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Garcia PS, Duchemin W, Flandrois JP, Gribaldo S, Grangeasse C, Brochier-Armanet C. A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes. Mol Biol Evol 2021; 38:2396-2412. [PMID: 33533884 PMCID: PMC8136486 DOI: 10.1093/molbev/msab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.
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Affiliation(s)
- Pierre S Garcia
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France.,Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Wandrille Duchemin
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
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2
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Sharma M, Singh DN, Budhraja R, Sood U, Rawat CD, Adrian L, Richnow HH, Singh Y, Negi RK, Lal R. Comparative proteomics unravelled the hexachlorocyclohexane (HCH) isomers specific responses in an archetypical HCH degrading bacterium Sphingobium indicum B90A. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41380-41395. [PMID: 33783707 DOI: 10.1007/s11356-021-13073-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Hexachlorocyclohexane (HCH) is a persistent organochlorine pesticide that poses threat to different life forms. Sphingobium indicum B90A that belong to sphingomonad is well-known for its ability to degrade HCH isomers (α-, β-, γ-, δ-), but effects of HCH isomers and adaptive mechanisms of strain B90A under HCH load remain obscure. To investigate the responses of strain B90A to HCH isomers, we followed the proteomics approach as this technique is considered as the powerful tool to study the microbial response to environmental stress. Strain B90A culture was exposed to α-, β-, γ-, δ-HCH (5 mgL-1) and control (without HCH) taken for comparison and changes in whole cell proteome were analyzed. In β- and δ-HCH-treated cultures growth decreased significantly when compared to control, α-, and γ-HCH-treated cultures. HCH residue analysis corroborated previous observations depicting the complete depletion of α- and γ-HCH, while only 66% β-HCH and 34% δ-HCH were depleted from culture broth. Comparative proteome analyses showed that β- and δ-HCH induced utmost systemic changes in strain B90A proteome, wherein stress-alleviating proteins such as histidine kinases, molecular chaperons, DNA binding proteins, ABC transporters, TonB proteins, antioxidant enzymes, and transcriptional regulators were significantly affected. Besides study confirmed constitutive expression of linA, linB, and linC genes that are crucial for the initiation of HCH isomers degradation, while increased abundance of LinM and LinN in presence of β- and δ-HCH suggested the important role of ABC transporter in depletion of these isomers. These results will help to understand the HCH-induced damages and adaptive strategies of strain B90A under HCH load which remained unravelled to date.
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Affiliation(s)
- Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Rohit Budhraja
- Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, 110007, India
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007, India
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India.
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India.
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3
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Molecular Basis for the Activation of Human Innate Immune Response by the Flagellin Derived from Plant-Pathogenic Bacterium, Acidovorax avenae. Int J Mol Sci 2021; 22:ijms22136920. [PMID: 34203170 PMCID: PMC8268093 DOI: 10.3390/ijms22136920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022] Open
Abstract
Acidovorax avenae is a flagellated, pathogenic bacterium to various plant crops that has also been found in human patients with haematological malignancy, fever, and sepsis; however, the exact mechanism for infection in humans is not known. We hypothesized that the human innate immune system could be responsive to the purified flagellin isolated from A. avenae, named FLA-AA. We observed the secretion of inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, and IL-8 by treating FLA-AA to human dermal fibroblasts, as well as macrophages. This response was exclusively through TLR5, which was confirmed by using TLR5-overexpression cell line, 293/hTLR5, as well as TLR5-specific inhibitor, TH1020. We also observed the secretion of inflammatory cytokine, IL-1β, by the activation of NLRC4 with FLA-AA. Overall, our results provide a molecular basis for the inflammatory response caused by FLA-AA in cell-based assays.
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4
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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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5
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Zhuang XY, Lo CJ. Construction and Loss of Bacterial Flagellar Filaments. Biomolecules 2020; 10:E1528. [PMID: 33182435 PMCID: PMC7696725 DOI: 10.3390/biom10111528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The bacterial flagellar filament is an extracellular tubular protein structure that acts as a propeller for bacterial swimming motility. It is connected to the membrane-anchored rotary bacterial flagellar motor through a short hook. The bacterial flagellar filament consists of approximately 20,000 flagellins and can be several micrometers long. In this article, we reviewed the experimental works and models of flagellar filament construction and the recent findings of flagellar filament ejection during the cell cycle. The length-dependent decay of flagellar filament growth data supports the injection-diffusion model. The decay of flagellar growth rate is due to reduced transportation of long-distance diffusion and jamming. However, the filament is not a permeant structure. Several bacterial species actively abandon their flagella under starvation. Flagellum is disassembled when the rod is broken, resulting in an ejection of the filament with a partial rod and hook. The inner membrane component is then diffused on the membrane before further breakdown. These new findings open a new field of bacterial macro-molecule assembly, disassembly, and signal transduction.
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Affiliation(s)
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Taoyuan City 32001, Taiwan;
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6
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Zhuang X, Guo S, Li Z, Zhao Z, Kojima S, Homma M, Wang P, Lo C, Bai F. Live‐cell fluorescence imaging reveals dynamic production and loss of bacterial flagella. Mol Microbiol 2020; 114:279-291. [DOI: 10.1111/mmi.14511] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Xiang‐Yu Zhuang
- Department of Physics and Graduate Institute of Biophysics National Central University Jhongli Taiwan, R.O.C
| | - Shihao Guo
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences Peking University Beijing China
- Department of General Surgery Peking University First Hospital Peking University Beijing China
| | - Zhuoran Li
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences Peking University Beijing China
| | - Ziyi Zhao
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences Peking University Beijing China
| | - Seiji Kojima
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
| | - Michio Homma
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
| | - Pengyuan Wang
- Department of General Surgery Peking University First Hospital Peking University Beijing China
| | - Chien‐Jung Lo
- Department of Physics and Graduate Institute of Biophysics National Central University Jhongli Taiwan, R.O.C
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences Peking University Beijing China
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7
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Murakami K, Kimura S, Nagafuchi O, Sekizuka T, Onozuka D, Mizukoshi F, Tsukagoshi H, Ishioka T, Asai T, Hirai S, Musashi M, Suzuki M, Ohnishi M, Oishi K, Saruki N, Kimura H, Iyoda S, Kuroda M, Fujimoto S. Flagellum expression and swimming activity by the zoonotic pathogen Escherichia albertii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:92-96. [PMID: 31845481 PMCID: PMC7003939 DOI: 10.1111/1758-2229.12818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Flagella are the well-known structural appendages used by bacteria for motility. Although generally reported to be non-motile, the enteropathogenic bacterial species Escherichia albertii produces flagella intermittently. We found that E. albertii expressed flagella under specific environmental conditions. After several generations (involving 4 to 12-h incubations), six of the twelve strains we investigated displayed swimming motility in various aquatic environments, including pond water containing nutrients from pigeon droppings (10% suspension) as well as in 20 × -diluted tryptic soy broth. The most significant motility determinant was a temperature between 15 and 30 °C. At 20 °C in the 10% pigeon-dropping suspension, microscopic observations revealed that some cells (1%-95% of six strains) showed swimming motility. Electron microscopy showed that the E. albertii cells expressed flagella. Lower concentrations of some substrates (including nutrients) may be of secondary importance for E. albertii flagella expression. Interestingly, the non-motile strains (n = 6/12) contained pseudogenes corresponding to essential flagella structural proteins. After being released from its host into surface water, E. albertii may express flagella to move toward nutrient sources or new hosts.
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Affiliation(s)
- Koichi Murakami
- Infectious Disease Surveillance CenterNational Institute of Infectious DiseasesMusashi‐MurayamaTokyoJapan
| | - Shinya Kimura
- Gunma Prefectural Institute of Public Health and Environmental SciencesMaebashiGunmaJapan
| | | | - Tsuyoshi Sekizuka
- Pathogen Genomics CenterNational Institute of Infectious DiseasesShinjukuTokyoJapan
| | - Daisuke Onozuka
- Department of Preventive Medicine and EpidemiologyNational Cerebral and Cardiovascular CenterSuitaOsakaJapan
| | - Fuminori Mizukoshi
- Department of MicrobiologyTochigi Prefectural Institute of Public Health and Environmental ScienceUtsunomiyaTochigiJapan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental SciencesMaebashiGunmaJapan
| | | | - Tetsuo Asai
- The United Graduate School of Veterinary SciencesGifu UniversityGifuJapan
| | - Shinichiro Hirai
- Infectious Disease Surveillance CenterNational Institute of Infectious DiseasesMusashi‐MurayamaTokyoJapan
| | - Manami Musashi
- Aomori Prefectural Public Health and Environment CenterAomoriJapan
| | - Motoi Suzuki
- Infectious Disease Surveillance CenterNational Institute of Infectious DiseasesMusashi‐MurayamaTokyoJapan
| | - Makoto Ohnishi
- Department of Bacteriology INational Institute of Infectious DiseasesShinjukuTokyoJapan
| | - Kazunori Oishi
- Infectious Disease Surveillance CenterNational Institute of Infectious DiseasesMusashi‐MurayamaTokyoJapan
| | - Nobuhiro Saruki
- Gunma Prefectural Institute of Public Health and Environmental SciencesMaebashiGunmaJapan
| | | | - Sunao Iyoda
- Department of Bacteriology INational Institute of Infectious DiseasesShinjukuTokyoJapan
| | - Makoto Kuroda
- Pathogen Genomics CenterNational Institute of Infectious DiseasesShinjukuTokyoJapan
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8
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Export Mechanisms and Energy Transduction in Type-III Secretion Machines. Curr Top Microbiol Immunol 2019; 427:143-159. [PMID: 31218506 DOI: 10.1007/82_2019_166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The remarkably complex architecture and organization of bacterial nanomachines originally raised the enigma to how they are assembled in a coordinated manner. Over the years, the assembly processes of the flagellum and evolutionary-related injectisome complexes have been deciphered and were shown to rely on a conserved protein secretion machine: the type-III secretion system. In this book chapter, we demonstrate how individually evolved mechanisms cooperate in highly versatile and robust secretion machinery to export and assemble the building blocks of those nanomachines.
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9
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Frequent pauses in Escherichia coli flagella elongation revealed by single cell real-time fluorescence imaging. Nat Commun 2018; 9:1885. [PMID: 29760469 PMCID: PMC5951861 DOI: 10.1038/s41467-018-04288-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/13/2018] [Indexed: 12/02/2022] Open
Abstract
The bacterial flagellum is a large extracellular protein organelle that extrudes from the cell surface. The flagellar filament is assembled from tens of thousands of flagellin subunits that are exported through the flagellar type III secretion system. Here, we measure the growth of Escherichia coli flagella in real time and find that, although the growth rate displays large variations at similar lengths, it decays on average as flagella lengthen. By tracking single flagella, we show that the large variations in growth rate occur as a result of frequent pauses. Furthermore, different flagella on the same cell show variable growth rates with correlation. Our observations are consistent with an injection-diffusion model, and we propose that an insufficient cytoplasmic flagellin supply is responsible for the pauses in flagellar growth in E. coli. The bacterial flagellar filament is assembled from tens of thousands of flagellin subunits that are exported by a dedicated secretion system. Here, the authors show that, on average, the growth rate of flagella in E. coli decays as flagella lengthen, with large variations due to frequent pauses.
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10
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Das C, Mokashi C, Mande SS, Saini S. Dynamics and Control of Flagella Assembly in Salmonella typhimurium. Front Cell Infect Microbiol 2018; 8:36. [PMID: 29473025 PMCID: PMC5809477 DOI: 10.3389/fcimb.2018.00036] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
The food-borne pathogen Salmonella typhimurium is a common cause of infections and diseases in a wide range of hosts. One of the major virulence factors associated to the infection process is flagella, which helps the bacterium swim to its preferred site of infection inside the host, the M-cells (Microfold cells) lining the lumen of the small intestine. The expression of flagellar genes is controlled by an intricate regulatory network. In this work, we investigate two aspects of flagella regulation and assembly: (a) distribution of the number of flagella in an isogenic population of bacteria and (b) dynamics of gene expression post cell division. More precisely, in a population of bacteria, we note a normal distribution of number of flagella assembled per cell. How is this distribution controlled, and what are the key regulators in the network which help the cell achieve this? In the second question, we explore the role of protein secretion in dictating gene expression dynamics post cell-division (when the number of hook basal bodies on the cell surface is reduced by a factor of two). We develop a mathematical model and perform stochastic simulations to address these questions. Simulations of the model predict that two accessory regulators of flagella gene expression, FliZ and FliT, have significant roles in maintaining population level distribution of flagella. In addition, FliT and FlgM were predicted to control the level and temporal order of flagellar gene expression when the cell adapts to post cell division consequences. Further, the model predicts that, the FliZ and FliT dependent feedback loops function under certain thresholds, alterations in which can substantially affect kinetics of flagellar genes. Thus, based on our results we propose that, the proteins FlgM, FliZ, and FliT, thought to have accessory roles in regulation of flagella, likely play a critical role controlling gene expression during cell division, and frequency distribution of flagella.
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Affiliation(s)
- Chandrani Das
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India.,Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India
| | - Chaitanya Mokashi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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11
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Renault TT, Abraham AO, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener JP, Minamino T, Erhardt M. Bacterial flagella grow through an injection-diffusion mechanism. eLife 2017; 6. [PMID: 28262091 PMCID: PMC5386592 DOI: 10.7554/elife.23136] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/04/2017] [Indexed: 11/30/2022] Open
Abstract
The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ∼1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell. DOI:http://dx.doi.org/10.7554/eLife.23136.001 Most bacteria are able to move in a directed manner towards nutrients or other locations of interest. Many move by rotating long tail-like filaments called flagella that stick out from the cell. The flagellum is a remarkably complex nanomachine. It is several times longer than the main body of the bacterial cell body and its external filament is made of thousands of building blocks of a single protein called flagellin. This protein is made inside the cell and a structure at the base of the flagellum known as a type III secretion system uses chemical energy to pump it out of the cell so that it can be incorporated into the growing flagellum. The exported building blocks travel through a narrow channel within the flagellum and self-assemble at the tip. It has been a mystery for several decades how bacteria manage to assemble the building blocks of flagella outside of the cell, where no discernible energy source is available. Renault et al. used mathematical modeling, biochemical and microscopy techniques to observe how the flagella of a bacterium called Salmonella enterica assemble in real time. The experiments demonstrate that simple biophysical principles regulate the assembly of the flagellum. The building blocks are pumped into the channel of the flagellum by the type III secretion system and then diffuse to the tip of the filament. Accordingly, the longer the flagellum gets, the slower it grows. This molecular mechanism also explains why the growth of bacterial flagella will eventually stop even without any other control mechanisms in place. Further work will be needed to understand how the type III secretion system harnesses chemical energy to drive the movement of flagellin out of the cell into the growing flagellum. A molecular understanding of these processes will aid the design of new antibiotics targeted against type III secretion systems. DOI:http://dx.doi.org/10.7554/eLife.23136.002
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Affiliation(s)
- Thibaud T Renault
- Junior Research Group, Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Anthony O Abraham
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Tobias Bergmiller
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Guillaume Paradis
- Department of Physics, Engineering Physics and Optics, Laval University, Quebec City, Quebec, Canada
| | - Simon Rainville
- Department of Physics, Engineering Physics and Optics, Laval University, Quebec City, Quebec, Canada
| | | | - Călin C Guet
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Yuhai Tu
- IBM Thomas J Watson Research Center, New York, United States
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,RIKEN Quantitative Biology Center, Suita, Japan
| | - James P Keener
- Department of Mathematics, University of Utah, Salt Lake City, United States
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Marc Erhardt
- Junior Research Group, Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
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12
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Growth rate control of flagellar assembly in Escherichia coli strain RP437. Sci Rep 2017; 7:41189. [PMID: 28117390 PMCID: PMC5259725 DOI: 10.1038/srep41189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/12/2016] [Indexed: 01/10/2023] Open
Abstract
The flagellum is a rotary motor that enables bacteria to swim in liquids and swarm over surfaces. Numerous global regulators control flagellar assembly in response to cellular and environmental factors. Previous studies have also shown that flagellar assembly is affected by the growth-rate of the cell. However, a systematic study has not yet been described under controlled growth conditions. Here, we investigated the effect of growth rate on flagellar assembly in Escherichia coli using steady-state chemostat cultures where we could precisely control the cell growth-rate. Our results demonstrate that flagellar abundance correlates with growth rate, where faster growing cells produce more flagella. They also demonstrate that this growth-rate dependent control occurs through the expression of the flagellar master regulator, FlhD4C2. Collectively, our results demonstrate that motility is intimately coupled to the growth-rate of the cell.
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13
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Chen M, Zhao Z, Yang J, Peng K, Baker MAB, Bai F, Lo CJ. Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging. eLife 2017; 6:e22140. [PMID: 28098557 PMCID: PMC5300704 DOI: 10.7554/elife.22140] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/15/2017] [Indexed: 01/27/2023] Open
Abstract
Bacterial flagella are extracellular filaments that drive swimming in bacteria. During motor assembly, flagellins are transported unfolded through the central channel in the flagellum to the growing tip. Here, we applied in vivo fluorescent imaging to monitor in real time the Vibrio alginolyticus polar flagella growth. The flagellar growth rate is found to be highly length-dependent. Initially, the flagellum grows at a constant rate (50 nm/min) when shorter than 1500 nm. The growth rate decays sharply when the flagellum grows longer, which decreases to ~9 nm/min at 7500 nm. We modeled flagellin transport inside the channel as a one-dimensional diffusive process with an injection force at its base. When the flagellum is short, its growth rate is determined by the loading speed at the base. Only when the flagellum grows longer does diffusion of flagellin become the rate-limiting step, dramatically reducing the growth rate. Our results shed new light on the dynamic building process of this complex extracellular structure.
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Affiliation(s)
- Meiting Chen
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan
| | - Ziyi Zhao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jin Yang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Kai Peng
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Matthew AB Baker
- EMBL Australia Node for Single Molecule Science, University of New South Wales, Sydney, Australia
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China, (FB)
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, (C-JL)
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14
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Schuhmacher JS, Thormann KM, Bange G. How bacteria maintain location and number of flagella? FEMS Microbiol Rev 2015. [PMID: 26195616 DOI: 10.1093/femsre/fuv034] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern). Despite the plethora of bacterial species, only a handful of these patterns exist. The correct flagellation pattern is a prerequisite for motility, but also relates to biofilm formation and the pathogenicity of disease-causing flagellated bacteria. However, the mechanisms that maintain location and number of flagella are far from being understood. Here, we review our knowledge on mechanisms that enable bacteria to maintain their appropriate flagellation pattern. While some peritrichous flagellation patterns might occur by rather simple stochastic processes, other bacterial species appear to rely on landmark systems to define the designated flagellar position. Such landmarks are the Tip system of Caulobacter crescentus or the signal recognition particle (SRP)-GTPase FlhF and the MinD/ParA-type ATPase FlhG (synonyms: FleN, YlxH and MinD2). The latter two proteins constitute a regulatory circuit essential for diverse flagellation patterns in many Gram-positive and negative species. The interactome of FlhF/G (e.g. C-ring proteins FliM, FliN, FliY or the transcriptional regulator FleQ/FlrA) seems evolutionary adapted to meet the specific needs for a respective pattern. This variability highlights the importance of the correct flagellation pattern for motile species.
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Affiliation(s)
- Jan S Schuhmacher
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | - Kai M Thormann
- Justus-Liebig University, Department of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
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15
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Lee PC, Rietsch A. Fueling type III secretion. Trends Microbiol 2015; 23:296-300. [PMID: 25701111 DOI: 10.1016/j.tim.2015.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
Abstract
Type III secretion systems (T3SSs) are complex nanomachines that export proteins from the bacterial cytoplasm across the cell envelope in a single step. They are at the core of the machinery used to assemble the bacterial flagellum, and the needle complex many Gram-negative pathogens use to inject effector proteins into host cells and cause disease. Several models have been put forward to explain how this export is energized, and the mechanism has been the subject of considerable debate. Here we present an overview of these models and discuss their relative merits. Recent evidence suggests that the proton motive force (pmf) is the primary energy source for type III secretion, although contribution from refolding of secreted proteins has not been ruled out. The mechanism by which the pmf is converted to protein export remains enigmatic.
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Affiliation(s)
- Pei-Chung Lee
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arne Rietsch
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106-4960, USA.
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16
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Mathematical model of flagella gene expression dynamics in Salmonella enterica serovar typhimurium. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:19-31. [PMID: 25972986 DOI: 10.1007/s11693-015-9160-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/11/2014] [Accepted: 01/21/2015] [Indexed: 01/11/2023]
Abstract
Flagellar assembly in Salmonella is controlled by an intricate genetic and biochemical network. This network comprises of a number of inter-connected feedback loops, which control the assembly process dynamically. Critical among these are the FliA-FlgM feedback, FliZ-mediated positive feedback, and FliT-mediated negative feedback. In this work, we develop a mathematical model to track the dynamics of flagellar gene expression in Salmonella. Analysis of our model demonstrates that the network is wired to not only control the transition of the cell from a non-flagellated to a flagellated state, but to also control dynamics of gene expression during cell division. Further, we predict that FliZ encoded in the flagellar regulon acts as a critical secretion-dependent molecular link between flagella and Salmonella Pathogenicity Island 1 gene expression. Sensitivity analysis of the model demonstrates that the flagellar regulatory network architecture is extremely robust to mutations.
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17
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Bai F, Morimoto YV, Yoshimura SDJ, Hara N, Kami-Ike N, Namba K, Minamino T. Assembly dynamics and the roles of FliI ATPase of the bacterial flagellar export apparatus. Sci Rep 2014; 4:6528. [PMID: 25284201 PMCID: PMC4185386 DOI: 10.1038/srep06528] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 09/15/2014] [Indexed: 11/09/2022] Open
Abstract
For construction of the bacterial flagellum, FliI ATPase forms the FliH2-FliI complex in the cytoplasm and localizes to the flagellar basal body (FBB) through the interaction of FliH with a C ring protein, FliN. FliI also assembles into a homo-hexamer to promote initial entry of export substrates into the export gate. The interaction of FliH with an export gate protein, FlhA, is required for stable anchoring of the FliI6 ring to the gate. Here we report the stoichiometry and assembly dynamics of FliI-YFP by fluorescence microscopy with single molecule precision. More than six FliI-YFP molecules were associated with the FBB through interactions of FliH with FliN and FlhA. Single FliI-YFP molecule exchanges between the FBB-localized and free-diffusing ones were observed several times per minute. Neither the number of FliI-YFP associated with the FBB nor FliI-YFP turnover rate were affected by catalytic mutations in FliI, indicating that ATP hydrolysis by FliI does not drive the assembly-disassembly cycle of FliI during flagellar assembly. We propose that the FliH2FliI complex and FliI6 ring function as a dynamic substrate carrier and a static substrate loader, respectively.
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Affiliation(s)
- Fan Bai
- 1] Biodynamic Optical Imaging Center, Peking University, Beijing, 100871, China [2] Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan [3]
| | - Yusuke V Morimoto
- 1] Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan [2] Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan [3]
| | - Shinsuke D J Yoshimura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Noritaka Hara
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobunori Kami-Ike
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- 1] Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan [2] Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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18
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Evans LDB, Hughes C, Fraser GM. Building a flagellum outside the bacterial cell. Trends Microbiol 2014; 22:566-72. [PMID: 24973293 PMCID: PMC4183434 DOI: 10.1016/j.tim.2014.05.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 12/30/2022]
Abstract
Flagella, the helical propellers that extend from the bacterial surface, are a paradigm for how complex molecular machines can be built outside the living cell. Their assembly requires ordered export of thousands of structural subunits across the cell membrane and this is achieved by a type III export machinery located at the flagellum base, after which subunits transit through a narrow channel at the core of the flagellum to reach the assembly site at the tip of the nascent structure, up to 20μm from the cell surface. Here we review recent findings that provide new insights into flagellar export and assembly, and a new and unanticipated mechanism for constant rate flagellum growth.
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Affiliation(s)
- Lewis D B Evans
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Colin Hughes
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Gillian M Fraser
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK.
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19
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Growth of flagellar filaments of Escherichia coli is independent of filament length. J Bacteriol 2012; 194:2437-42. [PMID: 22447900 DOI: 10.1128/jb.06735-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial flagellar filaments grow at their distal ends, from flagellin that travels through a central channel ∼2 nm in diameter. The flagellin is extruded from the cytoplasm by a pump powered by a proton motive force (PMF). We measured filament growth in cells near the mid-exponential-phase with flagellin bearing a specific cysteine-for-serine substitution, allowing filaments to be labeled with sulfhydryl-specific fluorescent dyes. We labeled filaments first with a green maleimide dye and then, following an additional period of growth, with a red maleimide dye. The contour lengths of the green and red segments were measured. The average lengths of red segments (∼2.3 μm) were the same regardless of the lengths of the green segments from which they grew (ranging from less than 1 to more than 9 μm in length). Thus, flagellar filaments do not grow at a rate that decreases exponentially with length, as formerly supposed. If flagellar filaments were broken by viscous shear, the broken filaments continued to grow. Identical results were obtained whether flagellin was expressed from fliC on the chromosome under the control of its native promoter or on a plasmid under the control of the arabinose promoter.
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20
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Koike M, Nishioka N, Kojima S, Homma M. Characterization of the flagellar motor composed of functional GFP-fusion derivatives of FliG in the Na +-driven polar flagellum of Vibrio alginolyticus. Biophysics (Nagoya-shi) 2011; 7:59-67. [PMID: 27857593 PMCID: PMC5036772 DOI: 10.2142/biophysics.7.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/18/2011] [Indexed: 12/01/2022] Open
Abstract
The polar flagellum of Vibrio alginolyticus is driven by sodium ion flux via a stator complex, composed of PomA and PomB, across the cell membrane. The interaction between PomA and the rotor component FliG is believed to generate torque required for flagellar rotation. Previous research reported that a GFP-fused FliG retained function in the Vibrio flagellar motor. In this study, we found that N-terminal or C-terminal fusion of GFP has different effects on both torque generation and the switching frequency of the direction of flagellar motor rotation. We could detect the GFP-fused FliG in the basal-body (rotor) fraction although its association with the basal body was less stable than that of intact FliG. Furthermore, the fusion of GFP to the C-terminus of FliG, which is believed to be directly involved in torque generation, resulted in very slow motility and prohibited the directional change of motor rotation. On the other hand, the fusion of GFP to the N-terminus of FliG conferred almost the same swimming speed as intact FliG. These results are consistent with the premise that the C-terminal domain of FliG is directly involved in torque generation and the GFP fusions are useful to analyze the functions of various domains of FliG.
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Affiliation(s)
- Masafumi Koike
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Noriko Nishioka
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
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21
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Chatterjee A, Cui Y, Chakrabarty P, Chatterjee AK. Regulation of motility in Erwinia carotovora subsp. carotovora: quorum-sensing signal controls FlhDC, the global regulator of flagellar and exoprotein genes, by modulating the production of RsmA, an RNA-binding protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1316-1323. [PMID: 20831410 DOI: 10.1094/mpmi-01-10-0017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Erwinia carotovora subsp. carotovora causes soft-rotting (tissue-macerating) disease in many plants and plant organs. Although pectinases are the primary determinants of virulence, several ancillary factors that augment bacterial virulence have also been identified. One such factor is bacterial motility. Flagellum formation and bacterial movement are regulated in many enterobacteria, including E. carotovora subsp. carotovora, by FlhDC, the master regulator of flagellar genes and FliA, a flagellum-specific σ factor. We document here that motility of E. carotovora subsp. carotovora is positively regulated by the quorum-sensing signal, N-acylhomoserine lactone (AHL), and negatively regulated by RsmA, a post-transcriptional regulator. RsmA, an RNA-binding protein, causes translational repression and promotes RNA decay. Our data show that RsmA negatively regulates flhDC and fliA expression. Moreover, the chemical stabilities of transcripts of these genes are greater in an RsmA- mutant than in RsmA+ bacteria. These observations contrast with positive regulation of flhDC and motility by CsrA (=RsmA) in Escherichia coli. In the absence of AHL, the AHL receptors ExpR1/ExpR2 (=AhlR) in Erwinia carotovora subsp. carotovora negatively regulate motility and expression of flhDC and fliA by activating RsmA production. In the presence of AHL, regulatory effects of ExpR1/ExpR2 are neutralized, resulting in reduced levels of rsmA expression and enhanced motility.
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22
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Algebraic and Geometric Understanding of Cells: Epigenetic Inheritance of Phenotypes Between Generations. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 124:55-81. [DOI: 10.1007/10_2010_97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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RsmC of Erwinia carotovora subsp. carotovora negatively controls motility, extracellular protein production, and virulence by binding FlhD and modulating transcriptional activity of the master regulator, FlhDC. J Bacteriol 2009; 191:4582-93. [PMID: 19447906 DOI: 10.1128/jb.00154-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RsmC and FlhDC are global regulators controlling extracellular proteins/enzymes, rsmB RNA, motility, and virulence of Erwinia carotovora subsp. carotovora. FlhDC, the master regulator of flagellar genes, controls these traits by positively regulating gacA, fliA, and rsmC and negatively regulating hexA. RsmC, on the other hand, is a negative regulator of extracellular proteins/enzymes, motility, and virulence since the deficiency of RsmC in FlhDC(+) strain results in overproduction of extracellular proteins/enzymes, hypermotility, and hypervirulence. These phenotypes are abolished in an RsmC(-) FlhDC(-) double mutant. We show that RsmC interferes with FlhDC action. Indeed, the expression of all three targets (i.e., gacA, rsmC, and fliA) positively regulated in E. carotovora subsp. carotovora by FlhDC is inhibited by RsmC. RsmC also partly relieves the inhibition of hexA expression by FlhDC. The results of yeast two-hybrid analysis revealed that RsmC binds FlhD and FlhDC, but not FlhC. We propose that binding of RsmC with FlhD/FlhDC interferes with its regulatory functions and that RsmC acts as an anti-FlhD(4)FlhC(2) factor. We document here for the first time that RsmC interferes with activation of fliA and motility in several members of the Enterobacteriaceae family. The extent of E. carotovora subsp. carotovora RsmC-mediated inhibition of FlhDC-dependent expression of fliA and motility varies depending upon enterobacterial species. The data presented here support the idea that differences in structural features in enterobacterial FlhD are responsible for differential susceptibility to E. carotovora subsp. carotovora RsmC action.
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24
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Deatherage BL, Lara JC, Bergsbaken T, Rassoulian Barrett SL, Lara S, Cookson BT. Biogenesis of bacterial membrane vesicles. Mol Microbiol 2009; 72:1395-407. [PMID: 19432795 DOI: 10.1111/j.1365-2958.2009.06731.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane vesicle (MV) release remains undefined, despite its conservation among replicating Gram-negative bacteria both in vitro and in vivo. Proteins identified in Salmonella MVs, derived from the envelope, control MV production via specific defined domains that promote outer membrane protein-peptidoglycan (OM-PG) and OM protein-inner membrane protein (OM-PG-IM) interactions within the envelope structure. Modulation of OM-PG and OM-PG-IM interactions along the cell body and at division septa, respectively, maintains membrane integrity while co-ordinating localized release of MVs with distinct size distribution and protein content. These data support a model of MV biogenesis, wherein bacterial growth and division invoke temporary, localized reductions in the density of OM-PG and OM-PG-IM associations within the envelope structure, thus releasing OM as MVs.
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Affiliation(s)
- Brooke L Deatherage
- Department of Microbiology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
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25
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Elizabeth Hulme S, DiLuzio WR, Shevkoplyas SS, Turner L, Mayer M, Berg HC, Whitesides GM. Using ratchets and sorters to fractionate motile cells of Escherichia coli by length. LAB ON A CHIP 2008; 8:1888-1895. [PMID: 18941690 DOI: 10.1039/b809892a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This paper describes the fabrication of a composite agar/PDMS device for enriching short cells in a population of motile Escherichia coli. The device incorporated ratcheting microchannels, which directed the motion of swimming cells of E. coli through the device, and three sorting junctions, which isolated successively shorter populations of bacteria. The ratcheting microchannels guided cells through the device with an average rate of displacement of (32 +/- 9) microm s(-1). Within the device, the average length of the cells decreased from 3.8 microm (Coefficient of Variation, CV: 21%) at the entrance, to 3.4 microm (CV: 16%) after the first sorting junction, to 3.2 mum (CV: 19%) after the second sorting junction, to 3.0 mum (CV: 19%) after the third sorting junction.
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Affiliation(s)
- S Elizabeth Hulme
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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26
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Martínez-Antonio A, Janga SC, Thieffry D. Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol 2008; 381:238-47. [PMID: 18599074 PMCID: PMC2726282 DOI: 10.1016/j.jmb.2008.05.054] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 05/21/2008] [Accepted: 05/22/2008] [Indexed: 02/05/2023]
Abstract
Taking advantage of available functional data associated with 115 transcription and 7 sigma factors, we have performed a structural analysis of the regulatory network of Escherichia coli. While the mode of regulatory interaction between transcription factors (TFs) is predominantly positive, TFs are frequently negatively autoregulated. Furthermore, feedback loops, regulatory motifs and regulatory pathways are unevenly distributed in this network. Short pathways, multiple feed-forward loops and negative autoregulatory interactions are particularly predominant in the subnetwork controlling metabolic functions such as the use of alternative carbon sources. In contrast, long hierarchical cascades and positive autoregulatory loops are overrepresented in the subnetworks controlling developmental processes for biofilm and chemotaxis. We propose that these long transcriptional cascades coupled with regulatory switches (positive loops) for external sensing enable the coexistence of multiple bacterial phenotypes. In contrast, short regulatory pathways and negative autoregulatory loops enable an efficient homeostatic control of crucial metabolites despite external variations. TFs at the core of the network coordinate the most basic endogenous processes by passing information onto multi-element circuits. Transcriptional expression data support broader and higher transcription of global TFs compared to specific ones. Global regulators are also more broadly conserved than specific regulators in bacteria, pointing to varying functional constraints.
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Affiliation(s)
- Agustino Martínez-Antonio
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Campus Guanajuato, Irapuato 36500, México.
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27
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Salvetti S, Ghelardi E, Celandroni F, Ceragioli M, Giannessi F, Senesi S. FlhF, a signal recognition particle-like GTPase, is involved in the regulation of flagellar arrangement, motility behaviour and protein secretion in Bacillus cereus. MICROBIOLOGY-SGM 2007; 153:2541-2552. [PMID: 17660418 DOI: 10.1099/mic.0.2006/005553-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Flagellar arrangement is a highly conserved feature within bacterial species. However, only a few genes regulating cell flagellation have been described in polar flagellate bacteria. This report demonstrates that the arrangement of flagella in the peritrichous flagellate Bacillus cereus is controlled by flhF. Disruption of flhF in B. cereus led to a reduction in the number of flagella from 10-12 to 1-3 filaments per cell in the insertion mutant MP06. Moreover, compared to the parental strain, MP06 exhibited: (i) shorter smooth swimming phases, causing reduced swimming motility but not affecting chemotaxis; (ii) complete inhibition of swarming motility, as differentiated swarm cells were never detected; (iii) an increased amount of extracellular proteins; and (iv) differential export of virulence determinants, such as haemolysin BL (HBL), phosphatidylcholine-preferring phospholipase C (PC-PLC) and non-haemolytic enterotoxin (NHE). Introduction of a plasmid harbouring flhF (pDGflhF) into MP06 completely restored the wild-type phenotype in the trans-complemented strain MP07. B. cereus flhF was found to constitute a monocistronic transcriptional unit and its overexpression did not produce abnormal features in the wild-type background. Characterization of a B. cereus mutant (MP05) carrying a partial flhF deletion indicated that the last C-terminal domain of FlhF is involved in protein export while not required for flagellar arrangement and motility behaviour. Taken together, these data suggest that B. cereus FlhF is a promising candidate for connecting diverse cellular functions, such as flagellar arrangement, motility behaviour, pattern of protein secretion and virulence phenotype.
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Affiliation(s)
- Sara Salvetti
- Dipartimento di Patologia Sperimentale, Biotecnologie Mediche, Infettivologia ed Epidemiologia, Università di Pisa, via San Zeno 37, 56127 Pisa, Italy
| | - Emilia Ghelardi
- Dipartimento di Patologia Sperimentale, Biotecnologie Mediche, Infettivologia ed Epidemiologia, Università di Pisa, via San Zeno 37, 56127 Pisa, Italy
| | - Francesco Celandroni
- Dipartimento di Patologia Sperimentale, Biotecnologie Mediche, Infettivologia ed Epidemiologia, Università di Pisa, via San Zeno 37, 56127 Pisa, Italy
| | - Mara Ceragioli
- Dipartimento di Biologia, Sezione di Microbiologia, Università di Pisa, via San Zeno 35, 56127 Pisa, Italy
| | - Francesco Giannessi
- Dipartimento di Morfologia Umana e Biologia Applicata, Università di Pisa, via Roma 55, 56126 Pisa, Italy
| | - Sonia Senesi
- Dipartimento di Biologia, Sezione di Microbiologia, Università di Pisa, via San Zeno 35, 56127 Pisa, Italy
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28
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Sorting of early and late flagellar subunits after docking at the membrane ATPase of the type III export pathway. J Mol Biol 2007; 374:877-82. [PMID: 17967465 PMCID: PMC2546511 DOI: 10.1016/j.jmb.2007.09.080] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 09/20/2007] [Accepted: 09/27/2007] [Indexed: 12/29/2022]
Abstract
The bacterial flagellum assembles in a strict order, with structural subunits delivered to the growing flagellum by a type III export pathway. Early rod-and-hook subunits are exported before completion of the hook, at which point a subunit-specificity switch allows export of late filament subunits. This implies that in bacteria with multiple flagella at different stages of assembly, each export pathway can discriminate and sort unchaperoned early and chaperoned late subunits. To establish whether subunit sorting is distinct from subunit transition from the cytosol to the membrane, in particular docking at the membrane-associated FliI ATPase, the pathway was manipulated in vivo. When ATP hydrolysis by the FliI ATPase was disabled and when the pathway was locked into an early export state, both unchaperoned early and chaperoned late subunits stalled and accumulated at the inner membrane. Furthermore, a chaperone that attenuates late subunit export by stalling when docked at the wild-type ATPase also stalled at the ATPase in an early-locked pathway and inhibited export of early subunits in both native and early-locked pathways. These data indicate that the pathways for early and late subunits converge at the FliI ATPase, independent of ATP hydrolysis, before a distinct, separable sorting step. To ascertain the likely signals for sorting, the export of recombinant subunits was assayed. Late filament subunits unable to bind their chaperones were still sorted accurately, but chaperoned late subunits were directed through an early-locked pathway when fused to early subunit N-terminal export signal regions. Furthermore, while an early subunit signal directed export of a heterologous type III export substrate through both native and early-locked pathways, a late subunit signal only directed export via native pathways. These data suggest that subunits are distinguished not by late chaperones but by N-terminal export signals of the subunits themselves.
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29
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Umehara S, Inoue I, Wakamoto Y, Yasuda K. Origin of individuality of two daughter cells during the division process examined by the simultaneous measurement of growth and swimming property using an on-chip single-cell cultivation system. Biophys J 2007; 93:1061-7. [PMID: 17496044 PMCID: PMC1913147 DOI: 10.1529/biophysj.106.098061] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examined the origin of individuality of two daughter cells born from an isolated single Escherichia coli mother cell during its cell division process by monitoring the change in its swimming behavior and tumbling frequency using an on-chip single-cell cultivation system. By keeping the isolated condition of an observed single cell, we compared its growth and swimming property within a generation and over up to seven generations. It revealed that running speed decreased as cell length smoothly increased within each generation, whereas tumbling frequency fluctuated among generations. Also found was an extraordinary tumbling mode characterized by the prolonged duration of pausing in predivisional cells after cell constriction. The observed prolonged pausing may imply the coexistence of two distinct control systems in a predivisional cell, indicating that individuality of daughter cells emerges after a mother cell initiates constriction and before it gets physically separated into two new cell bodies.
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Affiliation(s)
- Senkei Umehara
- Department of Biomedical Information, Division of Biosystems, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Tokyo 101-0062, Japan
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Umehara S, Hattori A, Inoue I, Yasuda K. Asynchrony in the growth and motility responses to environmental changes by individual bacterial cells. Biochem Biophys Res Commun 2007; 356:464-9. [PMID: 17350591 DOI: 10.1016/j.bbrc.2007.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Accepted: 03/01/2007] [Indexed: 11/28/2022]
Abstract
Knowing how individual cells respond to environmental changes helps one understand phenotypic diversity in a bacterial cell population, so we simultaneously monitored the growth and motility of isolated motile Escherichia coli cells over several generations by using a method called on-chip single-cell cultivation. Starved cells quickly stopped growing but remained motile for several hours before gradually becoming immotile. When nutrients were restored the cells soon resumed their growth and proliferation but remained immotile for up to six generations. A flagella visualization assay suggested that deflagellation underlies the observed loss of motility. This set of results demonstrates that single-cell transgenerational study under well-characterized environmental conditions can provide information that will help us understand distinct functions within individual cells.
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Affiliation(s)
- Senkei Umehara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
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31
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Ye F, Brauer T, Niehus E, Drlica K, Josenhans C, Suerbaum S. Flagellar and global gene regulation in Helicobacter pylori modulated by changes in DNA supercoiling. Int J Med Microbiol 2007; 297:65-81. [PMID: 17276136 DOI: 10.1016/j.ijmm.2006.11.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 11/13/2006] [Accepted: 11/17/2006] [Indexed: 12/20/2022] Open
Abstract
In Helicobacter pylori, a host-adapted bacterium with a small genome and few dedicated transcriptional regulators, promoter structure, and gene organization suggested a role for DNA topology in the transcriptional regulation of flagellar genes. H. pylori DNA supercoiling, monitored by a reporter plasmid, was relaxed by novobiocin, an inhibitor of DNA gyrase. A decrease in negative supercoiling coincided with lowered transcription of the late flagellin gene flaA. Targeted mutagenesis that either increased or decreased promoter spacer length in the flaA sigma(28) promoter lowered flaA transcript levels, expression of FlaA protein, and flagella formation. It also changed the promoter response to decreased superhelicity. Supercoiling of reporter plasmid DNA in H. pylori varied with growth phase in liquid culture. H. pylori sigma(28) promoters of various spacer length, as well as other supercoiling-sensitive genes, were differentially transcribed during the growth phases, consistent with supercoiling being associated with growth phase regulation. Genome-wide transcript analysis of wild-type H. pylori under conditions of reduced supercoiling identified flagellar, housekeeping, and virulence genes, the expression of which correlated with supercoiling change and/or growth phase. These data indicate that global supercoiling changes may help coordinate temporal (growth phase-related) regulation of flagellar biosynthesis and other cellular functions in Helicobacter.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- DNA, Bacterial/metabolism
- DNA, Superhelical/metabolism
- Flagella/genetics
- Flagella/ultrastructure
- Gene Expression Profiling
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Helicobacter pylori/genetics
- Helicobacter pylori/physiology
- Helicobacter pylori/ultrastructure
- Hydro-Lyases/biosynthesis
- Hydro-Lyases/genetics
- Microscopy, Electron, Transmission
- Novobiocin/pharmacology
- Oligonucleotide Array Sequence Analysis
- Oxidoreductases/biosynthesis
- Oxidoreductases/genetics
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Sequence Deletion
- Topoisomerase II Inhibitors
- Transcription, Genetic
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Affiliation(s)
- Fang Ye
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hanover, Germany
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32
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Darnton NC, Turner L, Rojevsky S, Berg HC. On torque and tumbling in swimming Escherichia coli. J Bacteriol 2006; 189:1756-64. [PMID: 17189361 PMCID: PMC1855780 DOI: 10.1128/jb.01501-06] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria swim by rotating long thin helical filaments, each driven at its base by a reversible rotary motor. When the motors of peritrichous cells turn counterclockwise (CCW), their filaments form bundles that drive the cells forward. We imaged fluorescently labeled cells of Escherichia coli with a high-speed charge-coupled-device camera (500 frames/s) and measured swimming speeds, rotation rates of cell bodies, and rotation rates of flagellar bundles. Using cells stuck to glass, we studied individual filaments, stopping their rotation by exposing the cells to high-intensity light. From these measurements we calculated approximate values for bundle torque and thrust and body torque and drag, and we estimated the filament stiffness. For both immobilized and swimming cells, the motor torque, as estimated using resistive force theory, was significantly lower than the motor torque reported previously. Also, a bundle of several flagella produced little more torque than a single flagellum produced. Motors driving individual filaments frequently changed directions of rotation. Usually, but not always, this led to a change in the handedness of the filament, which went through a sequence of polymorphic transformations, from normal to semicoiled to curly 1 and then, when the motor again spun CCW, back to normal. Motor reversals were necessary, although not always sufficient, to cause changes in filament chirality. Polymorphic transformations among helices having the same handedness occurred without changes in the sign of the applied torque.
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Jaakohuhta S, Härmä H, Tuomola M, Lövgren T. Sensitive Listeria spp. immunoassay based on europium(III) nanoparticulate labels using time-resolved fluorescence. Int J Food Microbiol 2006; 114:288-94. [PMID: 17173997 DOI: 10.1016/j.ijfoodmicro.2006.09.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 07/02/2006] [Accepted: 09/30/2006] [Indexed: 11/17/2022]
Abstract
Listeria spp. are Gram-positive rod shaped bacteria found universally in the environment. Pathogenic Listeria monocytogenes is seldom harmful to healthy adults, but can cause serious disease, listeriosis, especially to pregnant women, neonates, and elderly or immunocompromised people. Conventional methods for screening Listeria in food samples are time consuming and laborious, involving the use of a range of liquid media and plate cultures. In the current study, the total analysis time was shortened by employing a sensitive Listeria assay, which was able to detect the bacteria in low concentrations. Sensitivity of the sandwich immunoassay was substantially improved by utilizing europium(III)-chelate containing latex nanoparticles as tracers. Each 107 nm nanoparticle contained approximately 31000 europium(III)-chelates which enhanced the specific activity of the label. The sensitive nanoparticulate immunoassay developed for Listeria spp. was performed in one-step and two-step formats. One-step assay was notably faster, 15 min, and simpler to execute having analytical sensitivity of 300 CFU/ml and a dynamic range of three orders of magnitude. The sensitivity, 20 CFU/ml, of the 4 h two-step assay clearly exceeded that of the one-step assay, and the dynamic range was nearly five orders of magnitude. Food and environmental samples were measured against a commercial L. monocytogenes immunoassay with good correlation. The developed sensitive assay enabled shorter sample enrichment times and, therefore, faster analysis of Listeria spp. Obviously the detection of several other bacteria can also be enhanced by applying the nanoparticle assay technology.
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Rosu V, Hughes KT. sigma28-dependent transcription in Salmonella enterica is independent of flagellar shearing. J Bacteriol 2006; 188:5196-203. [PMID: 16816191 PMCID: PMC1539944 DOI: 10.1128/jb.00299-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The FlgM anti-sigma28 factor is secreted in response to flagellar hook-basal body completion to allow sigma28-dependent transcription of genes needed late in flagellar assembly, such as the flagellin structural gene, fliC. A long-standing hypothesis was that one role of FlgM secretion was to allow rapid expression of flagellin in response to shearing. We tested this hypothesis by following FlgM secretion and fliC transcription in response to flagellar shearing. Experiments showed that the level of FlgM inside the cell was unchanged after shearing whereas the extracellular FlgM levels increased in the growth medium as time passed. Identical results were obtained with cells that were not exposed to shear forces: internal FlgM levels remained constant while external FlgM levels rose with time at rates similar to those for the sheared culture. Consistent with this find, FlgM/sigma28-dependent class 3 gene expression was unaffected by flagellar shearing but was affected by the growth phase of the cell. Regardless of exposure to shear forces, flagellar class 3 transcription rose sharply and then declined. These results demonstrate that flagellar regrowth following shearing is independent of FlgM secretion.
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Affiliation(s)
- Valentina Rosu
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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35
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Crepin VF, Shaw R, Abe CM, Knutton S, Frankel G. Polarity of enteropathogenic Escherichia coli EspA filament assembly and protein secretion. J Bacteriol 2005; 187:2881-9. [PMID: 15805534 PMCID: PMC1070392 DOI: 10.1128/jb.187.8.2881-2889.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Type III secretion systems (TTSS) are sophisticated macromolecular structures that play an imperative role in bacterial infections and human disease. The TTSS needle complex is conserved among bacterial pathogens and shows broad similarity to the flagellar basal body. However, the TTSS of enteropathogenic and enterohemorrhagic Escherichia coli, two important human enteric pathogens, is unique in that it has an approximately 12-nm-diameter filamentous extension to the needle that is composed of the secreted translocator protein EspA. EspA filaments and flagellar structures have very similar helical symmetry parameters. In this study we investigated EspA filament assembly and the delivery of effector proteins across the bacterial cell wall. We show that EspA filaments are elongated by addition of EspA subunits to the tip of the growing filament. Moreover, EspA filament length is modulated by the availability of intracellular EspA subunits. Finally, we provide direct evidence that EspA filaments are hollow conduits through which effector proteins are delivered to the extremity of the bacterial cell (and subsequently into the host cell).
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Affiliation(s)
- Valérie F Crepin
- Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, UK
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36
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Hirano T, Shibata S, Ohnishi K, Tani T, Aizawa SI. N-terminal signal region of FliK is dispensable for length control of the flagellar hook. Mol Microbiol 2005; 56:346-60. [PMID: 15813729 DOI: 10.1111/j.1365-2958.2005.04615.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The length of the flagellar hook is regulated; it is 55 +/- 6 nm long in Salmonella. Five genes involved in hook-length regulation are fliK, flhB, fliG, fliM and fliN. The last four genes encode structural components of the protein export apparatus in the flagellar base, whereas FliK is soluble and secreted during flagellar assembly. The role of FliK, however, remains ambiguous. We constructed two kinds of FliK variants: N-terminally truncated FliK protein and FliK N-terminally fused with cyan fluorescent protein (CFP-FliK). Both N-terminally truncated FliK missing the first 99 amino acids (aa) and CFP-FliK fusion variants partially complemented a fliK null (polyhook) mutant to produce cells with filaments, allowing cells to swim; the hooks, however, were not normal but were polyhooks. When the N-terminally defective FliK variants were expressed at high levels, the average polyhook length was shortened coming close to the length of the wild-type hook, independently of the sizes of the FliK variants. These FliK variants were not secreted. CFP-FliK fusion proteins were observed to homogeneously distribute in the cytoplasm. We conclude that FliK does not need to be exported to control hook length and is unlikely to be a ruler; instead, we conclude that FliK controls hook length by the timely switching of secretion modes of the flagellar type III secretion system by the FliK C-terminal domain, and that the N-terminal region is dispensable for hook length control.
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Affiliation(s)
- Takanori Hirano
- CREST, Japan Science and Technology Agency (JST), 1064-18 Takahori, Hirata, Takanezawa, Shioya-gun, Tochigi 329-1206, Japan
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37
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Kalir S, Mangan S, Alon U. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 2005; 1:2005.0006. [PMID: 16729041 PMCID: PMC1681456 DOI: 10.1038/msb4100010] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 03/09/2005] [Indexed: 01/17/2023] Open
Abstract
Complex gene-regulation networks are made of simple recurring gene circuits called network motifs. The functions of several network motifs have recently been studied experimentally, including the coherent feed-forward loop (FFL) with an AND input function that acts as a sign-sensitive delay element. Here, we study the function of the coherent FFL with a sum input function (SUM-FFL). We analyze the dynamics of this motif by means of high-resolution expression measurements in the flagella gene-regulation network, the system that allows Escherichia coli to swim. In this system, the master regulator FlhDC activates a second regulator, FliA, and both activate in an additive fashion the operons that produce the flagella motor. We find that this motif prolongs flagella expression following deactivation of the master regulator, protecting flagella production from transient loss of input signal. Thus, in contrast to the AND-FFL that shows a delay following signal activation, the SUM-FFL shows delays after signal deactivation. The SUM-FFL in this system works as theoretically predicted despite being embedded in at least two additional feedback loops. The present function might be carried out by the SUM-FFL in systems found across organisms.
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Affiliation(s)
- Shiraz Kalir
- Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Shmoolik Mangan
- Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. Tel.: +972 8 934 4448; Fax: +972 8 9344125; E-mail:
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38
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O'Shea TM, Deloney-Marino CR, Shibata S, Aizawa SI, Wolfe AJ, Visick KL. Magnesium promotes flagellation of Vibrio fischeri. J Bacteriol 2005; 187:2058-65. [PMID: 15743954 PMCID: PMC1064065 DOI: 10.1128/jb.187.6.2058-2065.2005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 12/01/2004] [Indexed: 11/20/2022] Open
Abstract
The bacterium Vibrio fischeri requires bacterial motility to initiate colonization of the Hawaiian squid Euprymna scolopes. Once colonized, however, the bacterial population becomes largely unflagellated. To understand environmental influences on V. fischeri motility, we investigated migration of this organism in tryptone-based soft agar media supplemented with different salts. We found that optimal migration required divalent cations and, in particular, Mg2+. At concentrations naturally present in seawater, Mg2+ improved migration without altering the growth rate of the cells. Transmission electron microscopy and Western blot experiments suggested that Mg2+ addition enhanced flagellation, at least in part through an effect on the steady-state levels of flagellin protein.
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Affiliation(s)
- Therese M O'Shea
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
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39
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Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Just-in-time transcription program in metabolic pathways. Nat Genet 2004; 36:486-91. [PMID: 15107854 DOI: 10.1038/ng1348] [Citation(s) in RCA: 317] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Accepted: 03/11/2004] [Indexed: 11/09/2022]
Abstract
A primary goal of systems biology is to understand the design principles of the transcription networks that govern the timing of gene expression. Here we measured promoter activity for approximately 100 genes in parallel from living cells at a resolution of minutes and accuracy of 10%, based on GFP and Lux reporter libraries. Focusing on the amino-acid biosynthesis systems of Escherichia coli, we identified a previously unknown temporal expression program and expression hierarchy that matches the enzyme order in unbranched pathways. We identified two design principles: the closer the enzyme is to the beginning of the pathway, the shorter the response time of the activation of its promoter and the higher its maximal promoter activity. Mathematical analysis suggests that this 'just-in-time' (ref. 5) transcription program is optimal under constraints of rapidly reaching a production goal with minimal total enzyme production. Our findings suggest that metabolic regulation networks are designed to generate precision promoter timing and activity programs that can be understood using the engineering principles of production pipelines.
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Affiliation(s)
- Alon Zaslaver
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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40
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Abstract
The bacterial flagellum is both a motor organelle and a protein export/assembly apparatus. It extends from the cytoplasm to the cell exterior. All the protein subunits of the external elements have to be exported. Export employs a type III pathway, also utilized for secretion of virulence factors. Six of the components of the export apparatus are integral membrane proteins and are believed to be located within the flagellar basal body. Three others are soluble: the ATPase that drives export, a regulator of the ATPase, and a general chaperone. Exported substrates diffuse down a narrow channel in the growing structure and assemble at the distal end, often with the help of a capping structure.
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Affiliation(s)
- Robert M Macnab
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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41
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Abstract
Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.
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Affiliation(s)
- Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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Abstract
Sensory transcription networks generally control rapid and reversible gene expression responses to external stimuli. Developmental transcription networks carry out slow and irreversible temporal programs of gene expression during development. It is important to understand the design principles that underlie the structure of sensory and developmental transcription networks. Cascades, which are chains of regulatory reactions, are a basic structural element of transcription networks. When comparing databases of sensory and developmental transcription networks, a striking difference is found in the distribution of cascade lengths. Here, we suggest that delay times in the responses of the network present a design constraint that influences the network architecture. We experimentally studied the response times in simple cascades constructed of well-characterized repressors in Escherichia coli. Accurate kinetics at high temporal resolution was measured using green fluorescent protein (GFP) reporters. We find that transcription cascades can show long delays of about one cell-cycle time per cascade step. Mathematical analysis suggests that such a delay is characteristic of cascades that are designed to minimize the response times for both turning-on and turning-off gene expression. The need to achieve rapid reversible responses in sensory transcription networks may help explain the finding that long cascades are very rare in databases of E.coli and Saccharomyces cerevisiae sensory transcription networks. In contrast, long cascades are common in developmental transcription networks from sea urchin and from Drosophila melanogaster. Response delay constraints are likely to be less important for developmental networks, since they control irreversible processes on the timescale of cell-cycles. This study highlights a fundamental difference between the architecture of sensory and developmental transcription networks.
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Affiliation(s)
- Nitzan Rosenfeld
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
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Soutourina OA, Krin E, Laurent-Winter C, Hommais F, Danchin A, Bertin PN. Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1543-1551. [PMID: 11988529 DOI: 10.1099/00221287-148-5-1543] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The effect of detrimental conditions on bacterial motility in Escherichia coli was investigated. Expression profiling of mutant E. coli strains by DNA arrays and analysis of phenotypic traits demonstrated that motility and low-pH resistance are coordinately regulated. Analysis of transcriptional fusions suggests that bacterial motility in response to an acidic environment is mediated via the control by H-NS of flhDC expression. Moreover, the results suggested that the presence of an extended mRNA 5' end and DNA topology are required in this process. Finally, the presence of a similar regulatory region in several Gram-negative bacteria implies that this mechanism is largely conserved.
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Affiliation(s)
- Olga A Soutourina
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
| | - Evelyne Krin
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
| | - Christine Laurent-Winter
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
| | - Florence Hommais
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
| | - Philippe N Bertin
- Unité de Génétique des Génomes Bactériens1 and Génopole-Plateau Protéomique2, Institut Pasteur, Paris, France
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Josenhans C, Niehus E, Amersbach S, Hörster A, Betz C, Drescher B, Hughes KT, Suerbaum S. Functional characterization of the antagonistic flagellar late regulators FliA and FlgM of Helicobacter pylori and their effects on the H. pylori transcriptome. Mol Microbiol 2002; 43:307-22. [PMID: 11985711 DOI: 10.1046/j.1365-2958.2002.02765.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Helicobacter pylori is thought to regulate gene expression with a very small set of regulatory genes. We identified a previously unannotated open reading frame (ORF) in the H. pylori 26695 genome (HP1122) as a putative H. pylori flgM gene (sigma28 factor antagonist) by a motif-based bioinformatic approach. Deletion of HP1122 resulted in a fourfold increase in transcription of the sigma28-dependent major flagellin gene flaA, supporting the function of HP1122 as H. pylori FlgM. Helicobacter pylori FlgM lacks a conserved 20-amino-acid N-terminal domain of enterobacterial FlgM proteins, but was able to interact with the Salmonella typhimurium sigma28 (FliA) and inhibit the expression of FliA-dependent genes in Salmonella. Helicobacter pylori FlgM inhibited FliA to the same extent in a Salmonella strain with an intact flagellar export system and in an export-deficient strain. Helicobacter pylori FliA was able to drive transcription of FliA-dependent genes in Salmonella. The effects of mutations in the H. pylori flgM and fliA genes on the H. pylori transcriptome were analysed using whole genome DNA microarrays. The antagonistic roles of FlgM and FliA in controlling the transcription of the major flagellin gene flaA were confirmed, and two additional FliA/FlgM dependent operons (HP472 and HP1051/HP1052) were identified. None of the three genes contained in these operons has a known function in flagellar biogenesis in other bacteria. Like other motile bacteria, H. pylori has a FliA/FlgM pair of sigma and anti-sigma factors, but the genes controlled by these differ markedly from the Salmonella/Escherichia coli paradigm.
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45
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Bren A, Eisenbach M. Changing the direction of flagellar rotation in bacteria by modulating the ratio between the rotational states of the switch protein FliM. J Mol Biol 2001; 312:699-709. [PMID: 11575925 DOI: 10.1006/jmbi.2001.4992] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
One of the major questions in bacterial chemotaxis is how the switch, which controls the direction of flagellar rotation, functions. It is well established that binding of the signaling molecule CheY to the switch protein FliM shifts the rotation from the default direction, counterclockwise, to clockwise. How this shift is done is still a mystery. Our aim in this study was to determine the correlation between the fraction of FliM molecules in the clockwise state (i.e. occupied by CheY) and the probability of clockwise rotation. For this purpose we gradually expressed, from a plasmid, a clockwise FliM mutant protein in cells that express, from the chromosome, wild-type FliM but no chemotaxis proteins. We verified that plasmid-borne FliM exchanges chromosomal FliM in the switch. Surprisingly, a substantial clockwise probability was not obtained before the large majority of the FliM molecules in the switch were clockwise molecules. Thereafter, the rise in clockwise probability was very steep. These results suggest that an increase in the clockwise probability requires a high level of FliM occupancy by CheY approximately P. They further suggest that the steep increase in clockwise rotation upon increasing CheY levels, reported in several studies, is due, at least in part, to cooperativity of post-binding interactions within the switch. We also carried out the inverse experiment, in which wild-type FliM was gradually expressed in a background of a clockwise fliM mutant. In this case, the level of the clockwise mutant protein, required for establishing a certain clockwise probability, was lower than in the original experiment. If our system (in which the ratio between the rotational states of FliM in the switch is established by slow exchange) and the native system (in which the ratio is established by fast changes in FliM occupancy) are comparable, the results suggest that hysteresis is involved in the switch function. Such a situation might reflect a damping mechanism, which prevents a situation in which fluctuations in the phosphorylation level of CheY throw the switch from one direction of rotation to the other.
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Affiliation(s)
- A Bren
- Department of Biological Chemistry, The Weizmann Institute of Science,76100 Rehovot, Israel
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46
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Abstract
Polar flagella of Vibrio species can rotate at speeds as high as 100,000 rpm and effectively propel the bacteria in liquid as fast as 60 microm/s. The sodium motive force powers rotation of the filament, which acts as a propeller. The filament is complex, composed of multiple subunits, and sheathed by an extension of the cell outer membrane. The regulatory circuitry controlling expression of the polar flagellar genes of members of the Vibrionaceae is different from the peritrichous system of enteric bacteria or the polar system of Caulobacter crescentus. The scheme of gene control is also pertinent to other members of the gamma purple bacteria, in particular to Pseudomonas species. This review uses the framework of the polar flagellar system of Vibrio parahaemolyticus to provide a synthesis of what is known about polar motility systems of the Vibrionaceae. In addition to its propulsive role, the single polar flagellum of V. parahaemolyticus is believed to act as a tactile sensor controlling surface-induced gene expression. Under conditions that impede rotation of the polar flagellum, an alternate, lateral flagellar motility system is induced that enables movement through viscous environments and over surfaces. Although the dual flagellar systems possess no shared structural components and although distinct type III secretion systems direct the simultaneous placement and assembly of polar and lateral organelles, movement is coordinated by shared chemotaxis machinery.
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Affiliation(s)
- L L McCarter
- Department of Microbiology, The University of Iowa, Iowa City, IA 52242, USA.
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47
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Chilcott GS, Hughes KT. Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol Mol Biol Rev 2000; 64:694-708. [PMID: 11104815 PMCID: PMC99010 DOI: 10.1128/mmbr.64.4.694-708.2000] [Citation(s) in RCA: 494] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
How do organisms assess the degree of completion of a large structure, especially an extracellular structure such as a flagellum? Bacteria can do this. Mutants that lack key components needed early in assembly fail to express proteins that would normally be added at later assembly stages. In some cases, the regulatory circuitry is able to sense completion of structures beyond the cell surface, such as completion of the external hook structure. In Salmonella and Escherichia coli, regulation occurs at both transcriptional and posttranscriptional levels. One transcriptional regulatory mechanism involves a regulatory protein, FlgM, that escapes from the cell (and thus can no longer act) through a complete flagellum and is held inside when the structure has not reached a later stage of completion. FlgM prevents late flagellar gene transcription by binding the flagellum-specific transcription factor sigma(28). FlgM is itself regulated in response to the assembly of an incomplete flagellum known as the hook-basal body intermediate structure. Upon completion of the hook-basal body structure, FlgM is exported through this structure out of the cell. Inhibition of sigma(28)-dependent transcription is relieved, and genes required for the later assembly stages are expressed, allowing completion of the flagellar organelle. Distinct posttranscriptional regulatory mechanisms occur in response to assembly of the flagellar type III secretion apparatus and of ring structures in the peptidoglycan and lipopolysaccharide layers. The entire flagellar regulatory pathway is regulated in response to environmental cues. Cell cycle control and flagellar development are codependent. We discuss how all these levels of regulation ensure efficient assembly of the flagellum in response to environmental stimuli.
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Affiliation(s)
- G S Chilcott
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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48
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Karlinsey JE, Tanaka S, Bettenworth V, Yamaguchi S, Boos W, Aizawa SI, Hughes KT. Completion of the hook-basal body complex of the Salmonella typhimurium flagellum is coupled to FlgM secretion and fliC transcription. Mol Microbiol 2000; 37:1220-31. [PMID: 10972838 DOI: 10.1046/j.1365-2958.2000.02081.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The flhDC operon of Salmonella typhimurium is the master control operon required for the expression of the entire flagellar regulon. The flagellar master operon was placed under the tetracycline-inducible promoter PtetA using the T-POP transposon. Cells containing this construct are motile in the presence of tetracycline and non-motile without inducer present. No flagella were visible under the electron microscope when cells were grown without inducer. The class 1, class 2 and class 3 promoters of the flagellar regulon are temporally regulated. After addition of tetracycline, the class 1 flhDC operon was transcribed immediately. Transcription of flgM (which is transcribed from both class 2 and class 3 promoters) began 15 min after induction. At 20 min after induction, the class 2 fliA promoter became active and intracellular FliA protein levels increased; at 30 min after induction, the class 3 fliC promoter was activated. Induction of fliC gene expression coincides with the appearance of FlgM anti-sigma factor in the growth medium. This also coincides with the completion of hook-basal body structures. Rolling cells first appeared 35 min after induction, and excess hook protein (FlgE) was also found in the growth medium at this time. At 45 min after induction, nascent flagellar filaments became visible in electron micrographs and over 40% of the cells exhibited some swimming behaviour. Multiple flagella assemble and grow on individual cells after induction of the master operon. These results confirm that the flagellar regulatory hierarchy of S. typhimurium is temporally regulated after induction. Both FlgM secretion and class 3 gene expression occur upon completion of the hook-basal body structure.
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Affiliation(s)
- J E Karlinsey
- Department of Microbiology, Box 357242, University of Washington, Seattle, WA 98195, USA
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Tamano K, Aizawa S, Katayama E, Nonaka T, Imajoh-Ohmi S, Kuwae A, Nagai S, Sasakawa C. Supramolecular structure of the Shigella type III secretion machinery: the needle part is changeable in length and essential for delivery of effectors. EMBO J 2000; 19:3876-87. [PMID: 10921870 PMCID: PMC306602 DOI: 10.1093/emboj/19.15.3876] [Citation(s) in RCA: 187] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We investigated the supramolecular structure of the SHIGELLA: type III secretion machinery including its major components. Our results indicated that the machinery was composed of needle and basal parts with respective lengths of 45.4 +/- 3.3 and 31.6 +/- 0.3 nm, and contained MxiD, MxiG, MxiJ and MxiH. spa47, encoding a putative F(1)-type ATPase, was required for the secretion of effector proteins via the type III system and was involved in the formation of the needle. The spa47 mutant produced a defective, needle-less type III structure, which contained MxiD, MxiG and MxiJ but not MxiH. The mxiH mutant produced a defective type III structure lacking the needle and failed to secrete effector proteins. Upon overexpression of MxiH in the mxiH mutant, the bacteria produced type III structures with protruding dramatically long needles, and showed a remarkable increase in invasiveness. Our results suggest that MxiH is the major needle component of the type III machinery and is essential for delivery of the effector proteins, and that the level of MxiH affects the length of the needle.
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Affiliation(s)
- K Tamano
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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50
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Abstract
Vibrio parahaemolyticus has dual flagellar systems adapted for locomotion under different circumstances. A single, sheathed polar flagellum propels the swimmer cell in liquid environments. Numerous unsheathed lateral flagella move the swarmer cell over surfaces. The polar flagellum is produced continuously, whereas the synthesis of lateral flagella is induced under conditions that impede the function of the polar flagellum, e.g., in viscous environments or on surfaces. Thus, the organism possesses two large gene networks that orchestrate polar and lateral flagellar gene expression and assembly. In addition, the polar flagellum functions as a mechanosensor controlling lateral gene expression. In order to gain insight into the genetic circuitry controlling motility and surface sensing, we have sought to define the polar flagellar gene system. The hierarchy of regulation appears to be different from the polar system of Caulobacter crescentus or the peritrichous system of enteric bacteria but is pertinent to many Vibrio and Pseudomonas species. The gene identity and organization of 60 potential flagellar and chemotaxis genes are described. Conserved sequences are defined for two classes of polar flagellar promoters. Phenotypic and genotypic analysis of mutant strains with defects in swimming motility coupled with primer extension analysis of flagellar and chemotaxis transcription provides insight into the polar flagellar organelle, its assembly, and regulation of gene expression.
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Affiliation(s)
- Y K Kim
- Department of Microbiology, The University of Iowa, Iowa City, Iowa 52242, USA
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