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Minamino T, Kinoshita M. Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. EcoSal Plus 2023; 11:eesp00112023. [PMID: 37260402 DOI: 10.1128/ecosalplus.esp-0011-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 01/28/2024]
Abstract
Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of Salmonella enterica serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of Salmonella flagella.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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2
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Minamino T, Morimoto YV, Kinoshita M, Namba K. Multiple Roles of Flagellar Export Chaperones for Efficient and Robust Flagellar Filament Formation in Salmonella. Front Microbiol 2021; 12:756044. [PMID: 34691007 PMCID: PMC8527033 DOI: 10.3389/fmicb.2021.756044] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
FlgN, FliS, and FliT are flagellar export chaperones specific for FlgK/FlgL, FliC, and FliD, respectively, which are essential component proteins for filament formation. These chaperones facilitate the docking of their cognate substrates to a transmembrane export gate protein, FlhA, to facilitate their subsequent unfolding and export by the flagellar type III secretion system (fT3SS). Dynamic interactions of the chaperones with FlhA are thought to determine the substrate export order. To clarify the role of flagellar chaperones in filament assembly, we constructed cells lacking FlgN, FliS, and/or FliT. Removal of either FlgN, FliS, or FliT resulted in leakage of a large amount of unassembled FliC monomers into the culture media, indicating that these chaperones contribute to robust and efficient filament formation. The ∆flgN ∆fliS ∆fliT (∆NST) cells produced short filaments similarly to the ∆fliS mutant. Suppressor mutations of the ∆NST cells, which lengthened the filament, were all found in FliC and destabilized the folded structure of FliC monomer. Deletion of FliS inhibited FliC export and filament elongation only after FliC synthesis was complete. We propose that FliS is not involved in the transport of FliC upon onset of filament formation, but FliS-assisted unfolding of FliC by the fT3SS becomes essential for its rapid and efficient export to form a long filament when FliC becomes fully expressed in the cytoplasm.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yusuke V Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN SPring-8 Center and Center for Biosystems Dynamics Research, Suita, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Japan
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3
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Bacterial Flagellar Filament: A Supramolecular Multifunctional Nanostructure. Int J Mol Sci 2021; 22:ijms22147521. [PMID: 34299141 PMCID: PMC8306008 DOI: 10.3390/ijms22147521] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023] Open
Abstract
The bacterial flagellum is a complex and dynamic nanomachine that propels bacteria through liquids. It consists of a basal body, a hook, and a long filament. The flagellar filament is composed of thousands of copies of the protein flagellin (FliC) arranged helically and ending with a filament cap composed of an oligomer of the protein FliD. The overall structure of the filament core is preserved across bacterial species, while the outer domains exhibit high variability, and in some cases are even completely absent. Flagellar assembly is a complex and energetically costly process triggered by environmental stimuli and, accordingly, highly regulated on transcriptional, translational and post-translational levels. Apart from its role in locomotion, the filament is critically important in several other aspects of bacterial survival, reproduction and pathogenicity, such as adhesion to surfaces, secretion of virulence factors and formation of biofilms. Additionally, due to its ability to provoke potent immune responses, flagellins have a role as adjuvants in vaccine development. In this review, we summarize the latest knowledge on the structure of flagellins, capping proteins and filaments, as well as their regulation and role during the colonization and infection of the host.
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Bouteiller M, Dupont C, Bourigault Y, Latour X, Barbey C, Konto-Ghiorghi Y, Merieau A. Pseudomonas Flagella: Generalities and Specificities. Int J Mol Sci 2021; 22:ijms22073337. [PMID: 33805191 PMCID: PMC8036289 DOI: 10.3390/ijms22073337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Flagella-driven motility is an important trait for bacterial colonization and virulence. Flagella rotate and propel bacteria in liquid or semi-liquid media to ensure such bacterial fitness. Bacterial flagella are composed of three parts: a membrane complex, a flexible-hook, and a flagellin filament. The most widely studied models in terms of the flagellar apparatus are E. coli and Salmonella. However, there are many differences between these enteric bacteria and the bacteria of the Pseudomonas genus. Enteric bacteria possess peritrichous flagella, in contrast to Pseudomonads, which possess polar flagella. In addition, flagellar gene expression in Pseudomonas is under a four-tiered regulatory circuit, whereas enteric bacteria express flagellar genes in a three-step manner. Here, we use knowledge of E. coli and Salmonella flagella to describe the general properties of flagella and then focus on the specificities of Pseudomonas flagella. After a description of flagellar structure, which is highly conserved among Gram-negative bacteria, we focus on the steps of flagellar assembly that differ between enteric and polar-flagellated bacteria. In addition, we summarize generalities concerning the fuel used for the production and rotation of the flagellar macromolecular complex. The last part summarizes known regulatory pathways and potential links with the type-six secretion system (T6SS).
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Affiliation(s)
- Mathilde Bouteiller
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yvann Bourigault
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Corinne Barbey
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
- Correspondence:
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Zheng R, Wu S, Sun C. MerF is a novel regulator of deep-sea Pseudomonas stutzeri flagellum biogenesis and motility. Environ Microbiol 2020; 23:110-125. [PMID: 33047460 DOI: 10.1111/1462-2920.15275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022]
Abstract
MerF, a proposed bacterial mercury transporter, was surprisingly found to play key roles in the flagellum biogenesis and motility but not mercuric resistance of the deep-sea bacterium Pseudomonas stutzeri 273 in our previous study. However, the mechanism behind this interesting discovery has not been elucidated. Here, we firstly applied the combined transcriptomic and proteomic analysis to the P. stutzeri 273 wild type and merF deletion mutant. The results showed that expressions of extracellular flagellar components and FliS, a key factor controlling the biogenesis of extracellular flagellar filament, were significantly downregulated in the merF deletion mutant. In combination of genetic and biochemical methods, MerF was further demonstrated to regulate the expression of fliS via directly binding to its promoter, which is consistent with the discovery that MerF is essential for bacterial flagellum biogenesis and motility. Importantly, the expression of merF and fliS could be simultaneously upregulated by different heavy metals and MerF homologues exist in both bacterial and archaeal domains. To the best of our knowledge, this is the first report linking the heavy metal transporter and the flagellum biogenesis and motility in microorganisms, which provides a good model to investigate the unexplored adaptation strategies of deep-sea microbes against harsh conditions.
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Affiliation(s)
- Rikuan Zheng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shimei Wu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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6
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Two Tandem Mechanisms Control Bimodal Expression of the Flagellar Genes in Salmonella enterica. J Bacteriol 2020; 202:JB.00787-19. [PMID: 32312744 DOI: 10.1128/jb.00787-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/13/2020] [Indexed: 12/23/2022] Open
Abstract
Flagellar gene expression is bimodal in Salmonella enterica Under certain growth conditions, some cells express the flagellar genes whereas others do not. This results in mixed populations of motile and nonmotile cells. In the present study, we found that two independent mechanisms control bimodal expression of the flagellar genes. One was previously found to result from a double negative-feedback loop involving the flagellar regulators RflP and FliZ. This feedback loop governs bimodal expression of class 2 genes. In this work, a second mechanism was found to govern bimodal expression of class 3 genes. In particular, class 3 gene expression is still bimodal, even when class 2 gene expression is not. Using a combination of experimental and modeling approaches, we found that class 3 bimodality results from the σ28-FlgM developmental checkpoint.IMPORTANCE Many bacterial use flagella to swim in liquids and swarm over surface. In Salmonella enterica, over 50 genes are required to assemble flagella. The expression of these genes is tightly regulated. Previous studies have found that flagellar gene expression is bimodal in S. enterica, which means that only a fraction of cells express flagellar genes and are motile. In the present study, we found that two separate mechanisms induce this bimodal response. One mechanism, which was previously identified, tunes the fraction of motile cells in response to nutrients. The other results from a developmental checkpoint that couples flagellar gene expression to flagellar assembly. Collectively, these results further our understanding of how flagellar gene expression is regulated in S. enterica.
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Joshi C, Patel P, Godatwar P, Sharma S, Kothari V. Identifying the Molecular Targets of an Anti-pathogenic Hydroalcoholic Extract of Punica granatum Peel Against Multidrug-resistant Serratia marcescens. Curr Drug Discov Technol 2020; 18:391-404. [PMID: 32316896 DOI: 10.2174/1568009620666200421083120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antibiotic-resistant members of the family Enterobacteriaceae are among the serious threats to human health globally. This study reports the anti-pathogenic activity of Punica granatum peel extract (PGPE) against a multi-drug resistant, beta-lactamase producing member of this family i.e. Serratia marcescens. OBJECTIVE This study aimed at assessing the anti-pathogenic activity of PGPE against the gramnegative bacterial pathogen S. marcescens and identifying the molecular targets of this extract in the test bacterium. METHODS Effect of PGPE on S. marcescens growth and quorum sensing (QS)-regulated pigment production was assessed through broth dilution assay. In vivo anti-infective and prophylactic activity of PGPE was assessed employing the nematode worm Caenorhabditis elegans as a model host. Differential gene expression in PGPE-exposed S. marcescens was studied through a whole transcriptome approach. RESULTS PGPE was able to modulate QS-regulated pigment production in S. marcescens without exerting any heavy growth-inhibitory effect at concentrations as low as ≥2.5 μg/mL. It could attenuate the virulence of the test bacterium towards the worm host by 22-42% (p≤0.01) at even lower concentrations (≥0.5 μg/mL). PGPE also exerted a post-extract effect on S. marcescens. This extract was found to offer prophylactic benefit too, to the host worm, as PGPE-pre-fed worms scored better (34-51%; p≤0.001) survival in face of subsequent bacterial attack. Differential gene expression analysis revealed that PGPE affected the expression of a total of 66 genes in S. marcescens by ≥1.5 fold. CONCLUSION The anti-virulence effect of PGPE against S. marcescens is multifaceted, affecting stress-response machinery, efflux activity, iron homeostasis, and cellular energetics of this bacterium notably. Among the major molecular targets identified in this study are LPS export transporter permease (LptF), t-RNA pseudouridine synthase (TruB), etc.
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Affiliation(s)
- Chinmayi Joshi
- Institute of Science, Nirma University, Ahmedabad- 382481, India
| | - Pooja Patel
- Institute of Science, Nirma University, Ahmedabad- 382481, India
| | | | | | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad- 382481, India
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8
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Yang CL, Chen XK, Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Lin JQ, Chen LX. Essential Role of σ Factor RpoF in Flagellar Biosynthesis and Flagella-Mediated Motility of Acidithiobacillus caldus. Front Microbiol 2019; 10:1130. [PMID: 31178842 PMCID: PMC6543871 DOI: 10.3389/fmicb.2019.01130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/03/2019] [Indexed: 12/04/2022] Open
Abstract
Acidithiobacillaceae, an important family of acidophilic and chemoautotrophic sulfur or iron oxidizers, participate in geobiochemical circulation of the elements and drive the release of heavy metals in mining associated habitats. Because of their environmental adaptability and energy metabolic systems, Acidithiobacillus spp. have become the dominant bacteria used in bioleaching for heavy metal recovery. Flagella-driven motility is associated with bacterial chemotaxis and bacterial responses to environmental stimuli. However, little is known about how the flagellum of Acidithiobacillus spp. is regulated and how the flagellum affects the growth of these chemoautotrophic bacteria. In this study, we analyzed the flagellar gene clusters in Acidithiobacillus strains and uncovered the close relationship between flagella and the sulfur-oxidizing systems (Sox system). The σ28 gene (rpoF) knockout and overexpression strains of Acidithiobacillus caldus were constructed. Scanning electron microscopy shows that A. caldus ΔrpoF cells lacked flagella, indicating the essential role of RpoF in regulating flagella synthesis in these chemoautotrophic bacteria. Motility analysis suggests that the deletion of rpoF resulted in the reduction of swarming capability, while this capability was enhanced in the rpoF overexpression strain. Both static cultivation and low concentration of energy substrates (elemental sulfur or tetrathionate) led to weak growth of A. caldus ΔrpoF cells. The deletion of rpoF promoted bacterial attachment to the surface of elemental sulfur in static cultivation. The absence of RpoF caused an obvious change in transcription profile, including genes in flagellar cluster and those involved in biofilm formation. These results provide an understanding on the regulation of flagellar hierarchy and the flagellar function in these sulfur or iron oxidizers.
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Affiliation(s)
- Chun-Long Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xian-Ke Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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9
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Rudenko I, Ni B, Glatter T, Sourjik V. Inefficient Secretion of Anti-sigma Factor FlgM Inhibits Bacterial Motility at High Temperature. iScience 2019; 16:145-154. [PMID: 31170626 PMCID: PMC6551532 DOI: 10.1016/j.isci.2019.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/01/2019] [Accepted: 05/15/2019] [Indexed: 12/03/2022] Open
Abstract
Temperature is one of the key cues that enable microorganisms to adjust their physiology in response to environmental changes. Here we show that motility is the major cellular function of Escherichia coli that is differentially regulated between growth at normal host temperature of 37°C and the febrile temperature of 42°C. Expression of both class II and class III flagellar genes is reduced at 42°C because of lowered level of the upstream activator FlhD. Class III genes are additionally repressed because of the destabilization and malfunction of secretion apparatus at high temperature, which prevents secretion of the anti-sigma factor FlgM. This mechanism of repression apparently accelerates loss of motility at 42°C. We hypothesize that E. coli perceives high temperature as a sign of inflammation, downregulating flagella to escape detection by the immune system of the host. Secretion-dependent coupling of gene expression to the environmental temperature is likely common among many bacteria. E. coli motility is tightly turned off at febrile temperature (42°C) Repression of motility is achieved at two levels of hierarchical gene regulation Lowered FlhD level reduces expression of all flagellar genes Impaired FlgM secretion tightens repression of class III genes
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Affiliation(s)
- Iaroslav Rudenko
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Bin Ni
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Victor Sourjik
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany.
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Green CA, Kamble NS, Court EK, Bryant OJ, Hicks MG, Lennon C, Fraser GM, Wright PC, Stafford GP. Engineering the flagellar type III secretion system: improving capacity for secretion of recombinant protein. Microb Cell Fact 2019; 18:10. [PMID: 30657054 PMCID: PMC6337784 DOI: 10.1186/s12934-019-1058-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/08/2019] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Many valuable biopharmaceutical and biotechnological proteins have been produced in Escherichia coli, however these proteins are almost exclusively localised in the cytoplasm or periplasm. This presents challenges for purification, i.e. the removal of contaminating cellular constituents. One solution is secretion directly into the surrounding media, which we achieved via the 'hijack' of the flagellar type III secretion system (FT3SS). Ordinarily flagellar subunits are exported through the centre of the growing flagellum, before assembly at the tip. However, we exploit the fact that in the absence of certain flagellar components (e.g. cap proteins), monomeric flagellar proteins are secreted into the supernatant. RESULTS We report the creation and iterative improvement of an E. coli strain, by means of a modified FT3SS and a modular plasmid system, for secretion of exemplar proteins. We show that removal of the flagellin and HAP proteins (FliC and FlgKL) resulted in an optimal prototype. We next developed a high-throughput enzymatic secretion assay based on cutinase. This indicated that removal of the flagellar motor proteins, motAB (to reduce metabolic burden) and protein degradation machinery, clpX (to boost FT3SS levels intracellularly), result in high capacity secretion. We also show that a secretion construct comprising the 5'UTR and first 47 amino acidsof FliC from E. coli (but no 3'UTR) achieved the highest levels of secretion. Upon combination, we show a 24-fold improvement in secretion of a heterologous (cutinase) enzyme over the original strain. This improved strain could export a range of pharmaceutically relevant heterologous proteins [hGH, TrxA, ScFv (CH2)], achieving secreted yields of up to 0.29 mg L-1, in low cell density culture. CONCLUSIONS We have engineered an E. coli which secretes a range of recombinant proteins, through the FT3SS, to the extracellular media. With further developments, including cell culture process strategies, we envision further improvement to the secreted titre of recombinant protein, with the potential application for protein production for biotechnological purposes.
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Affiliation(s)
- Charlotte A Green
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK.,Sustainable Process Technologies, Chemical and Environmental Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nitin S Kamble
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Elizabeth K Court
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Owain J Bryant
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Matthew G Hicks
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Christopher Lennon
- FUJIFILM Diosynth Biotechnologies, Belasis Avenue, Stockton-on-Tees, Billingham, TS23 1LH, UK
| | - Gillian M Fraser
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Phillip C Wright
- School of Engineering, The Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle, NE1 7RU, UK
| | - Graham P Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK.
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11
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Piperine, an alkaloid inhibiting the super-relaxed state of myosin, binds to the myosin regulatory light chain. Arch Biochem Biophys 2018; 659:75-84. [PMID: 30287237 DOI: 10.1016/j.abb.2018.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/26/2018] [Accepted: 09/30/2018] [Indexed: 12/13/2022]
Abstract
Piperine, an alkaloid from black pepper, was found to inhibit the super-relaxed state (SRX) of myosin in fast-twitch skeletal muscle fibers. In this work we report that the piperine molecule binds heavy meromyosin (HMM), whereas it does not interact with the regulatory light chain (RLC)-free subfragment-1 (S1) or with control proteins from the same muscle molecular machinery, G-actin and tropomyosin. To further narrow down the location of piperine binding, we studied interactions between piperine and a fragment of skeletal myosin consisting of the full-length RLC and a fragment of the heavy chain (HCF). The sequence of HCF was designed to bind RLC and to dimerize via formation of a stable coiled coil, thus producing a well-folded isolated fragment of the myosin neck. Both chains were co-expressed in Escherichia coli, the RLC/HCF complex was purified and tested for stability, composition and binding to piperine. RLC and HCF chains formed a stable heterotetrameric complex (RLC/HCF)2 which was found to bind piperine. The piperine molecule was also found to bind isolated RLC. Piperine binding to RLC in (RLC/HCF)2 altered the compactness of the complex, suggesting that the mechanism of SRX inhibition by piperine is based on changing conformation of the myosin.
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12
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Inoue T, Barker CS, Matsunami H, Aizawa SI, Samatey FA. The FlaG regulator is involved in length control of the polar flagella of Campylobacter jejuni. MICROBIOLOGY-SGM 2018; 164:740-750. [PMID: 29595414 DOI: 10.1099/mic.0.000648] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Campylobacter jejuni cells have bipolar flagella. Both flagella have similar lengths of about one helical turn, or 3.53±0.52 µm. The flagellar filament is composed of two homologous flagellins: FlaA and FlaB. Mutant strains that express either FlaA or FlaB alone produce filaments that are shorter than those of the wild-type. It is reported that the flaG gene could affect filament length in some species of bacteria, but its function remains unknown. We introduced a flaG-deletion mutation into the C. jejuni wild-type strain and flaA- or flaB-deletion mutant strains, and observed their flagella by microscopy. The ΔflaG mutant cells produced long filaments of two helical turns in the wild-type background. The ΔflaAG double mutant cells produced very short FlaB filaments. On the other hand, ΔflaBG double mutant cells produced long FlaA filaments and their morphology was not helical but straight. Furthermore, FlaG was secreted, and a pulldown assay showed that sigma factor 28 was co-precipitated with purified polyhistidine-tagged FlaG. We conclude that FlaG controls flagella length by negatively regulating FlaA filament assembly and discuss the role of FlaA and FlaB flagellins in C. jejuni flagella formation.
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Affiliation(s)
- Tomoharu Inoue
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Onna, Onna-son, Okinawa 904-0495, Japan
| | - Clive S Barker
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Onna, Onna-son, Okinawa 904-0495, Japan
| | - Hideyuki Matsunami
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Onna, Onna-son, Okinawa 904-0495, Japan
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727-0023, Japan
| | - Fadel A Samatey
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Onna, Onna-son, Okinawa 904-0495, Japan
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13
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Lo YL, Chen CL, Shen L, Chen YC, Wang YH, Lee CC, Wang LC, Chuang CH, Janapatla RP, Chiu CH, Chang HY. Characterization of the role of global regulator FliA in the pathophysiology of Pseudomonas aeruginosa infection. Res Microbiol 2018; 169:135-144. [PMID: 29432810 DOI: 10.1016/j.resmic.2018.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 12/29/2022]
Abstract
FliA is known to be a sigma factor that regulates bacterial flagella gene expression. Accumulating evidence suggests that FliA is involved in bacterial behavior other than motility. To elucidate the contribution of FliA to Pseudomonas aeruginosa pathophysiology, we analyzed the biological properties and gene expression profiles of a ΔfliA mutant. Transcriptome analysis results demonstrated that the expression levels of flagella biogenesis genes decreased dramatically in the mutant; consequently, the ΔfliA mutant failed to synthesize flagella and exhibited reduced motility. The ΔfliA mutant displayed stronger hemolytic and caseinolytic activities, as well as pyocyanin production. The expression of type 6 secretion system-II genes and interbacterial competition activity was decreased in the ΔfliA mutant. Direct evidence of fliA participation in virulence was obtained from analysis of hypervirulent strain B136-33. Adhesion to and cytotoxicity toward mammalian cells and penetration through cell layers were noted; furthermore, the colonization ability of the fliA::Tn5 mutant in the intestines of laboratory mice was compromised. Notably, the fliA-overexpressing strain displayed phenotypes similar to that of the fliA-defective strain, indicating that optimal FliA levels are critical to bacterial physiology. Our findings indicate that FliA plays diverse roles in P. aeruginosa, not only in flagella biosynthesis, but also in pathophysiology.
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Affiliation(s)
- Yi-Ling Lo
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Lunda Shen
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Ying-Ching Chen
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chung-Chan Lee
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Lian-Chen Wang
- Division of Parasitology, Chang Gung University, Taoyuan, Taiwan
| | | | - Rajendra Prasad Janapatla
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
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14
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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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15
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Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat Commun 2018; 9:336. [PMID: 29362365 PMCID: PMC5780524 DOI: 10.1038/s41467-017-02522-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/07/2017] [Indexed: 11/29/2022] Open
Abstract
Most studies of bacterial motility have examined small-scale (micrometer–centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes. Interactions with other microbes may inhibit or facilitate the dispersal of bacteria. Here, Zhang et al. use cheese rind microbiomes as a model to show that physical networks created by filamentous fungi can affect the dispersal of motile bacteria and thus shape the diversity of microbial communities.
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16
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Radomska KA, Wösten MMSM, Ordoñez SR, Wagenaar JA, van Putten JPM. Importance of Campylobacter jejuni FliS and FliW in Flagella Biogenesis and Flagellin Secretion. Front Microbiol 2017; 8:1060. [PMID: 28659885 PMCID: PMC5466977 DOI: 10.3389/fmicb.2017.01060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/29/2017] [Indexed: 12/11/2022] Open
Abstract
Flagella-driven motility enables bacteria to reach their favorable niche within the host. The human foodborne pathogen Campylobacter jejuni produces two heavily glycosylated structural flagellins (FlaA and FlaB) that form the flagellar filament. It also encodes the non-structural FlaC flagellin which is secreted through the flagellum and has been implicated in host cell invasion. The mechanisms that regulate C. jejuni flagellin biogenesis and guide the proteins to the export apparatus are different from those in most other enteropathogens and are not fully understood. This work demonstrates the importance of the putative flagellar protein FliS in C. jejuni flagella assembly. A constructed fliS knockout strain was non-motile, displayed reduced levels of FlaA/B and FlaC flagellin, and carried severely truncated flagella. Pull-down and Far Western blot assays showed direct interaction of FliS with all three C. jejuni flagellins (FlaA, FlaB, and FlaC). This is in contrast to, the sensor and regulator of intracellular flagellin levels, FliW, which bound to FlaA and FlaB but not to FlaC. The FliS protein but not FliW preferred binding to glycosylated C. jejuni flagellins rather than to their non-glycosylated recombinant counterparts. Mapping of the binding region of FliS and FliW using a set of flagellin fragments showed that the C-terminal subdomain of the flagellin was required for FliS binding, whereas the N-terminal subdomain was essential for FliW binding. The separate binding subdomains required for FliS and FliW, the different substrate specificity, and the differential preference for binding of glycosylated flagellins ensure optimal processing and assembly of the C. jejuni flagellins.
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Affiliation(s)
- Katarzyna A Radomska
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Marc M S M Wösten
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Soledad R Ordoñez
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands.,Wageningen Bioveterinary ResearchLelystad, Netherlands.,WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for CampylobacteriosisUtrecht, Netherlands
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands.,WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for CampylobacteriosisUtrecht, Netherlands
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17
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Crystal structure of the flagellar chaperone FliS from Bacillus cereus and an invariant proline critical for FliS dimerization and flagellin recognition. Biochem Biophys Res Commun 2017; 487:381-387. [DOI: 10.1016/j.bbrc.2017.04.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 11/23/2022]
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18
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Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Sci Rep 2017; 7:862. [PMID: 28408760 PMCID: PMC5429845 DOI: 10.1038/s41598-017-00893-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/16/2017] [Indexed: 01/24/2023] Open
Abstract
The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteria.
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19
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De Maayer P, Cowan DA. Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus. BMC Genomics 2016; 17:913. [PMID: 27842516 PMCID: PMC5109656 DOI: 10.1186/s12864-016-3273-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/05/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. Post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many Gram-negative bacteria and Archaea. Several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, and virulence. However, little is known about this trait among Gram-positive bacteria. RESULTS Using comparative genomic approaches the flagellin glycosylation loci of multiple strains of the Gram-positive thermophilic genus Geobacillus were identified and characterized. Eighteen of thirty-six compared strains of the genus carry these loci, which show evidence of horizontal acquisition. The Geobacillus flagellin glycosylation islands (FGIs) can be clustered into five distinct types, which are predicted to encode highly variable glycans decorated with distinct and heavily modified sugars. CONCLUSIONS Our comparative genomic analyses showed that, while not universal, flagellin glycosylation islands are relatively common among members of the genus Geobacillus and that the encoded flagellin glycans are highly variable. This suggests that flagellin glycosylation plays an important role in the lifestyles of members of this thermophilic genus.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa.
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Pretoria, 0002, South Africa
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20
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Furukawa Y, Inoue Y, Sakaguchi A, Mori Y, Fukumura T, Miyata T, Namba K, Minamino T. Structural stability of flagellin subunit affects the rate of flagellin export in the absence of FliS chaperone. Mol Microbiol 2016; 102:405-416. [PMID: 27461872 DOI: 10.1111/mmi.13469] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2016] [Indexed: 12/17/2022]
Abstract
FliS chaperone binds to flagellin FliC in the cytoplasm and transfers FliC to a sorting platform of the flagellar type III export apparatus through the interaction between FliS and FlhA for rapid and efficient protein export during flagellar filament assembly. FliS also suppresses the secretion of an anti-σ factor, FlgM. Loss of FliS results in a short filament phenotype although the expression levels of FliC are increased considerably due to an increase in the secretion level of FlgM. Here to clarify the rate limiting step of FliC export in the absence of FliS, we isolated bypass mutants from a Salmonella ΔfliS mutant. All the bypass mutations were identified in FliC. These bypass mutations increased the export rate of FliC by ca. twofold, allowing the bypass mutant cells to produce longer filaments than the parental ΔfliS cells. Both far-UV CD measurements and limited proteolysis revealed that the bypass mutations significantly destabilize the folded structure of FliC monomer. These results suggest that an unfolding step of FliC limits the export rate of FliC in the ΔfliS mutant, thereby producing short filaments. We propose that FliS promotes FliC docking at the FlhA platform to facilitate subsequent unfolding of FliC.
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Affiliation(s)
- Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumi Inoue
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Aya Sakaguchi
- Department of Food Science and Nutrition, Faculty of Human Life and Science, Doshisha Women's College of Liberal Arts, Kyoto, 602-0893, Japan
| | - Yoko Mori
- Department of Food Science and Nutrition, Faculty of Human Life and Science, Doshisha Women's College of Liberal Arts, Kyoto, 602-0893, Japan
| | - Takuma Fukumura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Quantitative Biology Center, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Quantitative Biology Center, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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21
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Gupta SK, Gross R, Dandekar T. An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens. Gene 2016; 591:268-278. [PMID: 27425866 DOI: 10.1016/j.gene.2016.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/26/2016] [Accepted: 07/12/2016] [Indexed: 01/20/2023]
Abstract
We investigate a drug target screening pipeline comparing sequence, structure and network-based criteria for prioritization. Serratia marcescens, an opportunistic pathogen, serves as test case. We rank according to (i) availability of three dimensional structures and lead compounds, (ii) not occurring in man and general sequence conservation information, and (iii) network information on the importance of the protein (conserved protein-protein interactions; metabolism; reported to be an essential gene in other organisms). We identify 45 potential anti-microbial drug targets in S. marcescens with KdsA involved in LPS biosynthesis as top candidate drug target. LpxC and FlgB are further top-ranked targets identified by interactome analysis not suggested before for S. marcescens. Pipeline, targets and complementarity of the three approaches are evaluated by available experimental data and genetic evidence and against other antibiotic screening pipelines. This supports reliable drug target identification and prioritization for infectious agents (bacteria, parasites, fungi) by these bundled complementary criteria.
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Affiliation(s)
- Shishir K Gupta
- Department of Bioinformatics, Biocenter, Am Hubland, D-97074 Würzburg, Germany; Department of Microbiology, Biocenter, Am Hubland, D-97074 Würzburg, Germany.
| | - Roy Gross
- Department of Microbiology, Biocenter, Am Hubland, D-97074 Würzburg, Germany.
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, D-97074 Würzburg, Germany; EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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22
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Sajó R, Tőke O, Hajdú I, Jankovics H, Micsonai A, Dobó J, Kardos J, Vonderviszt F. Structural plasticity of the Salmonella FliS flagellar export chaperone. FEBS Lett 2016; 590:1103-13. [PMID: 27003324 DOI: 10.1002/1873-3468.12149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/11/2022]
Abstract
The Salmonella FliS flagellar export chaperone is a highly α-helical protein. Proteolytic experiments suggest that FliS has a compact core. However, the calorimetric melting profile of FliS does not show any melting transition in the 25-110 °C temperature range. Circular dichroism measurements reveal that FliS is losing its helical structure over a broad temperature range upon heating. These observations indicate that FliS unfolds in a noncooperative way and its native state shows features reminiscent of the molten globule state of proteins possessing substantial structural plasticity. As FliS has several binding partners within the cell, conformational adaptability seems to be an essential requirement to fulfill its multiple roles.
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Affiliation(s)
- Ráchel Sajó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Tőke
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Hajdú
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute for Chemical and Process Engineering, University of Pannonia, Veszprém, Hungary
| | - András Micsonai
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute for Chemical and Process Engineering, University of Pannonia, Veszprém, Hungary.,Institute of Technical Physics and Materials Science, Centre for Energy Research, Hungarian Academy of Sciences, Budapest, Hungary
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23
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Marcelletti S, Scortichini M. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits. PLoS One 2015; 10:e0131112. [PMID: 26147218 PMCID: PMC4492584 DOI: 10.1371/journal.pone.0131112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/28/2015] [Indexed: 01/26/2023] Open
Abstract
The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.
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Affiliation(s)
- Simone Marcelletti
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (C.R.A.)-Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, I-00134, Roma, Italy
| | - Marco Scortichini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (C.R.A.)-Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, I-00134, Roma, Italy
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (C.R.A.)-Unità di Ricerca per la Frutticoltura, Via Torrino 3, I-81100, Caserta, Italy
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24
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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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Functional role of bdm during flagella biogenesis in Escherichia coli. Curr Microbiol 2014; 70:369-73. [PMID: 25398323 DOI: 10.1007/s00284-014-0729-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
The biofilm-dependent modulation gene (bdm) has recently been shown to play a role in osmotic-induced formation of biofilm in Escherichia coli. In this study, we demonstrated that deletion of bdm results in down-regulation of flagella biosynthesis genes and, consequently, a defect in E. coli motility. In addition, we employed atomic force microscopy to confirm the absence of flagella-like structures on the surface of bdm-null cells. These findings indicate that bdm plays a key role in regulatory pathway for the formation of flagella.
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Sajó R, Liliom K, Muskotál A, Klein A, Závodszky P, Vonderviszt F, Dobó J. Soluble components of the flagellar export apparatus, FliI, FliJ, and FliH, do not deliver flagellin, the major filament protein, from the cytosol to the export gate. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2414-23. [PMID: 25068520 DOI: 10.1016/j.bbamcr.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/01/2014] [Accepted: 07/11/2014] [Indexed: 12/21/2022]
Abstract
Flagella, the locomotion organelles of bacteria, extend from the cytoplasm to the cell exterior. External flagellar proteins are synthesized in the cytoplasm and exported by the flagellar type III secretion system. Soluble components of the flagellar export apparatus, FliI, FliH, and FliJ, have been implicated to carry late export substrates in complex with their cognate chaperones from the cytoplasm to the export gate. The importance of the soluble components in the delivery of the three minor late substrates FlgK, FlgL (hook-filament junction) and FliD (filament-cap) has been convincingly demonstrated, but their role in the transport of the major filament component flagellin (FliC) is still unclear. We have used continuous ATPase activity measurements and quartz crystal microbalance (QCM) studies to characterize interactions between the soluble export components and flagellin or the FliC:FliS substrate-chaperone complex. As controls, interactions between soluble export component pairs were characterized providing Kd values. FliC or FliC:FliS did not influence the ATPase activity of FliI alone or in complex with FliH and/or FliJ suggesting lack of interaction in solution. Immobilized FliI, FliH, or FliJ did not interact with FliC or FliC:FliS detected by QCM. The lack of interaction in the fluid phase between FliC or FliC:FliS and the soluble export components, in particular with the ATPase FliI, suggests that cells use different mechanisms for the export of late minor substrates, and the major substrate, FliC. It seems that the abundantly produced flagellin does not require the assistance of the soluble export components to efficiently reach the export gate.
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Affiliation(s)
- Ráchel Sajó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary
| | - Károly Liliom
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary
| | - Adél Muskotál
- Bio-Nanosystems Laboratory, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, H-8200 Veszprém, Hungary
| | - Agnes Klein
- Bio-Nanosystems Laboratory, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, H-8200 Veszprém, Hungary
| | - Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, H-8200 Veszprém, Hungary
| | - József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
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Analysis of factors that affect FlgM-dependent type III secretion for protein purification with Salmonella enterica serovar Typhimurium. J Bacteriol 2014; 196:2333-47. [PMID: 24706743 DOI: 10.1128/jb.01572-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The FlgM protein is secreted in response to flagellar hook-basal body secretion and can be used as a secretion signal to direct selected protein secretion via the flagellar type III secretion (T3S) system [H. M. Singer, M. Erhardt, A. M. Steiner, M. M. Zhang, D. Yoshikami, G. Bulaj, B. M. Olivera, and K. T. Hughes, mBio 3(3):e00115-12, 2012, http://dx.doi.org/10.1128/mBio.00115-12]. Conditions known to affect flagellar gene expression, FlgM stability, and flagellar T3S were tested either alone or in combination to determine their effects on levels of secreted FlgM. These conditions included mutations that affect activity of the flagellar FlhD4C2 master regulatory protein complex or the FlgM T3S chaperone σ(28), the removal of Salmonella pathogenicity island 1 (Spi1), the removal of flagellar late secretion substrates that could compete with FlgM for secretion, and changes in the ionic strength of the growth medium. Conditions that enhanced FlgM secretion were combined in order to maximize levels of secreted FlgM. An optimized FlgM secretion strain was used to secrete and isolate otherwise difficult-to-produce proteins and peptides fused to the C terminus of FlgM. These include cysteine-rich, hydrophobic peptides (conotoxins δ-SVIE and MrVIA), nodule-specific, cysteine-rich antimicrobial peptides (NCR), and a malaria surface antigen domain of apical membrane antigen AMA-1.
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