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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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2
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Lucidi M, Tranca DE, Nichele L, Ünay D, Stanciu GA, Visca P, Holban AM, Hristu R, Cincotti G, Stanciu SG. SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells. Gigascience 2020; 9:giaa129. [PMID: 33231675 PMCID: PMC7684706 DOI: 10.1093/gigascience/giaa129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In recent years, a variety of imaging techniques operating at nanoscale resolution have been reported. These techniques have the potential to enrich our understanding of bacterial species relevant to human health, such as antibiotic-resistant pathogens. However, owing to the novelty of these techniques, their use is still confined to addressing very particular applications, and their availability is limited owing to associated costs and required expertise. Among these, scattering-type scanning near field optical microscopy (s-SNOM) has been demonstrated as a powerful tool for exploring important optical properties at nanoscale resolution, depending only on the size of a sharp tip. Despite its huge potential to resolve aspects that cannot be tackled otherwise, the penetration of s-SNOM into the life sciences is still proceeding at a slow pace for the aforementioned reasons. RESULTS In this work we introduce SSNOMBACTER, a set of s-SNOM images collected on 15 bacterial species. These come accompanied by registered Atomic Force Microscopy images, which are useful for placing nanoscale optical information in a relevant topographic context. CONCLUSIONS The proposed dataset aims to augment the popularity of s-SNOM and for accelerating its penetration in life sciences. Furthermore, we consider this dataset to be useful for the development and benchmarking of image analysis tools dedicated to s-SNOM imaging, which are scarce, despite the high need. In this latter context we discuss a series of image processing and analysis applications where SSNOMBACTER could be of help.
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Affiliation(s)
- Massimiliano Lucidi
- University Roma Tre, Department of Engineering, via Vito Volterra 62, Rome, 00146, Italy
| | - Denis E Tranca
- University Politehnica of Bucharest, Center for Microscopy-Microanalysis and Information Processing, 313 Splaiul Independentei, Bucharest,060042, Romania
| | - Lorenzo Nichele
- University Roma Tre, Department of Engineering, via Vito Volterra 62, Rome, 00146, Italy
| | - Devrim Ünay
- İzmir Democracy University, Faculty of Engineering, Electrical and Electronics Engineering, 14 Gürsel Aksel Bulvarı, İzmir, 35140, Turkey
| | - George A Stanciu
- University Politehnica of Bucharest, Center for Microscopy-Microanalysis and Information Processing, 313 Splaiul Independentei, Bucharest,060042, Romania
| | - Paolo Visca
- University Roma Tre, Department of Science, via Vito Volterra 62, Rome, 00146, Italy
| | - Alina Maria Holban
- University of Bucharest, Faculty of Biology, Department of Microbiology and Immunology, 1-3 Aleea Portocalelor, Bucharest, 060101, Romania
| | - Radu Hristu
- University Politehnica of Bucharest, Center for Microscopy-Microanalysis and Information Processing, 313 Splaiul Independentei, Bucharest,060042, Romania
| | - Gabriella Cincotti
- University Roma Tre, Department of Engineering, via Vito Volterra 62, Rome, 00146, Italy
| | - Stefan G Stanciu
- University Politehnica of Bucharest, Center for Microscopy-Microanalysis and Information Processing, 313 Splaiul Independentei, Bucharest,060042, Romania
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3
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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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4
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Kapanidis AN, Lepore A, El Karoui M. Rediscovering Bacteria through Single-Molecule Imaging in Living Cells. Biophys J 2018; 115:190-202. [PMID: 29680157 PMCID: PMC6050715 DOI: 10.1016/j.bpj.2018.03.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/16/2018] [Accepted: 03/26/2018] [Indexed: 12/23/2022] Open
Abstract
Bacteria are microorganisms central to health and disease, serving as important model systems for our understanding of molecular mechanisms and for developing new methodologies and vehicles for biotechnology. In the past few years, our understanding of bacterial cell functions has been enhanced substantially by powerful single-molecule imaging techniques. Using single fluorescent molecules as a means of breaking the optical microscopy limit, we can now reach resolutions of ∼20 nm inside single living cells, a spatial domain previously accessible only by electron microscopy. One can follow a single bacterial protein complex as it performs its functions and directly observe intricate cellular structures as they move and reorganize during the cell cycle. This toolbox enables the use of in vivo quantitative biology by counting molecules, characterizing their intracellular location and mobility, and identifying functionally distinct molecular distributions. Crucially, this can all be achieved while imaging large populations of cells, thus offering detailed views of the heterogeneity in bacterial communities. Here, we examine how this new scientific domain was born and discuss examples of applications to bacterial cellular mechanisms as well as emerging trends and applications.
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Affiliation(s)
- Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom.
| | - Alessia Lepore
- Institute of Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Meriem El Karoui
- Institute of Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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5
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Using transposition to introduce eGFP fusions in Sinorhizobium meliloti: A tool to analyze protein localization patterns in bacteria. J Biotechnol 2017; 257:139-149. [PMID: 28007516 DOI: 10.1016/j.jbiotec.2016.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/14/2016] [Accepted: 12/18/2016] [Indexed: 11/23/2022]
Abstract
Conventional methods used for the in vivo analysis of subcellular protein localizations and their spatio-temporal dynamics in prokaryotes are based on either the engineering of N(amino)- or C(carboxy)-terminal fusions of fluorescent proteins with the protein of interest, or involved probing internal sites for tag integration. In addition, the use of inducible or constitutive promoters for the expression of fluorescent fusion proteins can lead to overexpression and result in localization artifacts. Here, we describe a method for the synthesis of fluorescent fusion proteins using transposable elements, which can randomly integrate in the internal sections of the protein coding sequence to produce full-length fluorescent fusion proteins expressed at endogenous levels. The established method was used for investigating subcellular localization of proteins in the soil bacterium and plant symbiont Sinorhizobium meliloti. Two constructs for transposition-based insertion of the enhanced green fluorescent protein (eGFP), as well as for in vivo excision of the selection marker for the production of full-length proteins were engineered. Conjugation with pHB14 plasmid and induction of the transposition in S. meliloti produced approx. 3.22×104 transconjugant colonies harboring the fluorescent marker with the transposition efficiency of 0.8%. Sixteen randomly targeted proteins of diverse functions, fused to the eGFP were identified and analyzed in living cells by epifluorescence microscopy, demonstrating the suitability of the novel tool for massive, random production of fluorescent proteins and for following of these proteins with different localizations inside the prokaryotic cell.
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6
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Wei L, Ma Y, Zhu X, Xu J, Wang Y, Duan H, Xiao L. Sub-diffraction-limit localization imaging of a plasmonic nanoparticle pair with wavelength-resolved dark-field microscopy. NANOSCALE 2017; 9:8747-8755. [PMID: 28616948 DOI: 10.1039/c7nr02474f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, with wavelength-resolved dark-field microscopy, the center-of-mass localization information from nanoparticle pairs (i.e., spherical (45 nm in diameter) and rod (45 × 70 nm) shaped gold nanoparticle pairs with different gap distances and orientations) was explored and compared with the results determined by scanning electron microscopy (SEM) measurements. When the gap distance was less than 20 nm, the scattering spectrum of the nanoparticle pair was seriously modulated by the plasmonic coupling effect. The measured coordinate information determined by the optical method (Gaussian fitting) was not consistent with the true results determined by SEM measurement. A good correlation between the optical and SEM measurements was achieved when the gap distance was further increased (e.g., 20, 40 and 60 nm). Under these conditions, well-defined scattering peaks assigned to the corresponding individual nanoparticles could be distinguished from the obtained scattering spectrum. These results would afford valuable information for the studies on single plasmonic nanoparticle imaging applications with the optical microscopy method such as super-localization imaging, high precision single particle tracking in a crowding environment and so on.
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Affiliation(s)
- Lin Wei
- Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
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7
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Rowland DJ, Tuson HH, Biteen JS. Resolving Fast, Confined Diffusion in Bacteria with Image Correlation Spectroscopy. Biophys J 2017; 110:2241-51. [PMID: 27224489 DOI: 10.1016/j.bpj.2016.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 01/30/2023] Open
Abstract
By following single fluorescent molecules in a microscope, single-particle tracking (SPT) can measure diffusion and binding on the nanometer and millisecond scales. Still, although SPT can at its limits characterize the fastest biomolecules as they interact with subcellular environments, this measurement may require advanced illumination techniques such as stroboscopic illumination. Here, we address the challenge of measuring fast subcellular motion by instead analyzing single-molecule data with spatiotemporal image correlation spectroscopy (STICS) with a focus on measurements of confined motion. Our SPT and STICS analysis of simulations of the fast diffusion of confined molecules shows that image blur affects both STICS and SPT, and we find biased diffusion rate measurements for STICS analysis in the limits of fast diffusion and tight confinement due to fitting STICS correlation functions to a Gaussian approximation. However, we determine that with STICS, it is possible to correctly interpret the motion that blurs single-molecule images without advanced illumination techniques or fast cameras. In particular, we present a method to overcome the bias due to image blur by properly estimating the width of the correlation function by directly calculating the correlation function variance instead of using the typical Gaussian fitting procedure. Our simulation results are validated by applying the STICS method to experimental measurements of fast, confined motion: we measure the diffusion of cytosolic mMaple3 in living Escherichia coli cells at 25 frames/s under continuous illumination to illustrate the utility of STICS in an experimental parameter regime for which in-frame motion prevents SPT and tight confinement of fast diffusion precludes stroboscopic illumination. Overall, our application of STICS to freely diffusing cytosolic protein in small cells extends the utility of single-molecule experiments to the regime of fast confined diffusion without requiring advanced microscopy techniques.
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Affiliation(s)
- David J Rowland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Hannah H Tuson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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8
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Lee SA, Ponjavic A, Siv C, Lee SF, Biteen JS. Nanoscopic Cellular Imaging: Confinement Broadens Understanding. ACS NANO 2016; 10:8143-8153. [PMID: 27602688 DOI: 10.1021/acsnano.6b02863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.
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Affiliation(s)
- Stephen A Lee
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Aleks Ponjavic
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Chanrith Siv
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Steven F Lee
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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9
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Georgieva M, Cattoni DI, Fiche JB, Mutin T, Chamousset D, Nollmann M. Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging. Methods 2016; 105:44-55. [PMID: 27045944 DOI: 10.1016/j.ymeth.2016.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022] Open
Abstract
In order to study the detailed assembly and regulation mechanisms of complex structures and machineries in the cell, simultaneous in situ observation of all the individual interacting components should be achieved. Multi-color Single-Molecule Localization Microscopy (SMLM) is ideally suited for these quantifications. Here, we build on previous developments and thoroughly discuss a protocol for two-color SMLM combining PALM and STORM, including sample preparation details, image acquisition and data postprocessing analysis. We implement and evaluate a recently proposed colocalization analysis method (aCBC) that allows single-molecule colocalization quantification with the potential of revealing fine, nanometer-scaled, structural details of multicomponent complexes. Finally, using a doubly-labeled nuclear factor (Beaf-32) in Drosophila S2 cells we experimentally validate the colocalization quantification algorithm, highlight its advantages and discuss how using high molecular weight fluorescently labeled tags compromises colocalization precision in two-color SMLM experiments.
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Affiliation(s)
- Mariya Georgieva
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Thibaut Mutin
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Delphine Chamousset
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
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10
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Are the SSB-Interacting Proteins RecO, RecG, PriA and the DnaB-Interacting Protein Rep Bound to Progressing Replication Forks in Escherichia coli? PLoS One 2015; 10:e0134892. [PMID: 26244508 PMCID: PMC4526528 DOI: 10.1371/journal.pone.0134892] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
In all organisms several enzymes that are needed upon replication impediment are targeted to replication forks by interaction with a replication protein. In most cases these proteins interact with the polymerase clamp or with single-stranded DNA binding proteins (SSB). In Escherichia coli an accessory replicative helicase was also shown to interact with the DnaB replicative helicase. Here we have used cytological observation of Venus fluorescent fusion proteins expressed from their endogenous loci in live E. coli cells to determine whether DNA repair and replication restart proteins that interact with a replication protein travel with replication forks. A custom-made microscope that detects active replisome molecules provided that they are present in at least three copies was used. Neither the recombination proteins RecO and RecG, nor the replication accessory helicase Rep are detected specifically in replicating cells in our assay, indicating that either they are not present at progressing replication forks or they are present in less than three copies. The Venus-PriA fusion protein formed foci even in the absence of replication forks, which prevented us from reaching a conclusion.
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11
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Lagomarsino MC, Espéli O, Junier I. From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments. FEBS Lett 2015; 589:2996-3004. [PMID: 26171924 DOI: 10.1016/j.febslet.2015.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022]
Abstract
The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of experimental tools that have provided insights into the description of the bacterial chromosome, including genetic, biochemical and fluorescence microscopy techniques. We then explore the possibility of using comparative genomics to isolate functionally important features of chromosome organization, exploiting the fact that features shared between phylogenetically distant bacterial species reflect functional significance. Finally, we discuss possible future perspectives from the field of experimental evolution. Specifically, we propose novel experiments in which bacteria could be screened and selected on the basis of the structural properties of their chromosomes.
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Affiliation(s)
| | - Olivier Espéli
- CIRB-Collège de France, CNRS UMR 7241, INSERM U1050, Paris, France
| | - Ivan Junier
- Laboratoire Adaptation et Pathogénie des Micro-organismes - UMR 5163, Université Grenoble 1, CNRS, BP 170, F-38042 Grenoble Cedex 9, France; Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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12
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015. [PMID: 26088273 DOI: 10.1103/revmodphys.87.1183] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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13
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Moerner WEWE. Spektroskopie, Visualisierung und Photomanipulation einzelner Moleküle: die Grundlage für superhochauflösende Mikroskopie (Nobel-Aufsatz). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015; 54:8067-93. [PMID: 26088273 DOI: 10.1002/anie.201501949] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/10/2022]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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15
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Lemgruber L, Sant'Anna C, Griffths C, Abud Y, Mhlanga M, Wallich R, Frischknecht F. Nanoscopic Localization of Surface-Exposed Antigens of Borrelia burgdorferi. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:680-688. [PMID: 25739645 DOI: 10.1017/s1431927615000318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, is transmitted to humans through the bite of infected Ixodes spp. ticks. Successful infection of vertebrate hosts necessitates sophisticated means of the pathogen to escape the vertebrates' immune system. One strategy employed by Lyme disease spirochetes to evade adaptive immunity involves a highly coordinated regulation of the expression of outer surface proteins that is vital for infection, dissemination, and persistence. Here we characterized the expression pattern of bacterial surface antigens using different microscopy techniques, from fluorescent wide field to super-resolution and immunogold-scanning electron microscopy. A fluorescent strain of B. burgdorferi spirochetes was labeled with monoclonal antibodies directed against various bacterial surface antigens. Our results indicate that OspA is more evenly distributed over the surface than OspB and OspC that were present as punctate areas.
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Affiliation(s)
- Leandro Lemgruber
- 1Department of Infectious Diseases - Parasitology,Im Neuenheimer Feld 324,University of Heidelberg Medical School,69120, Heidelberg,Germany
| | - Celso Sant'Anna
- 2Laboratory of Microscopy for Life Sciences,Diretoria de Metrologia Aplicada às Ciências da Vida - Dimav,Instituto Nacional de Metrologia,Qualidade e Tecnologia - Inmetro,25250-020,Duque de Caxias,Rio de Janeiro,Brazil
| | - Caron Griffths
- 4Gene Expression and Biophysics Group,Synthetic Biology Emerging Research Area,Council for Scientific and Industrial Research,Box 395,Pretoria 0001S,South Africa
| | - Yuri Abud
- 2Laboratory of Microscopy for Life Sciences,Diretoria de Metrologia Aplicada às Ciências da Vida - Dimav,Instituto Nacional de Metrologia,Qualidade e Tecnologia - Inmetro,25250-020,Duque de Caxias,Rio de Janeiro,Brazil
| | - Musa Mhlanga
- 4Gene Expression and Biophysics Group,Synthetic Biology Emerging Research Area,Council for Scientific and Industrial Research,Box 395,Pretoria 0001S,South Africa
| | - Reinhard Wallich
- 5Institute for Immunology,Im Neuenheimer Feld 305,University of Heidelberg Medical School,69120,Heidelberg,Germany
| | - Friedrich Frischknecht
- 1Department of Infectious Diseases - Parasitology,Im Neuenheimer Feld 324,University of Heidelberg Medical School,69120, Heidelberg,Germany
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16
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Innovative techniques, sensors, and approaches for imaging biofilms at different scales. Trends Microbiol 2015; 23:233-42. [DOI: 10.1016/j.tim.2014.12.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/19/2014] [Indexed: 11/19/2022]
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17
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Tuson HH, Biteen JS. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal Chem 2014; 87:42-63. [PMID: 25380480 DOI: 10.1021/ac5041346] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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18
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Malt LM, Perrett CA, Humphrey S, Jepson MA. Applications of microscopy in Salmonella research. Methods Mol Biol 2014; 1225:165-98. [PMID: 25253256 DOI: 10.1007/978-1-4939-1625-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.
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Affiliation(s)
- Layla M Malt
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Tyndall Avenue, Bristol, BS8 1TD, UK
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Bakshi S, Dalrymple RM, Li W, Choi H, Weisshaar JC. Partitioning of RNA polymerase activity in live Escherichia coli from analysis of single-molecule diffusive trajectories. Biophys J 2014; 105:2676-86. [PMID: 24359739 DOI: 10.1016/j.bpj.2013.10.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/20/2013] [Accepted: 10/23/2013] [Indexed: 11/28/2022] Open
Abstract
Superresolution fluorescence microscopy is used to locate single copies of RNA polymerase (RNAP) in live Escherichia coli and track their diffusive motion. On a timescale of 0.1-1 s, most copies separate remarkably cleanly into two diffusive states. The "slow" RNAPs, which move indistinguishably from DNA loci, are assigned to specifically bound copies (with fractional population ftrxn) that are initiating transcription, elongating, pausing, or awaiting termination. The "mixed-state" RNAP copies, with effective diffusion constant Dmixed = 0.21 μm(2) s(-1), are assigned as a rapidly exchanging mixture of nonspecifically bound copies (fns) and copies undergoing free, three-dimensional diffusion within the nucleoids (ffree). Longer trajectories of 7-s duration reveal transitions between the slow and mixed states, corroborating the assignments. Short trajectories of 20-ms duration enable direct observation of the freely diffusing RNAP copies, yielding Dfree = 0.7 μm(2) s(-1). Analysis of single-particle trajectories provides quantitative estimates of the partitioning of RNAP into different states of activity: ftrxn = 0.54 ± 0.07, fns = 0.28 ± 0.05, ffree = 0.12 ± 0.03, and fnb = 0.06 ± 0.05 (fraction unable to bind to DNA on a 1-s timescale). These fractions disagree with earlier estimates.
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Affiliation(s)
- Somenath Bakshi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Renée M Dalrymple
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wenting Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Heejun Choi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin; Molecular Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin.
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20
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Han R, Li Z, Fan Y, Jiang Y. Recent Advances in Super-Resolution Fluorescence Imaging and Its Applications in Biology. J Genet Genomics 2013; 40:583-95. [DOI: 10.1016/j.jgg.2013.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 11/16/2022]
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21
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Cattoni DI, Fiche JB, Valeri A, Mignot T, Nöllmann M. Super-resolution imaging of bacteria in a microfluidics device. PLoS One 2013; 8:e76268. [PMID: 24146850 PMCID: PMC3797773 DOI: 10.1371/journal.pone.0076268] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved complex, highly-coordinated, multi-component cellular engines to achieve high degrees of efficiency, accuracy, adaptability, and redundancy. Super-resolution fluorescence microscopy methods are ideally suited to investigate the internal composition, architecture, and dynamics of molecular machines and large cellular complexes. These techniques require the long-term stability of samples, high signal-to-noise-ratios, low chromatic aberrations and surface flatness, conditions difficult to meet with traditional immobilization methods. We present a method in which cells are functionalized to a microfluidics device and fluorophores are injected and imaged sequentially. This method has several advantages, as it permits the long-term immobilization of cells and proper correction of drift, avoids chromatic aberrations caused by the use of different filter sets, and allows for the flat immobilization of cells on the surface. In addition, we show that different surface chemistries can be used to image bacteria at different time-scales, and we introduce an automated cell detection and image analysis procedure that can be used to obtain cell-to-cell, single-molecule localization and dynamic heterogeneity as well as average properties at the super-resolution level.
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Affiliation(s)
- Diego I. Cattoni
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Alessandro Valeri
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Centre National de la Recherche Scientifique, Aix-Marseille University, Unité Mixte de Recherche 7283, Marseille, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
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22
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Kedrov A, Kusters I, Driessen AJM. Single-Molecule Studies of Bacterial Protein Translocation. Biochemistry 2013; 52:6740-54. [DOI: 10.1021/bi400913x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alexej Kedrov
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Ilja Kusters
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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