolution, an additional benefit is the molecular characterization of biomolecular complexes directly in an intact cell. Single-molecule localization microscopy, as one technology out of the toolbox of super-resolution methods, generates images by detecting the position of single fluorophore labels and is particularly suited for molecular quantification. We review imaging and analysis methods employing single-molecule localization microscopy and extract molecule numbers.
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Affiliation(s)
- Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.
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10
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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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11
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Endesfelder U. From single bacterial cell imaging towards in vivo single-molecule biochemistry studies. Essays Biochem 2019; 63:187-196. [PMID: 31197072 PMCID: PMC6610453 DOI: 10.1042/ebc20190002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022]
Abstract
Bacteria as single-cell organisms are important model systems to study cellular mechanisms and functions. In recent years and with the help of advanced fluorescence microscopy techniques, immense progress has been made in characterizing and quantifying the behavior of single bacterial cells on the basis of molecular interactions and assemblies in the complex environment of live cultures. Importantly, single-molecule imaging enables the in vivo determination of the stoichiometry and molecular architecture of subcellular structures, yielding detailed, quantitative, spatiotemporally resolved molecular maps and unraveling dynamic heterogeneities and subpopulations on the subcellular level. Nevertheless, open challenges remain. Here, we review the past and current status of the field, discuss example applications and give insights into future trends.
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Affiliation(s)
- Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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12
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Turkowyd B, Müller-Esparza H, Climenti V, Steube N, Endesfelder U, Randau L. Live-cell single-particle tracking photoactivated localization microscopy of Cascade-mediated DNA surveillance. Methods Enzymol 2019; 616:133-171. [PMID: 30691641 DOI: 10.1016/bs.mie.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Type I CRISPR-Cas systems utilize small CRISPR RNA (crRNA) molecules to scan DNA strands for target regions. Different crRNAs are bound by several CRISPR-associated (Cas) protein subunits that form the stable ribonucleoprotein complex Cascade. The Cascade-mediated DNA surveillance process requires a sufficient degree of base-complementarity between crRNA and target sequences and relies on the recognition of small DNA motifs, termed protospacer adjacent motifs. Recently, super-resolution microscopy and single-particle tracking methods have been developed to follow individual protein complexes in live cells. Here, we described how this technology can be adapted to visualize the DNA scanning process of Cascade assemblies in Escherichia coli cells. The activity of recombinant Type I-Fv Cascade complexes of Shewanella putrefaciens CN-32 serves as a model system that facilitates comparative studies for many of the diverse CRISPR-Cas systems.
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Affiliation(s)
- Bartosz Turkowyd
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vanessa Climenti
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Niklas Steube
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Lennart Randau
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany; Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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13
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Spahn CK, Glaesmann M, Grimm JB, Ayala AX, Lavis LD, Heilemann M. A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels. Sci Rep 2018; 8:14768. [PMID: 30282984 PMCID: PMC6170473 DOI: 10.1038/s41598-018-33052-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022] Open
Abstract
Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.
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Affiliation(s)
- Christoph K Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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14
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Mohr MA, Pantazis P. Primed Conversion: The New Kid on the Block for Photoconversion. Chemistry 2018; 24:8268-8274. [PMID: 29430743 DOI: 10.1002/chem.201705651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 11/07/2022]
Abstract
In 2015, a novel way to convert photoconvertible fluorescent proteins was reported that uses the intercept of blue and far-red light instead of traditional violet or near-UV light illumination. This Minireview describes and contrasts this distinct two-step mechanism termed primed conversion with traditional photoconversion. We provide a comprehensive overview of what is known to date about primed conversion and focus on the molecular requirements for it to take place. We provide examples of its application to axially confined photoconversion in complex tissues as well as super-resolution microscopy. Further, we describe why and when it is useful, including its advantages and disadvantages, and give an insight into potential future development in the field.
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Affiliation(s)
- Manuel Alexander Mohr
- Department for Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Periklis Pantazis
- Department for Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
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