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Liu J, Li Y, Chen T, Zhang F, Xu F. Machine Learning for Single-Molecule Localization Microscopy: From Data Analysis to Quantification. Anal Chem 2024; 96:11103-11114. [PMID: 38946062 DOI: 10.1021/acs.analchem.3c05857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a versatile tool for realizing nanoscale imaging with visible light and providing unprecedented opportunities to observe bioprocesses. The integration of machine learning with SMLM enhances data analysis by improving efficiency and accuracy. This tutorial aims to provide a comprehensive overview of the data analysis process and theoretical aspects of SMLM, while also highlighting the typical applications of machine learning in this field. By leveraging advanced analytical techniques, SMLM is becoming a powerful quantitative analysis tool for biological research.
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Affiliation(s)
- Jianli Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yumian Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Tailong Chen
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Fan Xu
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
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2
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Vignolini T, Capitanio M, Caldini C, Gardini L, Pavone FS. Highly inclined light sheet allows volumetric super-resolution imaging of efflux pumps distribution in bacterial biofilms. Sci Rep 2024; 14:12902. [PMID: 38839922 PMCID: PMC11153600 DOI: 10.1038/s41598-024-63729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
Bacterial biofilms are highly complex communities in which isogenic bacteria display different gene expression patterns and organize in a three-dimensional mesh gaining enhanced resistance to biocides. The molecular mechanisms behind such increased resistance remain mostly unknown, also because of the technical difficulties in biofilm investigation at the sub-cellular and molecular level. In this work we focus on the AcrAB-TolC protein complex, a multidrug efflux pump found in Enterobacteriaceae, whose overexpression is associated with most multiple drug resistance (MDR) phenotypes occurring in Gram-negative bacteria. We propose an optical method to quantify the expression level of the AcrAB-TolC pump within the biofilm volume at the sub-cellular level, with single-molecule sensitivity. Through a combination of super-resolution PALM with single objective light sheet and precision genome editing, we can directly quantify the spatial distribution of endogenous AcrAB-TolC pumps expressed in both planktonic bacteria and, importantly, within the bacterial biofilm volume. We observe a gradient of pump density within the biofilm volume and over the course of biofilm maturation. Notably, we propose an optical method that could be broadly employed to achieve volumetric super-resolution imaging of thick samples.
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Affiliation(s)
- T Vignolini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy.
- Parasite RNA Biology Group, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
| | - M Capitanio
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - C Caldini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - L Gardini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- National Institute of Optics, National Research Council, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
| | - F S Pavone
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
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3
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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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4
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Vojnovic I, Caspari OD, Hoşkan MA, Endesfelder U. Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level. Open Biol 2024; 14:230414. [PMID: 38320620 PMCID: PMC10846934 DOI: 10.1098/rsob.230414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).
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Affiliation(s)
- Ilijana Vojnovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oliver D. Caspari
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Microbiology, Institute Pasteur, Paris, France
| | - Mehmet Ali Hoşkan
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - 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, Carnegie Mellon University, Pittsburgh, PA, USA
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5
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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6
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Platzer R, Hellmeier J, Göhring J, Perez ID, Schatzlmaier P, Bodner C, Focke‐Tejkl M, Schütz GJ, Sevcsik E, Stockinger H, Brameshuber M, Huppa JB. Monomeric agonist peptide/MHCII complexes activate T-cells in an autonomous fashion. EMBO Rep 2023; 24:e57842. [PMID: 37768718 PMCID: PMC10626418 DOI: 10.15252/embr.202357842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular crowding of agonist peptide/MHC class II complexes (pMHCIIs) with structurally similar, yet per se non-stimulatory endogenous pMHCIIs is postulated to sensitize T-cells for the recognition of single antigens on the surface of dendritic cells and B-cells. When testing this premise with the use of advanced live cell microscopy, we observe pMHCIIs as monomeric, randomly distributed entities diffusing rapidly after entering the APC surface. Synaptic TCR engagement of highly abundant endogenous pMHCIIs is low or non-existent and affects neither TCR engagement of rare agonist pMHCII in early and advanced synapses nor agonist-induced TCR-proximal signaling. Our findings highlight the capacity of single freely diffusing agonist pMHCIIs to elicit the full T-cell response in an autonomous and peptide-specific fashion with consequences for adaptive immunity and immunotherapeutic approaches.
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Affiliation(s)
- René Platzer
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Joschka Hellmeier
- TU Wien, Institute of Applied PhysicsViennaAustria
- Present address:
Max Planck Institute of Biochemistry, Molecular Imaging and BionanotechnologyMartinsriedGermany
| | - Janett Göhring
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Iago Doel Perez
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
- Present address:
Takeda Manufacturing Austria AGViennaAustria
| | - Philipp Schatzlmaier
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Clara Bodner
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Margarete Focke‐Tejkl
- Center for Pathophysiology, Infectiology, Immunology, Institute for Pathophysiology and Allergy ResearchMedical University of ViennaViennaAustria
| | | | - Eva Sevcsik
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Hannes Stockinger
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | | | - Johannes B Huppa
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
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7
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Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
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Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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8
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Fan J, El Sayyed H, Pambos OJ, Stracy M, Kyropoulos J, Kapanidis AN. RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons. Nucleic Acids Res 2023; 51:8085-8101. [PMID: 37351576 PMCID: PMC10450203 DOI: 10.1093/nar/gkad511] [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: 02/02/2022] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Bacterial transcription by RNA polymerase (RNAP) is spatially organized. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich medium, with several studies linking RNAP clustering and transcription of rRNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons (Δrrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting five or six of the seven chromosomal rrn operons. Spatial analysis in Δrrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at cell endcaps, where the remaining rrn operons reside. These results support a model where RNAPs in Δrrn strains relocate to copies of the remaining rrn operons. In rich medium, Δrrn strains redistribute RNAP to minimize growth defects due to rrn deletions, with very high RNAP densities on rrn genes leading to genomic instability. Our study links RNAP clusters and rrn transcription, and offers insight into how bacteria maintain growth in the presence of only 1-2 rrn operons.
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Affiliation(s)
- Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
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9
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Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA. Proc Natl Acad Sci U S A 2023; 120:e2303849120. [PMID: 37406096 PMCID: PMC10334767 DOI: 10.1073/pnas.2303849120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in the cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryotic Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so are unclear. We used multiwavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the Escherichia coli transcription cycle. In our experiments, RapA at <5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post termination complex (PTC)-consisting of core RNA polymerase (RNAP)-bound sequence nonspecifically to double-stranded DNA-and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription reinitiation in proteobacterial genomes.
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Affiliation(s)
- Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, MA02453
| | | | | | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA02453
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10
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Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA.. [DOI: 10.1101/2023.03.22.533849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
ABSTRACTFree-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in theE. colitranscription cycle. In our experiments, RapA at < 5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post-termination complex (PTC) -- consisting of core RNA polymerase (RNAP) bound to dsDNA -- and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription re-initiation in proteobacterial genomes.SIGNIFICANCERNA synthesis is an essential conduit of genetic information in all organisms. After transcribing an RNA, the bacterial RNA polymerase (RNAP) must be reused to make subsequent RNAs, but the steps that enable RNAP reuse are unclear. We directly observed the dynamics of individual molecules of fluorescently labeled RNAP and the enzyme RapA as they colocalized with DNA during and after RNA synthesis. Our studies show that RapA uses ATP hydrolysis to remove RNAP from DNA after the RNA is released from RNAP and reveal essential features of the mechanism by which this removal occurs. These studies fill in key missing pieces in our current understanding of the events that occur after RNA is released and that enable RNAP reuse.
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11
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Scalisi S, Ahmad A, D'Annunzio S, Rousseau D, Zippo A. Quantitative Analysis of PcG-Associated Condensates by Stochastic Optical Reconstruction Microscopy (STORM). Methods Mol Biol 2023; 2655:183-200. [PMID: 37212997 DOI: 10.1007/978-1-0716-3143-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The polycomb group (PcG) proteins play a central role in the maintenance of a repressive state of gene expression. Recent findings demonstrate that PcG components are organized into nuclear condensates, contributing to the reshaping of chromatin architecture in physiological and pathological conditions, thus affecting the nuclear mechanics. In this context, direct stochastic optical reconstruction microscopy (dSTORM) provides an effective tool to achieve a detailed characterization of PcG condensates by visualizing them at a nanometric level. Furthermore, by analyzing dSTORM datasets with cluster analysis algorithms, quantitative information can be yielded regarding protein numbers, grouping, and spatial organization. Here, we describe how to set up a dSTORM experiment and perform the data analysis to study PcG complexes' components in adhesion cells quantitatively.
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Affiliation(s)
- Silvia Scalisi
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Ali Ahmad
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
| | - Sarah D'Annunzio
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - David Rousseau
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
| | - Alessio Zippo
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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12
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Joyeux M. Organization of the bacterial nucleoid by DNA-bridging proteins and globular crowders. Front Microbiol 2023; 14:1116776. [PMID: 36925468 PMCID: PMC10011147 DOI: 10.3389/fmicb.2023.1116776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most important contributions to the compaction of the DNA coil are the cross-linking of the DNA by nucleoid proteins (like H-NS and StpA) and the demixing of DNA and other abundant globular macromolecules which do not bind to the DNA (like ribosomes). The present work deals with the interplay of DNA-bridging proteins and globular macromolecular crowders, with the goal of determining the extent to which they collaborate in organizing the nucleoid. In order to answer this question, a coarse-grained model was developed and its properties were investigated through Brownian dynamics simulations. These simulations reveal that the radius of gyration of the DNA coil decreases linearly with the effective volume ratio of globular crowders and the number of DNA bridges formed by nucleoid proteins in the whole range of physiological values. Moreover, simulations highlight the fact that the number of DNA bridges formed by nucleoid proteins depends crucially on their ability to self-associate (oligomerize). An explanation for this result is proposed in terms of the mean distance between DNA segments and the capacity of proteins to maintain DNA-bridging in spite of the thermal fluctuations of the DNA network. Finally, simulations indicate that non-associating proteins preserve a high mobility inside the nucleoid while contributing to its compaction, leading to a DNA/protein complex which looks like a liquid droplet. In contrast, self-associating proteins form a little deformable network which cross-links the DNA chain, with the consequence that the DNA/protein complex looks more like a gel.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, St Martin d'Hères, France
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13
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Verzelli P, Nold A, Sun C, Heilemann M, Schuman EM, Tchumatchenko T. Unbiased choice of global clustering parameters for single-molecule localization microscopy. Sci Rep 2022. [PMID: 36581654 DOI: 10.1101/2021.02.22.432198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Single-molecule localization microscopy resolves objects below the diffraction limit of light via sparse, stochastic detection of target molecules. Single molecules appear as clustered detection events after image reconstruction. However, identification of clusters of localizations is often complicated by the spatial proximity of target molecules and by background noise. Clustering results of existing algorithms often depend on user-generated training data or user-selected parameters, which can lead to unintentional clustering errors. Here we suggest an unbiased algorithm (FINDER) based on adaptive global parameter selection and demonstrate that the algorithm is robust to noise inclusion and target molecule density. We benchmarked FINDER against the most common density based clustering algorithms in test scenarios based on experimental datasets. We show that FINDER can keep the number of false positive inclusions low while also maintaining a low number of false negative detections in densely populated regions.
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Affiliation(s)
- Pietro Verzelli
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Nold
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
- Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Chao Sun
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Erin M Schuman
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Tatjana Tchumatchenko
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany.
- Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
- Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany.
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14
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Verzelli P, Nold A, Sun C, Heilemann M, Schuman EM, Tchumatchenko T. Unbiased choice of global clustering parameters for single-molecule localization microscopy. Sci Rep 2022; 12:22561. [PMID: 36581654 PMCID: PMC9800574 DOI: 10.1038/s41598-022-27074-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Single-molecule localization microscopy resolves objects below the diffraction limit of light via sparse, stochastic detection of target molecules. Single molecules appear as clustered detection events after image reconstruction. However, identification of clusters of localizations is often complicated by the spatial proximity of target molecules and by background noise. Clustering results of existing algorithms often depend on user-generated training data or user-selected parameters, which can lead to unintentional clustering errors. Here we suggest an unbiased algorithm (FINDER) based on adaptive global parameter selection and demonstrate that the algorithm is robust to noise inclusion and target molecule density. We benchmarked FINDER against the most common density based clustering algorithms in test scenarios based on experimental datasets. We show that FINDER can keep the number of false positive inclusions low while also maintaining a low number of false negative detections in densely populated regions.
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Affiliation(s)
- Pietro Verzelli
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Nold
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany ,grid.419505.c0000 0004 0491 3878Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Chao Sun
- grid.419505.c0000 0004 0491 3878Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Mike Heilemann
- grid.7839.50000 0004 1936 9721Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Tatjana Tchumatchenko
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany ,grid.410607.4Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany ,grid.419505.c0000 0004 0491 3878Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
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15
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Zhang Y, Lu Y, El Sayyed H, Bian J, Lin J, Li X. Transcription factor dynamics in plants: Insights and technologies for in vivo imaging. PLANT PHYSIOLOGY 2022; 189:23-36. [PMID: 35134239 PMCID: PMC9070795 DOI: 10.1093/plphys/kiac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Biochemical and genetic approaches have been extensively used to study transcription factor (TF) functions, but their dynamic behaviors and the complex ways in which they regulate transcription in plant cells remain unexplored, particularly behaviors such as translocation and binding to DNA. Recent developments in labeling and imaging techniques provide the necessary sensitivity and resolution to study these behaviors in living cells. In this review, we present an up-to-date portrait of the dynamics and regulation of TFs under physiologically relevant conditions and then summarize recent advances in fluorescent labeling strategies and imaging techniques. We then discuss future prospects and challenges associated with the application of these techniques to examine TFs' intricate dance in living plants.
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Affiliation(s)
- Yuan Zhang
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yuqing Lu
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Jiahui Bian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
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16
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Nunes Vicente F, Lelek M, Tinevez JY, Tran QD, Pehau-Arnaudet G, Zimmer C, Etienne-Manneville S, Giannone G, Leduc C. Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging. SCIENCE ADVANCES 2022; 8:eabm2696. [PMID: 35213220 PMCID: PMC8880768 DOI: 10.1126/sciadv.abm2696] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/11/2022] [Indexed: 05/30/2023]
Abstract
Intermediate filaments (IFs) are involved in key cellular functions including polarization, migration, and protection against large deformations. These functions are related to their remarkable ability to extend without breaking, a capacity that should be determined by the molecular organization of subunits within filaments. However, this structure-mechanics relationship remains poorly understood at the molecular level. Here, using super-resolution microscopy (SRM), we show that vimentin filaments exhibit a ~49-nanometer axial repeat both in cells and in vitro. As unit-length filaments (ULFs) were measured at ~59 nanometers, this demonstrates a partial overlap of ULFs during filament assembly. Using an SRM-compatible stretching device, we also provide evidence that the extensibility of vimentin is due to the unfolding of its subunits and not to their sliding, thus establishing a direct link between the structural organization and its mechanical properties. Overall, our results pave the way for future studies of IF assembly, mechanical, and structural properties in cells.
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Affiliation(s)
- Filipe Nunes Vicente
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Mickael Lelek
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, 2RT / DTPS, Institut Pasteur, Paris F-75015 , France
| | - Quang D. Tran
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
| | - Gerard Pehau-Arnaudet
- CNRS UMR 3528, Institut Pasteur, Paris F-75015, France
- Ultrastructural BioImaging Platform, Institut Pasteur, Paris F-75015, France
| | - Christophe Zimmer
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
| | - Gregory Giannone
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Cécile Leduc
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
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17
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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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18
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Cassaro CJ, Uphoff S. Super-Resolution Microscopy and Tracking of DNA-Binding Proteins in Bacterial Cells. Methods Mol Biol 2022; 2476:191-208. [PMID: 35635706 DOI: 10.1007/978-1-0716-2221-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ability to detect individual fluorescent molecules inside living cells has enabled a range of powerful microscopy techniques that resolve biological processes on the molecular scale. These methods have also transformed the study of bacterial cell biology, which was previously obstructed by the limited spatial resolution of conventional microscopy. In the case of DNA-binding proteins, super-resolution microscopy can visualize the detailed spatial organization of DNA replication, transcription, and repair processes by reconstructing a map of single-molecule localizations. Furthermore, DNA-binding activities can be observed directly by tracking protein movement in real time. This allows identifying subpopulations of DNA-bound and diffusing proteins, and can be used to measure DNA-binding times in vivo. This chapter provides a detailed protocol for super-resolution microscopy and tracking of DNA-binding proteins in Escherichia coli cells. The protocol covers the genetic engineering and fluorescent labeling of strains and describes data acquisition and analysis procedures, such as super-resolution image reconstruction, mapping single-molecule tracks, computing diffusion coefficients to identify molecular subpopulations with different mobility, and analysis of DNA-binding kinetics. While the focus is on the study of bacterial chromosome biology, these approaches are generally applicable to other molecular processes and cell types.
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Affiliation(s)
- Chloé J Cassaro
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford, UK.
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19
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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20
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Troung SF, Sukhodolets MV. The bacterial protein Hfq: Stable modifications and growth phase-dependent changes in SPAM profiles. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1183:122958. [PMID: 34628185 DOI: 10.1016/j.jchromb.2021.122958] [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: 07/06/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022]
Abstract
In bacteria transcription is coupled to translation, and while it is broadly accepted that transcription-translation complexes (TTCs) are formed in growing bacterial cells, the exact spatial organization of these macromolecular assemblies is not known with certainty. Recent studies indicated the formation of orderly cytosolic superstructures in growing E. coli cells. The bacterial nucleic acid (NA)-binding protein Hfq has been shown to function at the interface of RNA synthesis-degradation machinery; multiple, independent studies link Hfq to orderly cytosolic assemblies. In this work, using fast cell lysis/2D-PAGE and in vitro reconstitution analyses we studied the Hfq modifications and small protein-associated molecules (SPAM). We demonstrate that native Hfq carries stable modifications and simulate 2D patterns of native Hfq-SPAM complexes in reconstitution experiments with purified Hfq and synthetic NA probes. We also demonstrate that genetically engineered Hfq lacking the conserved arginine residues positioned near the rim of the disc formed by the subunits' N-terminal domains binds DNA with a reduced affinity in comparison with wild-type Hfq. These results are consistent with the proposed Hfq-mediated DNA remodeling and point to the involvement of this patch of conserved arginines in interactions with DNA.
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Affiliation(s)
- Stanley F Troung
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States.
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21
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Herdly L, Janin P, Bauer R, van de Linde S. Tunable Wide-Field Illumination and Single-Molecule Photoswitching with a Single MEMS Mirror. ACS PHOTONICS 2021; 8:2728-2736. [PMID: 34553004 PMCID: PMC8447260 DOI: 10.1021/acsphotonics.1c00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Homogeneous illumination in single-molecule localization microscopy (SMLM) is key for the quantitative analysis of super-resolution images. Therefore, different approaches for flat-field illumination have been introduced as alternative to the conventional Gaussian illumination. Here, we introduce a single microelectromechanical systems (MEMS) mirror as a tunable and cost-effective device for adapting wide-field illumination in SMLM. In flat-field mode the MEMS allowed for consistent SMLM metrics across the entire field of view. Employing single-molecule photoswitching, we developed a simple yet powerful routine to benchmark different illumination schemes on the basis of local emitter brightness and ON-state lifetime. Moreover, we propose that tuning the MEMS beyond optimal flat-field conditions enables to study the kinetics of photoswitchable fluorophores within a single acquisition.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Paul Janin
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Ralf Bauer
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
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22
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Singh MK, Kenney LJ. Super-resolution imaging of bacterial pathogens and visualization of their secreted effectors. FEMS Microbiol Rev 2021; 45:5911101. [PMID: 32970796 DOI: 10.1093/femsre/fuaa050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Recent advances in super-resolution imaging techniques, together with new fluorescent probes have enhanced our understanding of bacterial pathogenesis and their interplay within the host. In this review, we provide an overview of what these techniques have taught us about the bacterial lifestyle, the nucleoid organization, its complex protein secretion systems, as well as the secreted virulence factors.
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Affiliation(s)
- Moirangthem Kiran Singh
- Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Linda J Kenney
- Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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23
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Jung Y, Ha BY. Collapse transition of a heterogeneous polymer in a crowded medium. J Chem Phys 2021; 155:054902. [PMID: 34364346 DOI: 10.1063/5.0056446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Long chain molecules can be entropically compacted in a crowded medium. We study the compaction transition of a heterogeneous polymer with ring topology by crowding effects in a free or confined space. For this, we use molecular dynamics simulations in which the effects of crowders are taken into account through effective interactions between chain segments. Our parameter choices are inspired by the Escherichia coli chromosome. The polymer consists of small and big monomers; the big monomers dispersed along the backbone are to mimic the binding of RNA polymerases. Our results show that the compaction transition is a two-step process: initial compaction induced by the association (clustering) of big monomers followed by a gradual overall compaction. They also indicate that cylindrical confinement makes the initial transition more effective; for representative parameter choices, the initial compaction accounts for about 60% reduction in the chain size. Our simulation results support the view that crowding promotes clustering of active transcription units into transcription factories.
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Affiliation(s)
- Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 34141, South Korea
| | - Bae-Yeun Ha
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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24
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McQuail J, Carpousis AJ, Wigneshweraraj S. The association between Hfq and RNase E in long-term nitrogen-starved Escherichia coli. Mol Microbiol 2021; 117:54-66. [PMID: 34219284 DOI: 10.1111/mmi.14782] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/27/2022]
Abstract
Under conditions of nutrient adversity, bacteria adjust metabolism to minimize cellular energy usage. This is often achieved by controlling the synthesis and degradation of RNA. In Escherichia coli, RNase E is the central enzyme involved in RNA degradation and serves as a scaffold for the assembly of the multiprotein complex known as the RNA degradosome. The activity of RNase E against specific mRNAs can also be regulated by the action of small RNAs (sRNA). In this case, the ubiquitous bacterial chaperone Hfq bound to sRNAs can interact with the RNA degradosome for the sRNA guided degradation of target RNAs. The RNA degradosome and Hfq have never been visualized together in live bacteria. We now show that in long-term nitrogen starved E. coli, both RNase E and Hfq co-localize in a single, large focus. This subcellular assembly, which we refer to as the H-body, forms by a liquid-liquid phase separation type mechanism and includes components of the RNA degradosome, namely, the helicase RhlB and the exoribonuclease polynucleotide phosphorylase. The results support the existence of a hitherto unreported subcellular compartmentalization of a process(s) associated with RNA management in stressed bacteria.
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Affiliation(s)
- Josh McQuail
- MRC Centre for Molecular Bacteriology, Imperial College London, London, UK
| | - Agamemnon J Carpousis
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, Toulouse, France
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25
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Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods 2021; 18:669-677. [PMID: 34059826 PMCID: PMC9040192 DOI: 10.1038/s41592-021-01154-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/12/2021] [Indexed: 02/04/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on obtaining the true pairwise distance distribution of different fluorophores naturally from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that, using the true pairwise distribution, we can define and maximize the likelihood, obtaining a set of localizations void of blinking artifacts. DDC results in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications, enabling accurate reconstruction and quantification of SMLM images.
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Affiliation(s)
- Christopher H. Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Tenner
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Melike Lakadamyali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
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26
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Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods 2021. [PMID: 34059826 DOI: 10.1101/768051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on obtaining the true pairwise distance distribution of different fluorophores naturally from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that, using the true pairwise distribution, we can define and maximize the likelihood, obtaining a set of localizations void of blinking artifacts. DDC results in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications, enabling accurate reconstruction and quantification of SMLM images.
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Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Tenner
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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27
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Roles of liquid-liquid phase separation in bacterial RNA metabolism. Curr Opin Microbiol 2021; 61:91-98. [PMID: 33878678 DOI: 10.1016/j.mib.2021.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/01/2023]
Abstract
While bacteria typically lack membrane bound organelles, the mechanisms of subcellular organization have been unclear. Bacteria have recently been found to harbor membraneless organelles containing enzymes of many biochemical pathways. These organelles, called biomolecular condensates, have been found to commonly form through the process of liquid-liquid phase separation and are typically enriched in nucleic acid binding proteins. Interestingly, eukaryote and bacterial transcription and RNA decay machinery have been found to form biomolecular condensates. Additionally, DEAD Box ATPases from eukaryotes and bacteria have also been found to modulate biomolecular condensates. The shared ability of RNA metabolic enzymes to assemble into biomolecular condensates across domains suggests that this mode of subcellular organization aids in the control of RNA metabolism.
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28
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Stracy M, Schweizer J, Sherratt DJ, Kapanidis AN, Uphoff S, Lesterlin C. Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins. Mol Cell 2021; 81:1499-1514.e6. [PMID: 33621478 PMCID: PMC8022225 DOI: 10.1016/j.molcel.2021.01.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/24/2020] [Accepted: 01/27/2021] [Indexed: 12/18/2022]
Abstract
Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Toward identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid is not a physical barrier for protein diffusion but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58%–99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome crowding likely has important implications for the function of all DNA-binding proteins. Protein motion was compared between unperturbed cells and DNA-free cells Protein mobility was dictated by DNA interactions rather than molecular weight The nucleoid is not a physical barrier for protein diffusion The proteins studied spend most (58%–99%) of their search time bound to DNA
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Affiliation(s)
- Mathew Stracy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Jakob Schweizer
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, INSERM, UMR5086, 69007 Lyon, France.
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29
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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30
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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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31
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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32
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McQuail J, Switzer A, Burchell L, Wigneshweraraj S. The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli. J Biol Chem 2020; 295:12355-12367. [PMID: 32532816 PMCID: PMC7458820 DOI: 10.1074/jbc.ra120.014107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Indexed: 11/13/2022] Open
Abstract
The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.
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Affiliation(s)
- Josh McQuail
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Amy Switzer
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Lynn Burchell
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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33
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Wu YL, Tschanz A, Krupnik L, Ries J. Quantitative Data Analysis in Single-Molecule Localization Microscopy. Trends Cell Biol 2020; 30:837-851. [PMID: 32830013 DOI: 10.1016/j.tcb.2020.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Super-resolution microscopy, and specifically single-molecule localization microscopy (SMLM), is becoming a transformative technology for cell biology, as it allows the study of cellular structures with nanometer resolution. Here, we review a wide range of data analyses approaches for SMLM that extract quantitative information about the distribution, size, shape, spatial organization, and stoichiometry of macromolecular complexes to guide biological interpretation. We present a case study using the nuclear pore complex as an example that highlights the power of combining complementary approaches by identifying its symmetry, ringlike structure, and protein copy number. In face of recent technical and computational advances, this review serves as a guideline for selecting appropriate analysis tools and controls to exploit the potential of SMLM for a wide range of biological questions.
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Affiliation(s)
- Yu-Le Wu
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Aline Tschanz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Leonard Krupnik
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Faculty of Chemistry and Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
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34
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Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation. Proc Natl Acad Sci U S A 2020; 117:18540-18549. [PMID: 32675239 PMCID: PMC7414142 DOI: 10.1073/pnas.2005019117] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid–liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid–liquid phase separation is a common mechanism for intracellular organization in both eukaryotic and prokaryotic cells. Once described as mere “bags of enzymes,” bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid–liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.
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35
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Hidalgo-Soria M, Barkai E. Hitchhiker model for Laplace diffusion processes. Phys Rev E 2020; 102:012109. [PMID: 32794941 DOI: 10.1103/physreve.102.012109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Brownian motion is a Gaussian process describing normal diffusion with a variance increasing linearly with time. Recently, intracellular single-molecule tracking experiments have recorded exponentially decaying propagators, a phenomenon called Laplace diffusion. Inspired by these developments we study a many-body approach, called the Hitchhiker model, providing a microscopic description of the widely observed behavior. Our model explains how Laplace diffusion is controlled by size fluctuations of single molecules, independently of the diffusion law which they follow. By means of numerical simulations Laplace diffusion is recovered and we show how single-molecule tracking and data analysis, in a many-body system, is highly nontrivial as tracking of a single particle or many in parallel yields vastly different estimates for the diffusivity. We quantify the differences between these two commonly used approaches, showing how the single-molecule estimate of diffusivity is larger if compared to the full tagging method.
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Affiliation(s)
- M Hidalgo-Soria
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - E Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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36
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Joyeux M. Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling. Biophys J 2020; 118:2141-2150. [PMID: 31629479 PMCID: PMC7202931 DOI: 10.1016/j.bpj.2019.09.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this work, we investigate the interplay of these two mechanisms with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime in which the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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37
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Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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38
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Otterstrom J, Castells-Garcia A, Vicario C, Gomez-Garcia PA, Cosma MP, Lakadamyali M. Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo. Nucleic Acids Res 2019; 47:8470-8484. [PMID: 31287868 PMCID: PMC6895258 DOI: 10.1093/nar/gkz593] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/31/2019] [Accepted: 07/04/2019] [Indexed: 01/28/2023] Open
Abstract
Chromatin organization is crucial for regulating gene expression. Previously, we showed that nucleosomes form groups, termed clutches. Clutch size correlated with the pluripotency grade of mouse embryonic stem cells and human induced pluripotent stem cells. Recently, it was also shown that regions of the chromatin containing activating epigenetic marks were composed of small and dispersed chromatin nanodomains with lower DNA density compared to the larger silenced domains. Overall, these results suggest that clutch size may regulate DNA packing density and gene activity. To directly test this model, we carried out 3D, two-color super-resolution microscopy of histones and DNA with and without increased histone tail acetylation. Our results showed that lower percentage of DNA was associated with nucleosome clutches in hyperacetylated cells. We further showed that the radius and compaction level of clutch-associated DNA decreased in hyperacetylated cells, especially in regions containing several neighboring clutches. Importantly, this change was independent of clutch size but dependent on the acetylation state of the clutch. Our results directly link the epigenetic state of nucleosome clutches to their DNA packing density. Our results further provide in vivo support to previous in vitro models that showed a disruption of nucleosome-DNA interactions upon hyperacetylation.
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Affiliation(s)
- Jason Otterstrom
- ICFO-Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona
| | - Alvaro Castells-Garcia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Vicario
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Pablo A Gomez-Garcia
- ICFO-Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China.,Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China
| | - Melike Lakadamyali
- ICFO-Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona.,Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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Sun Z, Cagliero C, Izard J, Chen Y, Zhou YN, Heinz WF, Schneider TD, Jin DJ. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. Nucleic Acids Res 2019; 47:3970-3985. [PMID: 30843055 DOI: 10.1093/nar/gkz159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
RNA polymerase (RNAP), the transcription machinery, shows dynamic binding across the genomic DNA under different growth conditions. The genomic features that selectively redistribute the limited RNAP molecules to dictate genome-wide transcription in response to environmental cues remain largely unknown. We chose the bacterial osmotic stress response model to determine genomic features that direct genome-wide redistribution of RNAP during the stress. Genomic mapping of RNAP and transcriptome profiles corresponding to the different temporal states after salt shock were determined. We found rapid redistribution of RNAP across the genome, primarily at σ70 promoters. Three subsets of genes exhibiting differential salt sensitivities were identified. Sequence analysis using an information-theory based σ70 model indicates that the intergenic regions of salt-responsive genes are enriched with a higher density of σ70 promoter-like sites than those of salt-sensitive genes. In addition, the density of promoter-like sites has a positive linear correlation with RNAP binding at different salt concentrations. The RNAP binding contributed by the non-initiating promoter-like sites is important for gene transcription at high salt concentration. Our study demonstrates that hyperdensity of σ70 promoter-like sites in the intergenic regions of salt-responsive genes drives the RNAP redistribution for reprograming the transcriptome to counter osmotic stress.
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Affiliation(s)
- Zhe Sun
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Cedric Cagliero
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jerome Izard
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yixiong Chen
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yan Ning Zhou
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Thomas D Schneider
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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40
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Lu YC, Chang YR. Gene expression in E. coli influences the position and motion of the lac operon and vicinal loci. Biochem Biophys Res Commun 2019; 519:438-443. [PMID: 31522813 DOI: 10.1016/j.bbrc.2019.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 10/26/2022]
Abstract
Transcription and translation of active genes play an important role in determining the global organization of the chromosome. To further elucidate this phenomenon, we examined how the expression of either the lacY or the cfp gene in the native lac operon influences adjacent chromosomal segments by fluorescently labeling loci upstream and downstream of the expressed gene. Based on the positions and motile behaviors of these loci, our results reveal that the local organization of the vicinal chromosomal segments and its position in the nucleoid are both influenced by gene expression. Furthermore, we found that the effects on local organization depend on whether the expressed gene encodes a membrane protein or a cytoplasmic protein. Our measurements showing the movement of loci toward the membrane and the correlation between the motions of the upstream and downstream loci support the conclusion that the expression of genes encoding membrane proteins greatly influences chromosome dynamics.
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Affiliation(s)
- Yuan-Chu Lu
- Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, 88, Sec.4, Ting-Chou Rd., Taipei, 116, Taiwan
| | - Yi-Ren Chang
- Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, 88, Sec.4, Ting-Chou Rd., Taipei, 116, Taiwan.
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41
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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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42
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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43
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Alqahtany M, Khadka P, Niyonshuti I, Krishnamurthi VR, Sadoon AA, Challapalli SD, Chen J, Wang Y. Nanoscale reorganizations of histone-like nucleoid structuring proteins in Escherichia coli are caused by silver nanoparticles. NANOTECHNOLOGY 2019; 30:385101. [PMID: 31212266 DOI: 10.1088/1361-6528/ab2a9f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Silver nanoparticles (AgNPs) and ions (Ag+) have recently gained broad attention due to their antimicrobial effects against bacteria and other microbes. In this work, we demonstrate the use of super-resolution fluorescence microscopy for investigating and quantifying the antimicrobial effect of AgNPs at the molecular level. We found that subjecting Escherichia coli (E. coli) bacteria to AgNPs led to nanoscale reorganization of histone-like nucleoid structuring (H-NS) proteins, an essential nucleoid associated protein in bacteria. We observed that H-NS proteins formed denser and larger clusters at the center of the bacteria after exposure to AgNPs. We quantified the spatial reorganizations of H-NS proteins by examining the changes of various spatial parameters, including the inter-molecular distances and molecular densities. Clustering analysis based on Voronoi-tessellation were also performed to characterize the change of H-NS proteins' clustering behavior. We found that AgNP-treatment led to an increase in the fraction of H-NS proteins forming clusters. Similar effects were observed for bacteria exposed to Ag+ ions, suggesting that the release of Ag+ ions plays an important role in the toxicity of AgNPs. On the other hand, we observed that AgNPs with two surface coatings showed difference in the nanoscale reorganization of H-NS proteins, indicating that particle-specific effects also contribute to the antimicrobial activities of AgNPs. Our results suggested that H-NS proteins were significantly affected by AgNPs and Ag+ ions, which has been overlooked previously. In addition, we examined the dynamic motion of AgNPs that were attached to the surface of bacteria. We expect that the current methodology can be readily applied to broadly and quantitatively study the spatial reorganization of biological macromolecules at the scale of nanometers caused by metal nanoparticles, which are expected to shed new light on the antimicrobial mechanism of metal nanoparticles.
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Affiliation(s)
- Meaad Alqahtany
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, United States of America. Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States of America
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44
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Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:20115-20123. [PMID: 31527272 DOI: 10.1073/pnas.1903968116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ70 was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.
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45
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Joyeux M. Preferential Localization of the Bacterial Nucleoid. Microorganisms 2019; 7:E204. [PMID: 31331025 PMCID: PMC6680996 DOI: 10.3390/microorganisms7070204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 11/18/2022] Open
Abstract
Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show that such spherical nucleoids are invariably positioned at the center of mononucleoid cells. The present work aims to determine whether such preferential localization results from generic (entropic) interactions between the nucleoid and the cell membrane or instead requires some specific mechanism, like the tethering of DNA at mid-cell or periodic fluctuations of the concentration gradient of given chemical species. To this end, we performed numerical simulations using a coarse-grained model based on the assumption that the formation of the nucleoid results from a segregative phase separation mechanism driven by the de-mixing of the DNA and non-binding globular macromolecules. These simulations show that the abrupt compaction of the DNA coil, which takes place at large crowder density, close to the jamming threshold, is accompanied by the re-localization of the DNA coil close to the regions of the bounding wall with the largest curvature, like the hemispherical caps of rod-like cells, as if the DNA coil were suddenly acquiring the localization properties of a solid sphere. This work therefore supports the hypothesis that the localization of compact nucleoids at regular cell positions involves either some anchoring of the DNA to the cell membrane or some dynamical localization mechanism.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38400 Grenoble, France.
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46
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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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47
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Kramm K, Endesfelder U, Grohmann D. A Single-Molecule View of Archaeal Transcription. J Mol Biol 2019; 431:4116-4131. [PMID: 31207238 DOI: 10.1016/j.jmb.2019.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023]
Abstract
The discovery of the archaeal domain of life is tightly connected to an in-depth analysis of the prokaryotic RNA world. In addition to Carl Woese's approach to use the sequence of the 16S rRNA gene as phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP but are more complex enzymes that resemble the eukaryotic RNAPII was one of the key findings supporting the idea that archaea constitute the third major branch on the tree of life. This breakthrough in transcriptional research 40years ago paved the way for in-depth studies of the transcription machinery in archaea. However, although the archaeal RNAP and the basal transcription factors that fine-tune the activity of the RNAP during the transcription cycle are long known, we still lack information concerning the architecture and dynamics of archaeal transcription complexes. In this context, single-molecule measurements were instrumental as they provided crucial insights into the process of transcription initiation, the architecture of the initiation complex and the dynamics of mobile elements of the RNAP. In this review, we discuss single-molecule approaches suitable to examine molecular mechanisms of transcription and highlight findings that shaped our understanding of the archaeal transcription apparatus. We furthermore explore the possibilities and challenges of next-generation single-molecule techniques, for example, super-resolution microscopy and single-molecule tracking, and ask whether these approaches will ultimately allow us to investigate archaeal transcription in vivo.
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Affiliation(s)
- Kevin Kramm
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
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48
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Liew ATF, Foo YH, Gao Y, Zangoui P, Singh MK, Gulvady R, Kenney LJ. Single cell, super-resolution imaging reveals an acid pH-dependent conformational switch in SsrB regulates SPI-2. eLife 2019; 8:e45311. [PMID: 31033442 PMCID: PMC6557628 DOI: 10.7554/elife.45311] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022] Open
Abstract
After Salmonella is phagocytosed, it resides in an acidic vacuole. Its cytoplasm acidifies to pH 5.6; acidification activates pathogenicity island 2 (SPI-2). SPI-2 encodes a type three secretion system whose effectors modify the vacuole, driving endosomal tubulation. Using super-resolution imaging in single bacterial cells, we show that low pH induces expression of the SPI-2 SsrA/B signaling system. Single particle tracking, atomic force microscopy, and single molecule unzipping assays identified pH-dependent stimulation of DNA binding by SsrB. A so-called phosphomimetic form (D56E) was unable to bind to DNA in live cells. Acid-dependent DNA binding was not intrinsic to regulators, as PhoP and OmpR binding was not pH-sensitive. The low level of SPI-2 injectisomes observed in single cells is not due to fluctuating SsrB levels. This work highlights the surprising role that acid pH plays in virulence and intracellular lifestyles of Salmonella; modifying acid survival pathways represents a target for inhibiting Salmonella.
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Affiliation(s)
- Andrew Tze Fui Liew
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yunfeng Gao
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Parisa Zangoui
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | | | - Ranjit Gulvady
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Linda J Kenney
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
- Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUnited States
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49
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Baldering TN, Dietz MS, Gatterdam K, Karathanasis C, Wieneke R, Tampé R, Heilemann M. Synthetic and genetic dimers as quantification ruler for single-molecule counting with PALM. Mol Biol Cell 2019; 30:1369-1376. [PMID: 30969885 PMCID: PMC6724688 DOI: 10.1091/mbc.e18-10-0661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How membrane proteins oligomerize determines their function. Superresolution microscopy can report on protein clustering and extract quantitative molecular information. Here, we evaluate the blinking kinetics of four photoactivatable fluorescent proteins for quantitative single-molecule microscopy. We identified mEos3.2 and mMaple3 to be suitable for molecular quantification through blinking histogram analysis. We designed synthetic and genetic dimers of mEos3.2 as well as fusion proteins of monomeric and dimeric membrane proteins as reference structures, and we demonstrate their versatile use for quantitative superresolution imaging in vitro and in situ. We further found that the blinking behavior of mEos3.2 and mMaple3 is modified by a reducing agent, offering the possibility to adjust blinking parameters according to experimental needs.
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Affiliation(s)
- Tim N Baldering
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Karl Gatterdam
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Christos Karathanasis
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Ralph Wieneke
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
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50
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Kim J, Goñi‐Moreno A, Calles B, de Lorenzo V. Spatial organization of the gene expression hardware in
Pseudomonas putida. Environ Microbiol 2019; 21:1645-1658. [DOI: 10.1111/1462-2920.14544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/09/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Belén Calles
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
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