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Ding L, Wang X, Wang J, Wang H, Yu L, Liu J, Yu J, Xue T, Yang X, Xue L. Fluorogenic Probes for Real-Time Tracking of Bacterial Cell Wall Dynamics with Nanoscopy. ACS NANO 2025; 19:14389-14403. [PMID: 40173278 DOI: 10.1021/acsnano.5c01930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]
Abstract
The bacterial cell wall, an essential structure for maintaining cell morphology and protecting against environmental hazards, is predominantly composed of peptidoglycan (PG). This intricate macromolecule undergoes dynamic synthesis and remodeling throughout the cell cycle. Despite its importance, monitoring PG dynamics in live cells, particularly with detailed spatial distribution, poses significant challenges. To this end, we present a series of rhodamine-based fluorogenic probes specifically optimized for real-time and super-resolution imaging of PG synthesis. By fine-tuning the self-aggregation of the probes through the incorporation of hydrophobic linkers, we achieved a substantial reduction in background fluorescence and significant fluorogenicity after labeling. These advancements have enabled us to attain wash-free labeling across a diverse array of bacterial species. Our approach facilitates the direct visualization of PG synthesis patterns, enabling the quantification of septal PG (sPG) synthesis rates in living bacterial cells. Furthermore, it allows for simultaneous imaging of cell division machinery in living cells via both two-dimensional (2D) and three-dimensional (3D) STED microscopy. This study provides a powerful toolkit for investigating the architecture and dynamics of the bacterial cell wall, paving new paths for research on PG-related cellular processes.
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Affiliation(s)
- Lihao Ding
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xinci Wang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiajia Wang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Hui Wang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Anhui Basic Discipline Research Center of Artificial Intelligence Biotechnology and Synthetic Biology, Hefei 230027, China
| | - Le Yu
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiang Liu
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiangliu Yu
- College of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Ting Xue
- College of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Xinxing Yang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Anhui Basic Discipline Research Center of Artificial Intelligence Biotechnology and Synthetic Biology, Hefei 230027, China
| | - Lin Xue
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Anhui Basic Discipline Research Center of Artificial Intelligence Biotechnology and Synthetic Biology, Hefei 230027, China
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Carsten A, Wolters M, Aepfelbacher M. Super-resolution fluorescence microscopy for investigating bacterial cell biology. Mol Microbiol 2024; 121:646-658. [PMID: 38041391 DOI: 10.1111/mmi.15203] [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: 08/04/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
Super-resolution fluorescence microscopy technologies developed over the past two decades have pushed the resolution limit for fluorescently labeled molecules into the nanometer range. These technologies have the potential to study bacterial structures, for example, macromolecular assemblies such as secretion systems, with single-molecule resolution on a millisecond time scale. Here we review recent applications of super-resolution fluorescence microscopy with a focus on bacterial secretion systems. We also describe MINFLUX fluorescence nanoscopy, a relatively new technique that promises to one day produce molecular movies of molecular machines in action.
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Affiliation(s)
- Alexander Carsten
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Manuel Wolters
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
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Golmohammadzadeh M, Sexton DL, Parmar S, Tocheva EI. Advanced imaging techniques: Microscopy. ADVANCES IN APPLIED MICROBIOLOGY 2023; 122:1-25. [PMID: 37085191 DOI: 10.1016/bs.aambs.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
For decades, bacteria were thought of as "bags" of enzymes, lacking organelles and significant subcellular structures. This stood in sharp contrast with eukaryotes, where intracellular compartmentalization and the role of large-scale order had been known for a long time. However, the emerging field of Bacterial Cell Biology has established that bacteria are in fact highly organized, with most macromolecular components having specific subcellular locations that can change depending on the cell's physiological state (Barry & Gitai, 2011; Lenz & Søgaard-Andersen, 2011; Thanbichler & Shapiro, 2008). For example, we now know that many processes in bacteria are orchestrated by cytoskeletal proteins, which polymerize into surprisingly diverse superstructures, such as rings, sheets, and tread-milling rods (Pilhofer & Jensen, 2013). These superstructures connect individual proteins, macromolecular assemblies, and even two neighboring cells, to affect essential higher-order processes including cell division, DNA segregation, and motility. Understanding these processes requires resolving the in vivo dynamics and ultrastructure at different functional stages of the cell, at macromolecular resolution and in 3-dimensions (3D). Fluorescence light microscopy (fLM) of tagged proteins is highly valuable for investigating protein localization and dynamics, and the resolution power of transmission electron microscopy (TEM) is required to elucidate the structure of macromolecular complexes in vivo and in vitro. This chapter summarizes the most recent advances in LM and TEM approaches that have revolutionized our knowledge and understanding of the microbial world.
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Affiliation(s)
- Mona Golmohammadzadeh
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Danielle L Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Shweta Parmar
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada.
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Shrestha J, Razavi Bazaz S, Ding L, Vasilescu S, Idrees S, Söderström B, Hansbro PM, Ghadiri M, Ebrahimi Warkiani M. Rapid separation of bacteria from primary nasal samples using inertial microfluidics. LAB ON A CHIP 2022; 23:146-156. [PMID: 36484411 DOI: 10.1039/d2lc00794k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.
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Affiliation(s)
- Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Lin Ding
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Steven Vasilescu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Maliheh Ghadiri
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
- Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
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Söderström B, Pittorino MJ, Daley DO, Duggin IG. Assembly dynamics of FtsZ and DamX during infection-related filamentation and division in uropathogenic E. coli. Nat Commun 2022; 13:3648. [PMID: 35752634 PMCID: PMC9233674 DOI: 10.1038/s41467-022-31378-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
During infection of bladder epithelial cells, uropathogenic Escherichia coli (UPEC) can stop dividing and grow into highly filamentous forms. Here, we find that some filaments of E. coli UTI89 released from infected cells grow very rapidly and by more than 100 μm before initiating division, whereas others do not survive, suggesting that infection-related filamentation (IRF) is a stress response that promotes bacterial dispersal. IRF is accompanied by unstable, dynamic repositioning of FtsZ division rings. In contrast, DamX, which is associated with normal cell division and is also essential for IRF, is distributed uniformly around the cell envelope during filamentation. When filaments initiate division to regenerate rod cells, DamX condenses into stable rings prior to division. The DamX rings maintain consistent thickness during constriction and remain at the septum until after membrane fusion. Deletion of damX affects vegetative cell division in UTI89 (but not in the model E. coli K-12), and, during infection, blocks filamentation and reduces bacterial cell integrity. IRF therefore involves DamX distribution throughout the membrane and prevention of FtsZ ring stabilization, leading to cell division arrest. DamX then reassembles into stable division rings for filament division, promoting dispersal and survival during infection.
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Affiliation(s)
- Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia.
| | - Matthew J Pittorino
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 106 91, Sweden
| | - Iain G Duggin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia
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Thomas GH. Microbial Musings - December 2020. MICROBIOLOGY (READING, ENGLAND) 2020; 166:1107-1109. [PMID: 33353584 PMCID: PMC7819357 DOI: 10.1099/mic.0.001019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 11/18/2022]
Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, York, YO10 5YW, UK
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