1
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Marrin ME, Foster MR, Santana CM, Choi Y, Jassal AS, Rancic SJ, Greenwald CR, Drucker MN, Feldman DT, Thrall ES. The translesion polymerase Pol Y1 is a constitutive component of the B. subtilis replication machinery. Nucleic Acids Res 2024:gkae637. [PMID: 39051562 DOI: 10.1093/nar/gkae637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Unrepaired DNA damage encountered by the cellular replication machinery can stall DNA replication, ultimately leading to cell death. In the DNA damage tolerance pathway translesion synthesis (TLS), replication stalling is alleviated by the recruitment of specialized polymerases to synthesize short stretches of DNA near a lesion. Although TLS promotes cell survival, most TLS polymerases are low-fidelity and must be tightly regulated to avoid harmful mutagenesis. The gram-negative bacterium Escherichia coli has served as the model organism for studies of the molecular mechanisms of bacterial TLS. However, it is poorly understood whether these same mechanisms apply to other bacteria. Here, we use in vivo single-molecule fluorescence microscopy to investigate the TLS polymerase Pol Y1 in the model gram-positive bacterium Bacillus subtilis. We find significant differences in the localization and dynamics of Pol Y1 in comparison to its E. coli homolog, Pol IV. Notably, Pol Y1 is constitutively enriched at or near sites of replication in the absence of DNA damage through interactions with the DnaN clamp; in contrast, Pol IV has been shown to be selectively enriched only upon replication stalling. These results suggest key differences in the roles and mechanisms of regulation of TLS polymerases across different bacterial species.
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Affiliation(s)
- McKayla E Marrin
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Michael R Foster
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Chloe M Santana
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Yoonhee Choi
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Avtar S Jassal
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Sarah J Rancic
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Carolyn R Greenwald
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Madeline N Drucker
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Denholm T Feldman
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Elizabeth S Thrall
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
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2
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Zhai F, Hao L, Chen X, Jiang T, Guo Q, Xie L, Ma Y, Du X, Zheng Z, Chen K, Fan J. Single-molecule tracking of PprI in D. radiodurans without interference of autoblinking. Front Microbiol 2023; 14:1256711. [PMID: 38029090 PMCID: PMC10652783 DOI: 10.3389/fmicb.2023.1256711] [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: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Autoblinking is a widespread phenomenon and exhibits high level of intensity in some bacteria. In Deinococcus radiodurans (D. radiodurans), strong autoblinking was found to be indistinguishable from PAmCherry and greatly prevented single-molecule tracking of proteins of interest. Here we employed the bright photoswitchable fluorescent protein mMaple3 to label PprI, one essential DNA repair factor, and characterized systematically the fluorescence intensity and bleaching kinetics of both autoblinking and PprI-mMaple3 molecules within cells grown under three different conditions. Under minimal media, we can largely separate autoblinking from mMaple3 molecules and perform reliably single-molecule tracking of PprI in D. radiodurans, by means of applying signal-to-noise ratio and constraining the minimal length for linking the trajectories. We observed three states of PprI molecules, which bear different subcellular localizations and distinct functionalities. Our strategy provides a useful means to study the dynamics and distributions of proteins of interest in bacterial cells with high level of autoblinking.
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Affiliation(s)
- Fanfan Zhai
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Li Hao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaomin Chen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Jiang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Qianhong Guo
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Liping Xie
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ying Ma
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Xiaobo Du
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Zhiqin Zheng
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
- School of Biological Engineering and Wuliangye Liquor, Sichuan University of Science and Engineering, Yibin, Sichuan, China
| | - Kun Chen
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
| | - Jun Fan
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
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3
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Computerized fluorescence microscopy of microbial cells. World J Microbiol Biotechnol 2021; 37:189. [PMID: 34617135 DOI: 10.1007/s11274-021-03159-3] [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: 07/27/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
The upgrading of fluorescence microscopy by the introduction of computer technologies has led to the creation of a new methodology, computerized fluorescence microscopy (CFM). CFM improves subjective visualization and combines it with objective quantitative analysis of the microscopic data. CFM has opened up two fundamentally new opportunities for studying microorganisms. The first is the quantitative measurement of the fluorescence parameters of the targeted fluorophores in association with certain structures of individual cells. The second is the expansion of the boundaries of visualization/resolution of intracellular components beyond the "diffraction limit" of light microscopy into the nanometer range. This enables to obtain unique information about the localization and dynamics of intracellular processes at the molecular level. The purpose of this review is to demonstrate the potential of CFM in the study of fundamental aspects of the structural and functional organization of microbial cells. The basics of computer processing and analysis of digital images are briefly described. The fluorescent molecules used in CFM with an emphasis on fluorescent proteins are characterized. The main methods of super-resolution microscopy (nanoscopy) are presented. The capabilities of various CFM methods for exploring microbial cells at the subcellular level are illustrated by the examples of various studies on yeast and bacteria.
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4
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Shi M, Geng X, Wang C, Guan Y. Quantification of Low Copy Number Proteins in Single Cells. Anal Chem 2019; 91:11493-11496. [PMID: 31476854 DOI: 10.1021/acs.analchem.9b02989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed an ultrasensitive and highly selective method to quantify low copy number intracellular proteins in a single cell using a low-cost laser-induced fluorescence (LIF) detector and a BV605 fluorescent probe. Active caspase3 proteins in cells were labeled by corresponding antibody-BV605 fluorescent binding, and a cell was injected into a 20 cm × 50 μm i.d. capillary column, followed by in situ lysis and capillary electrophoresis (CE)-LIF analysis. About seven active caspase3 protein molecules in a detection volume of 91 pL could be detected. In our method, cross-bounding proteins other than active caspase3 could be separated and distinguished by differences of retention time. By using Si photodiode assembly as a fluorescent detector instead of PMT, the dynamic range of the LIF is over 4 orders of magnitude. In this experiment, we found that the number of active caspase3 molecules in 98 single Jurkat cells were from 629 to 12171, reflecting significant heterogeneity among the cells although they were from the same batch. For extended application, it could also be applied to quantify other types of low copy number proteins in a single cell as long as the corresponding antibodies are provided. This high-sensitive method could also be a promising tool for earlier cancer diagnosis and related disease pathway research which is relevant to low copy number proteins. In addition, this low-cost system could also be easily expanded to an array system for high-throughput quantitation of low copy proteins in single cells.
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Affiliation(s)
- Meng Shi
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Xuhui Geng
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
| | - Chengye Wang
- Department of Thoracic Surgery , The Second Hospital of Dalian Medical University , No. 467, Zhongshan Road , Dalian , Liaoning 116023 , China
| | - Yafeng Guan
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
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5
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Ho HN, Zalami D, Köhler J, van Oijen AM, Ghodke H. Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells. Biophys J 2019; 117:950-961. [PMID: 31383358 DOI: 10.1016/j.bpj.2019.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 01/20/2023] Open
Abstract
Understanding how multiprotein complexes function in cells requires detailed quantitative understanding of their association and dissociation kinetics. Analysis of the heterogeneity of binding lifetimes enables the interrogation of the various intermediate states formed during the reaction. Single-molecule fluorescence imaging permits the measurement of reaction kinetics inside living organisms with minimal perturbation. However, poor photophysical properties of fluorescent probes limit the dynamic range and accuracy of measurements of off rates in live cells. Time-lapse single-molecule fluorescence imaging can partially overcome the limits of photobleaching; however, limitations of this technique remain uncharacterized. Here, we present a structured analysis of which timescales are most accessible using the time-lapse imaging approach and explore uncertainties in determining kinetic subpopulations. We demonstrate the effect of shot noise on the precision of the measurements as well as the resolution and dynamic range limits that are inherent to the method. Our work provides a convenient implementation to determine theoretical errors from measurements and to support interpretation of experimental data.
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Affiliation(s)
- Han N Ho
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Daniel Zalami
- Spectroscopy of Soft Matter, University of Bayreuth, Bayreuth, Germany
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Bayreuth, Germany; Bavarian Polymer Institute, Bayreuth, Germany; Bayreuth Institute of Macromolecular Research, University of Bayreuth, Bayreuth, Germany
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia.
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia.
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6
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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7
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Davis JL, Dong B, Sun C, Zhang HF. Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-14. [PMID: 30334394 PMCID: PMC6210800 DOI: 10.1117/1.jbo.23.10.106501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/21/2018] [Indexed: 05/04/2023]
Abstract
The existence of fluorescent impurities has been a long-standing obstacle in single-molecule imaging, which results in sample misidentification and higher localization uncertainty. Spectroscopic single-molecule localization microscopy can record the full fluorescent spectrum of every stochastic single-molecule emission event. This capability allows us to quantify the spatial and spectral characteristics of fluorescent impurities introduced by sample preparation steps, based on which we developed a method to effectively separate fluorescent impurities from target molecules.
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Affiliation(s)
- Janel L. Davis
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Biqin Dong
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
- Northwestern University, Department of Mechanical Engineering, Evanston, Illinois, United States
| | - Cheng Sun
- Northwestern University, Department of Mechanical Engineering, Evanston, Illinois, United States
| | - Hao F. Zhang
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
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8
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Floc'h K, Lacroix F, Barbieri L, Servant P, Galland R, Butler C, Sibarita JB, Bourgeois D, Timmins J. Bacterial cell wall nanoimaging by autoblinking microscopy. Sci Rep 2018; 8:14038. [PMID: 30232348 PMCID: PMC6145920 DOI: 10.1038/s41598-018-32335-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/06/2018] [Indexed: 01/02/2023] Open
Abstract
Spurious blinking fluorescent spots are often seen in bacteria during single-molecule localization microscopy experiments. Although this 'autoblinking' phenomenon is widespread, its origin remains unclear. In Deinococcus strains, we observed particularly strong autoblinking at the periphery of the bacteria, facilitating its comprehensive characterization. A systematic evaluation of the contributions of different components of the sample environment to autoblinking levels and the in-depth analysis of the photophysical properties of autoblinking molecules indicate that the phenomenon results from transient binding of fluorophores originating mostly from the growth medium to the bacterial cell wall, which produces single-molecule fluorescence through a Point Accumulation for Imaging in Nanoscale Topography (PAINT) mechanism. Our data suggest that the autoblinking molecules preferentially bind to the plasma membrane of bacterial cells. Autoblinking microscopy was used to acquire nanoscale images of live, unlabeled D. radiodurans and could be combined with PALM imaging of PAmCherry-labeled bacteria in two-color experiments. Autoblinking-based super-resolved images provided insight into the formation of septa in dividing bacteria and revealed heterogeneities in the distribution and dynamics of autoblinking molecules within the cell wall.
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Affiliation(s)
- Kevin Floc'h
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | | | | | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Remi Galland
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Corey Butler
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Jean-Baptiste Sibarita
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
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9
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Byrdin M, Duan C, Bourgeois D, Brettel K. A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins. J Am Chem Soc 2018; 140:2897-2905. [PMID: 29394055 DOI: 10.1021/jacs.7b12755] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").
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Affiliation(s)
- Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay , F-91198 Gif-sur-Yvette cedex, France
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10
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Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance. Biochem Soc Trans 2017; 46:23-35. [PMID: 29196610 DOI: 10.1042/bst20170055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/19/2023]
Abstract
Genomic DNA is constantly under threat from intracellular and environmental factors that damage its chemical structure. Uncorrected DNA damage may impede cellular propagation or even result in cell death, making it critical to restore genomic integrity. Decades of research have revealed a wide range of mechanisms through which repair factors recognize damage and co-ordinate repair processes. In recent years, single-molecule live-cell imaging methods have further enriched our understanding of how repair factors operate in the crowded intracellular environment. The ability to follow individual biochemical events, as they occur in live cells, makes single-molecule techniques tremendously powerful to uncover the spatial organization and temporal regulation of repair factors during DNA-repair reactions. In this review, we will cover practical aspects of single-molecule live-cell imaging and highlight recent advances accomplished by the application of these experimental approaches to the study of DNA-repair processes in prokaryotes.
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11
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Liao Y, Li Y, Schroeder JW, Simmons LA, Biteen JS. Single-Molecule DNA Polymerase Dynamics at a Bacterial Replisome in Live Cells. Biophys J 2017; 111:2562-2569. [PMID: 28002733 DOI: 10.1016/j.bpj.2016.11.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/16/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022] Open
Abstract
PolC is one of two essential replicative DNA polymerases found in the Gram-positive bacterium Bacillus subtilis. The B. subtilis replisome is eukaryotic-like in that it relies on a two DNA polymerase system for chromosomal replication. To quantitatively image how the replicative DNA polymerase PolC functions in B. subtilis, we applied photobleaching-assisted microscopy, three-dimensional superresolution imaging, and single-particle tracking to examine the in vivo behavior of PolC at single-molecule resolution. We report the stoichiometry of PolC proteins within each cell and within each replisome, we elucidate the diffusion characteristics of individual PolC molecules, and we quantify the exchange dynamics for PolC engaged in lagging strand synthesis. We show that PolC is highly dynamic: this DNA polymerase is constantly recruited to and released from a centrally located replisome, providing, to our knowledge, new insight into the organization and dynamics of the replisome in bacterial cells.
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Affiliation(s)
- Yi Liao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Yilai Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jeremy W Schroeder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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12
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Lee SA, Ponjavic A, Siv C, Lee SF, Biteen JS. Nanoscopic Cellular Imaging: Confinement Broadens Understanding. ACS NANO 2016; 10:8143-8153. [PMID: 27602688 DOI: 10.1021/acsnano.6b02863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.
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Affiliation(s)
- Stephen A Lee
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Aleks Ponjavic
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Chanrith Siv
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Steven F Lee
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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