1
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Nat Commun 2024; 15:331. [PMID: 38184686 PMCID: PMC10771500 DOI: 10.1038/s41467-023-44606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.
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2
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de Amorim GC, Bardiaux B, Izadi-Pruneyre N. Structural Analysis of Proteins from Bacterial Secretion Systems and Their Assemblies by NMR Spectroscopy. Methods Mol Biol 2024; 2715:503-517. [PMID: 37930547 DOI: 10.1007/978-1-0716-3445-5_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are built up from proteins with different physicochemical characteristics, such as highly hydrophobic transmembrane polypeptides, and soluble periplasmic or intracellular domains. A single complex can be composed of more than ten proteins with distinct features, spreading through different cellular compartments. The membrane and multicompartment nature of the proteins, and their large molecular weight make their study challenging. However, information on their structure and assemblies is required to understand their mechanisms and interfere with them. An alternative strategy is to work with soluble domains and peptides corresponding to the regions of interest of the proteins.Here, we describe a simple and fast protocol to evaluate the stability, folding, and interaction of protein sub-complexes by using solution-state Nuclear Magnetic Resonance (NMR) spectroscopy. This technique is widely used for protein structure and protein-ligand interaction analysis in solution.
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Affiliation(s)
- Gisele Cardoso de Amorim
- Núcleo Multidisciplinar de Pesquisa em Biologia, Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
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3
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552980. [PMID: 37609138 PMCID: PMC10441417 DOI: 10.1101/2023.08.11.552980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
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4
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Donegan RK. The role of host heme in bacterial infection. Biol Chem 2022; 403:1017-1029. [PMID: 36228088 DOI: 10.1515/hsz-2022-0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022]
Abstract
Heme is an indispensable cofactor for almost all aerobic life, including the human host and many bacterial pathogens. During infection, heme and hemoproteins are the largest source of bioavailable iron, and pathogens have evolved various heme acquisition pathways to satisfy their need for iron and heme. Many of these pathways are regulated transcriptionally by intracellular iron levels, however, host heme availability and intracellular heme levels have also been found to regulate heme uptake in some species. Knowledge of these pathways has helped to uncover not only how these bacteria incorporate host heme into their metabolism but also provided insight into the importance of host heme as a nutrient source during infection. Within this review is covered multiple aspects of the role of heme at the host pathogen interface, including the various routes of heme biosynthesis, how heme is sequestered by the host, and how heme is scavenged by bacterial pathogens. Also discussed is how heme and hemoproteins alter the behavior of the host immune system and bacterial pathogens. Finally, some unanswered questions about the regulation of heme uptake and how host heme is integrated into bacterial metabolism are highlighted.
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Affiliation(s)
- Rebecca K Donegan
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY, 10027, USA
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5
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Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguéné VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P. Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog. Commun Biol 2022; 5:355. [PMID: 35418619 PMCID: PMC9008036 DOI: 10.1038/s42003-022-03306-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/22/2022] [Indexed: 01/20/2023] Open
Abstract
ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.
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Affiliation(s)
- Valérie Biou
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Ricardo Jorge Diogo Adaixo
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Pierre-Damien Coureux
- grid.10877.390000000121581279Laboratoire de Biologie Structurale de la Cellule, BIOC, UMR7654 CNRS/Ecole polytechnique, Palaiseau, France
| | - Benoist Laurent
- grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France ,grid.508487.60000 0004 7885 7602Plateforme de Bioinformatique, Université de Paris, FRC 550 CNRS, F-75005 Paris, France
| | - Véronique Yvette Ntsogo Enguéné
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France ,grid.5335.00000000121885934Present Address: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Gisele Cardoso de Amorim
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS, USR3756 Paris, France ,grid.8536.80000 0001 2294 473XPresent Address: Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ Brasil
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS, USR3756 Paris, France
| | - Christian Malosse
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, 75015 Paris, France
| | - Julia Chamot-Rooke
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, 75015 Paris, France
| | - Henning Stahlberg
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland ,grid.9851.50000 0001 2165 4204Present Address: Centre d’imagerie Dubochet UNIL-EPFL-UNIGE & Laboratoire de microscopie électronique biologique UNIL-EPFL, Lausanne, Switzerland
| | - Philippe Delepelaire
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France
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6
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Extracellular haem utilization by the opportunistic pathogen Pseudomonas aeruginosa and its role in virulence and pathogenesis. Adv Microb Physiol 2021; 79:89-132. [PMID: 34836613 DOI: 10.1016/bs.ampbs.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Iron is an essential micronutrient for all bacteria but presents a significant challenge given its limited bioavailability. Furthermore, iron's toxicity combined with the need to maintain iron levels within a narrow physiological range requires integrated systems to sense, regulate and transport a variety of iron complexes. Most bacteria encode systems to chelate and transport ferric iron (Fe3+) via siderophore receptor mediated uptake or via cytoplasmic energy dependent transport systems. Pathogenic bacteria have further lowered the barrier to iron acquisition by employing systems to utilize haem as a source of iron. Haem, a lipophilic and toxic molecule, presents a significant challenge for transport into the cell. As such pathogenic bacteria have evolved sophisticated cell surface signaling (CSS) and transport systems to sense and obtain haem from the host. Once internalized haem is cleaved by both oxidative and non-oxidative mechanisms to release iron. Herein we summarize our current understanding of the mechanism of haem sensing, uptake and utilization in Pseudomonas aeruginosa, its role in pathogenesis and virulence, and the potential of these systems as antimicrobial targets.
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7
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FusB Energizes Import across the Outer Membrane through Direct Interaction with Its Ferredoxin Substrate. mBio 2020; 11:mBio.02081-20. [PMID: 33109756 PMCID: PMC7593965 DOI: 10.1128/mbio.02081-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Phytopathogenic Pectobacterium spp. import ferredoxin into the periplasm for proteolytic processing and iron release via the ferredoxin uptake system. Although the ferredoxin receptor FusA and the processing protease FusC have been identified, the mechanistic basis of ferredoxin import is poorly understood. In this work, we demonstrate that protein translocation across the outer membrane is dependent on the TonB-like protein FusB. In contrast to the loss of FusC, loss of FusB or FusA abolishes ferredoxin transport to the periplasm, demonstrating that FusA and FusB work in concert to transport ferredoxin across the outer membrane. In addition to an interaction with the "TonB box" region of FusA, FusB also forms a complex with the ferredoxin substrate, with complex formation required for substrate transport. These data suggest that ferredoxin transport requires energy transduction from the cytoplasmic membrane via FusB both for removal of the FusA plug domain and for substrate translocation through the FusA barrel.IMPORTANCE The ability to acquire iron is key to the ability of bacteria to cause infection. Plant-pathogenic Pectobacterium spp. are able to acquire iron from plants by transporting the iron-containing protein ferredoxin into the cell from proteolytic processing. In this work, we show that the TonB-like protein FusB plays a key role in transporting ferredoxin across the bacterial outer membrane by directly energizing its transport into the cell. The direct interaction of the TonB-like protein with substrate is unprecedented and explains the requirement for the system-specific TonB homologue in the ferredoxin uptake system. Since multiple genes encoding TonB-like proteins are commonly found in the genomes of Gram-negative bacteria, this may be a common mechanism for the uptake of atypical substrates via TonB-dependent receptors.
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8
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Biodegradation of 3-chlorobenzoic acid with electron shuttle systems: pathways and molecular identification. Arch Microbiol 2020; 202:2471-2480. [PMID: 32613418 DOI: 10.1007/s00203-020-01965-1] [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: 11/15/2019] [Revised: 05/28/2020] [Accepted: 06/24/2020] [Indexed: 10/24/2022]
Abstract
A synergy of biodegradation and electron shuttle systems is a promising strategy for eliminating pollutants including chlorinated aromatic compounds. The present work studies the degradation products of 3-chlorobenzoic acid by Pseudomonas putida in the presence of an electron shuttle system (ESS) composed of citrate and pyruvate as electron donors and the pollutant as an electron acceptor. Chromatographic results showed different pathways involved in the biodegradation process under the influence of electron shuttle systems. These routes depend on oxidation and reduction reactions for output byproducts to be easily mineralized by the bacterium under investigation. A nucleotide sequence with about 380 bp of a ton B gene was detected in P. putida and it resembles Escherichia coli Ton B. The relatedness tree of the selected gene reveals a high similarity and is comparable to P. aeruginosa (100%) and the highest variation with that of P. citronellolis (21.99%). Accordingly, in the presence of electron shuttle systems, the genes responsible for bacterial influx were activated to ease the biodegradation process. In an application model, the remediated-water samples were handled by two recycling processes using Scenedesmus obliquus and Trigonella foenum-graecum to evaluate the efficiency of this non-conventional treatment. In conclusion, this strategy succeeded in remediating the polluted water with chlorinated aromatic compounds for further applications.
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9
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Celia H, Noinaj N, Buchanan SK. Structure and Stoichiometry of the Ton Molecular Motor. Int J Mol Sci 2020; 21:E375. [PMID: 31936081 PMCID: PMC7014051 DOI: 10.3390/ijms21020375] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
The Ton complex is a molecular motor that uses the proton gradient at the inner membrane of Gram-negative bacteria to generate force and movement, which are transmitted to transporters at the outer membrane, allowing the entry of nutrients into the periplasmic space. Despite decades of investigation and the recent flurry of structures being reported by X-ray crystallography and cryoEM, the mode of action of the Ton molecular motor has remained elusive, and the precise stoichiometry of its subunits is still a matter of debate. This review summarizes the latest findings on the Ton system by presenting the recently reported structures and related reports on the stoichiometry of the fully assembled complex.
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Affiliation(s)
- Herve Celia
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA;
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA;
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA;
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10
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Richard KL, Kelley BR, Johnson JG. Heme Uptake and Utilization by Gram-Negative Bacterial Pathogens. Front Cell Infect Microbiol 2019; 9:81. [PMID: 30984629 PMCID: PMC6449446 DOI: 10.3389/fcimb.2019.00081] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Iron is a transition metal utilized by nearly all forms of life for essential cellular processes, such as DNA synthesis and cellular respiration. During infection by bacterial pathogens, the host utilizes various strategies to sequester iron in a process termed, nutritional immunity. To circumvent these defenses, Gram-negative pathogens have evolved numerous mechanisms to obtain iron from heme. In this review we outline the systems that exist in several Gram-negative pathogens that are associated with heme transport and utilization, beginning with hemolysis and concluding with heme degradation. In addition, Gram-negative pathogens must also closely regulate the intracellular concentrations of iron and heme, since high levels of iron can lead to the generation of toxic reactive oxygen species. As such, we also provide several examples of regulatory pathways that control heme utilization, showing that co-regulation with other cellular processes is complex and often not completely understood.
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Affiliation(s)
- Kaylie L Richard
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Brittni R Kelley
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Jeremiah G Johnson
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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11
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Oeemig JS, Ollila OS, Iwaï H. NMR structure of the C-terminal domain of TonB protein from Pseudomonas aeruginosa. PeerJ 2018; 6:e5412. [PMID: 30186676 PMCID: PMC6118199 DOI: 10.7717/peerj.5412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
The TonB protein plays an essential role in the energy transduction system to drive active transport across the outer membrane (OM) using the proton-motive force of the cytoplasmic membrane of Gram-negative bacteria. The C-terminal domain (CTD) of TonB protein is known to interact with the conserved TonB box motif of TonB-dependent OM transporters, which likely induces structural changes in the OM transporters. Several distinct conformations of differently dissected CTDs of Escherichia coli TonB have been previously reported. Here we determined the solution NMR structure of a 96-residue fragment of Pseudomonas aeruginosa TonB (PaTonB-96). The structure shows a monomeric structure with the flexible C-terminal region (residues 338-342), different from the NMR structure of E. coli TonB (EcTonB-137). The extended and flexible C-terminal residues are confirmed by 15N relaxation analysis and molecular dynamics simulation. We created models for the PaTonB-96/TonB box interaction and propose that the internal fluctuations of PaTonB-96 makes it more accessible for the interactions with the TonB box and possibly plays a role in disrupting the plug domain of the TonB-dependent OM transporters.
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Affiliation(s)
- Jesper S. Oeemig
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- VIB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel, Brussels, Belgium
| | - O.H. Samuli Ollila
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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12
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Abstract
Iron is essential for the survival of most bacteria but presents a significant challenge given its limited bioavailability. Furthermore, the toxicity of iron combined with the need to maintain physiological iron levels within a narrow concentration range requires sophisticated systems to sense, regulate, and transport iron. Most bacteria have evolved mechanisms to chelate and transport ferric iron (Fe3+) via siderophore receptor systems, and pathogenic bacteria have further lowered this barrier by employing mechanisms to utilize the host's hemoproteins. Once internalized, heme is cleaved by both oxidative and nonoxidative mechanisms to release iron. Heme, itself a lipophilic and toxic molecule, presents a significant challenge for transport into the cell. As such, pathogenic bacteria have evolved sophisticated cell surface signaling and transport systems to obtain heme from the host. In this review, we summarize the structure and function of the heme-sensing and transport systems of pathogenic bacteria and the potential of these systems as antimicrobial targets.
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Affiliation(s)
- Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201;
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201;
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13
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Ciragan A, Aranko AS, Tascon I, Iwaï H. Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool. J Mol Biol 2016; 428:4573-4588. [PMID: 27720988 DOI: 10.1016/j.jmb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 10/20/2022]
Abstract
Intervening protein sequences (inteins) from extremely halophilic haloarchaea can be inactive under low salinity but could be activated by increasing the salt content to a specific concentration for each intein. The halo-obligatory inteins confer high solubility under both low and high salinity conditions. We showed the broad utility of salt-dependent protein splicing in cis and trans by demonstrating backbone cyclization, self-cleavage for purification, and scarless protein ligation for segmental isotopic labeling. Artificially split MCM2 intein derived from Halorhabdus utahensis remained highly soluble and was capable of protein trans-splicing with excellent ligation kinetics by reassembly under high salinity conditions. Importantly, the MCM2 intein has the active site residue of Ser at the +1 position, which remains in the ligated product, instead of Cys as found in many other efficient split inteins. Since Ser is more abundant than Cys in proteins, the novel split intein could widen the applications of segmental labeling in protein NMR spectroscopy and traceless protein ligation by exploiting a Ser residue in the native sequences as the +1 position of the MCM2 intein. The split halo-obligatory intein was successfully used to demonstrate the utility in NMR investigation of intact proteins by producing segmentally isotope-labeled intact TonB protein from Helicobacter pylori.
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Affiliation(s)
- Annika Ciragan
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Igor Tascon
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.
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14
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Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach. Biochem J 2016; 473:2239-48. [PMID: 27208170 PMCID: PMC4941744 DOI: 10.1042/bcj20160131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/13/2016] [Indexed: 01/19/2023]
Abstract
In bacteria, some scarce nutrients are sensed, bound and internalized by their specific transporter. In the present study, using an integrative structural approach, we study HasR, a bacterial haem transporter in both its free and its loaded forms. Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling process that up-regulates the expression of genes of various functions, from uptake of nutrient to production of virulence factors. Although proteins involved in this process have been identified, signal transduction through this family of transporters is not well understood. In the present study, using an integrative approach (EM, SAXS, X-ray crystallography and NMR), we have studied the structure of the haem transporter HasR captured in two stages of the signalling process, i.e. before and after the arrival of signalling activators (haem and its carrier protein). We show for the first time that the HasR domain responsible for signal transfer: (i) is highly flexible in two stages of signalling; (ii) extends into the periplasm at approximately 70–90 Å (1 Å=0.1 nm) from the HasR β-barrel; and (iii) exhibits local conformational changes in response to the arrival of signalling activators. These features would favour the signal transfer from HasR to its cytoplasmic membrane partners.
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Delepelaire P, Izadi-Pruneyre N, Delepierre M, Ghigo JM, Schwartz M. A tribute to Cécile Wandersman. Res Microbiol 2015; 166:393-8. [PMID: 26258186 DOI: 10.1016/j.resmic.2015.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Zhu L, Yang Z, Yang Q, Tu Z, Ma L, Shi Z, Li X. Degradation of dexamethasone by acclimated strain of Pseudomonas Alcaligenes. Int J Clin Exp Med 2015; 8:10971-10978. [PMID: 26379892 PMCID: PMC4565275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/10/2015] [Indexed: 06/05/2023]
Abstract
This study is to investigate the use of microbial remediation technology for degradation of dexamethasone in polluted water. A strain of Pseudomonas Alcaligenes with the ability of dexamethasone degradation was isolated from hospital polluted water. This strain was further acclimated into a bacterial strain that could highly degrade dexamethasone. Domesticated bacterial proteins were separated by osmotic shock method and were analyzed using SDS-PAGE. Enzyme activity of dexamethasone degradation was detected by high performance liquid chromatography. Protein bands with different molecular weight were found in all regions of the bacteria and a band with molecular weight of about 100 kDa was most obvious. In intracellular and periplasmic liquid, there was a band with molecular weight of about 41 kDa. Enzyme activity mainly existed in intracellular liquid. The 41 kDa protease was purified using ammonium sulfate precipitation, DEAE-52 ion exchange column and Sephadex G-100 column. Dexamethasone and dexamethasone sodium phosphate degrading rates of the purified enzyme were 36% and 95%, respectively. The 100 kDa protein had a 19% coverage rate to TonB receptor dependent protein, with 11 peptides matching. The 41 kDa protein had a 56% coverage rate to isovaleryl coenzyme A dehydrogenase, with 5 peptides matching. The 41 kDa protein had good degradation between the temperature of 25-40°C and PH value of 6.5-8.5. The enzyme kinetics equation was Ct = C0 e(-0.1769t), in accordance with the first-order kinetic equation. This study laid the foundation for further preparation of bioremediation agents for clearance of dexamethasone pollution in water.
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Affiliation(s)
- Lili Zhu
- Department of Pathogenic Biology, Basic Medical College of Chongqing Medical UniversityChongqing 400016, P. R. China
| | - Zhibang Yang
- Laboratory of Pathogenic Biology and Immunology, Basic Medical Experimental Teaching Center, Chongqing Medical UniversityChongqing 400016, P. R. China
| | - Qian Yang
- Department of Pathogenic Biology, Basic Medical College of Chongqing Medical UniversityChongqing 400016, P. R. China
| | - Zeng Tu
- Department of Pathogenic Biology, Basic Medical College of Chongqing Medical UniversityChongqing 400016, P. R. China
| | - Lianju Ma
- Pharmacy Experimental Teaching Center, Chongqing Medical UniversityChongqing 400016, P. R. China
| | - Zhongquan Shi
- Department of Immunology and Pathogenic Biology, Chongqing Three Gorges Medical CollegeChongqing 404120, P. R. China
| | - Xiaoyu Li
- Department of Pathogenic Biology, Basic Medical College of Chongqing Medical UniversityChongqing 400016, P. R. China
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Ascenzi P, di Masi A, Leboffe L, Frangipani E, Nardini M, Verde C, Visca P. Structural Biology of Bacterial Haemophores. Adv Microb Physiol 2015; 67:127-76. [PMID: 26616517 DOI: 10.1016/bs.ampbs.2015.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Iron plays a key role in a wide range of metabolic and signalling functions representing an essential nutrient for almost all forms of life. However, the ferric form is hardly soluble, whereas the ferrous form is highly toxic. Thus, in biological fluids, most of the iron is sequestered in iron- or haem-binding proteins and the level of free iron is low, making haem and iron acquisition a challenge for pathogenic bacteria during infections. Although toxic to the host, free haem is a major and readily available source of iron for several pathogenic microorganisms. Both Gram-positive and Gram-negative bacteria have developed several strategies to acquire free haem-Fe and protein-bound haem-Fe. Haemophores are a class of secreted and cell surface-exposed proteins promoting free-haem uptake, haem extraction from host haem proteins, and haem presentation to specific outer-membrane receptors that internalize the metal-porphyrins. Here, structural biology of bacterial haemophores is reviewed focusing on haem acquisition, haem internalization, and haem-degrading systems.
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Affiliation(s)
- Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Roma, Italy; Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Napoli, Italy.
| | | | - Loris Leboffe
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
| | | | - Marco Nardini
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy
| | - Cinzia Verde
- Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Napoli, Italy; Dipartimento di Scienze, Università Roma Tre, Roma, Italy
| | - Paolo Visca
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
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Malki I, Simenel C, Wojtowicz H, Cardoso de Amorim G, Prochnicka-Chalufour A, Hoos S, Raynal B, England P, Chaffotte A, Delepierre M, Delepelaire P, Izadi-Pruneyre N. Interaction of a partially disordered antisigma factor with its partner, the signaling domain of the TonB-dependent transporter HasR. PLoS One 2014; 9:e89502. [PMID: 24727671 PMCID: PMC3984077 DOI: 10.1371/journal.pone.0089502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/21/2022] Open
Abstract
Bacteria use diverse signaling pathways to control gene expression in response to external stimuli. In Gram-negative bacteria, the binding of a nutrient is sensed by an outer membrane transporter. This signal is then transmitted to an antisigma factor and subsequently to the cytoplasm where an ECF sigma factor induces expression of genes related to the acquisition of this nutrient. The molecular interactions involved in this transmembrane signaling are poorly understood and structural data on this family of antisigma factor are rare. Here, we present the first structural study of the periplasmic domain of an antisigma factor and its interaction with the transporter. The study concerns the signaling in the heme acquisition system (Has) of Serratia marcescens. Our data support unprecedented partially disordered periplasmic domain of an anti-sigma factor HasS in contact with a membrane-mimicking environment. We solved the 3D structure of the signaling domain of HasR transporter and identified the residues at the HasS-HasR interface. Their conservation in several bacteria suggests wider significance of the proposed model for the understanding of bacterial transmembrane signaling.
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Affiliation(s)
- Idir Malki
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Catherine Simenel
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Halina Wojtowicz
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Gisele Cardoso de Amorim
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Ada Prochnicka-Chalufour
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Sylviane Hoos
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Patrick England
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Alain Chaffotte
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Muriel Delepierre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Philippe Delepelaire
- Institut de Biologie Physico-Chimique, CNRS Université Paris-Diderot UMR 7099, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
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Contreras H, Chim N, Credali A, Goulding CW. Heme uptake in bacterial pathogens. Curr Opin Chem Biol 2014; 19:34-41. [PMID: 24780277 DOI: 10.1016/j.cbpa.2013.12.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 11/30/2022]
Abstract
Iron is an essential nutrient for the survival of organisms. Bacterial pathogens possess specialized pathways to acquire heme from their human hosts. In this review, we present recent structural and biochemical data that provide mechanistic insights into several bacterial heme uptake pathways, encompassing the sequestration of heme from human hemoproteins to secreted or membrane-associated bacterial proteins, the transport of heme across bacterial membranes, and the degradation of heme within the bacterial cytosol to liberate iron. The pathways for heme transport into the bacterial cytosol are divergent, harboring non-homologous protein sequences, novel structures, varying numbers of proteins, and different mechanisms. Congruously, the breakdown of heme within the bacterial cytosol by sequence-divergent proteins releases iron and distinct degradation products.
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Affiliation(s)
- Heidi Contreras
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Nicholas Chim
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Alfredo Credali
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, UCI, Irvine, CA 92697, USA.
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Porcheron G, Garénaux A, Proulx J, Sabri M, Dozois CM. Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence. Front Cell Infect Microbiol 2013; 3:90. [PMID: 24367764 PMCID: PMC3852070 DOI: 10.3389/fcimb.2013.00090] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/18/2013] [Indexed: 02/05/2023] Open
Abstract
For all microorganisms, acquisition of metal ions is essential for survival in the environment or in their infected host. Metal ions are required in many biological processes as components of metalloproteins and serve as cofactors or structural elements for enzymes. However, it is critical for bacteria to ensure that metal uptake and availability is in accordance with physiological needs, as an imbalance in bacterial metal homeostasis is deleterious. Indeed, host defense strategies against infection either consist of metal starvation by sequestration or toxicity by the highly concentrated release of metals. To overcome these host strategies, bacteria employ a variety of metal uptake and export systems and finely regulate metal homeostasis by numerous transcriptional regulators, allowing them to adapt to changing environmental conditions. As a consequence, iron, zinc, manganese, and copper uptake systems significantly contribute to the virulence of many pathogenic bacteria. However, during the course of our experiments on the role of iron and manganese transporters in extraintestinal Escherichia coli (ExPEC) virulence, we observed that depending on the strain tested, the importance of tested systems in virulence may be different. This could be due to the different set of systems present in these strains, but literature also suggests that as each pathogen must adapt to the particular microenvironment of its site of infection, the role of each acquisition system in virulence can differ from a particular strain to another. In this review, we present the systems involved in metal transport by Enterobacteria and the main regulators responsible for their controlled expression. We also discuss the relative role of these systems depending on the pathogen and the tissues they infect.
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Affiliation(s)
- Gaëlle Porcheron
- INRS-Institut Armand Frappier Laval, QC, Canada ; Centre de Recherche en Infectiologie Porcine et Aviaire, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada
| | - Amélie Garénaux
- INRS-Institut Armand Frappier Laval, QC, Canada ; Centre de Recherche en Infectiologie Porcine et Aviaire, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada
| | - Julie Proulx
- INRS-Institut Armand Frappier Laval, QC, Canada ; Centre de Recherche en Infectiologie Porcine et Aviaire, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada
| | - Mourad Sabri
- INRS-Institut Armand Frappier Laval, QC, Canada ; Centre de Recherche en Infectiologie Porcine et Aviaire, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada
| | - Charles M Dozois
- INRS-Institut Armand Frappier Laval, QC, Canada ; Centre de Recherche en Infectiologie Porcine et Aviaire, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada ; Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, QC, Canada
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