1
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Rivera M. Mobilization of iron stored in bacterioferritin, a new target for perturbing iron homeostasis and developing antibacterial and antibiofilm molecules. J Inorg Biochem 2023; 247:112306. [PMID: 37451083 DOI: 10.1016/j.jinorgbio.2023.112306] [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] [Received: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Antibiotic resistance is a global public health threat. The care of chronic infections is complicated by bacterial biofilms. Biofilm embedded cells can be up to 1000-fold more tolerant to antibiotic treatment than planktonic cells. Antibiotic tolerance is a condition which does not involve mutation and enables bacteria to survive in the presence of antibiotics. The antibiotic tolerance of biofilm-cells often renders antibiotics ineffective, even against strains that do not carry resistance-impairing mutations. This review discusses bacterial iron homeostasis and the strategies being developed to target this bacterial vulnerability, with emphasis on a recently proposed approach which aims at targeting the iron storage protein bacterioferritin (Bfr) and its physiological partner, the ferredoxin Bfd. Bfr regulates cytosolic iron concentrations by oxidizing Fe2+ and storing Fe3+ in its internal cavity, and by forming a complex with Bfd to reduce Fe3+ in the internal cavity and release Fe2+ to the cytosol. Blocking the Bfr-Bfd complex in P. aeruginosa cells causes an irreversible accumulation of Fe3+ in BfrB and simultaneous cytosolic iron depletion, which leads to impaired biofilm maintenance and biofilm cell death. Recently discovered small molecule inhibitors of the Bfr-Bfd complex, which bind Bfr at the Bfd binding site, inhibit iron mobilization, and elicit biofilm cell death.
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Affiliation(s)
- Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA.
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2
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Jobichen C, Ying Chong T, Rattinam R, Basak S, Srinivasan M, Choong YK, Pandey KP, Ngoc TB, Shi J, Angayarkanni J, Sivaraman J. Bacterioferritin nanocage structures uncover the biomineralization process in ferritins. PNAS NEXUS 2023; 2:pgad235. [PMID: 37529551 PMCID: PMC10388152 DOI: 10.1093/pnasnexus/pgad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023]
Abstract
Iron is an essential element involved in various metabolic processes. The ferritin family of proteins forms nanocage assembly and is involved in iron oxidation, storage, and mineralization. Although several structures of human ferritins and bacterioferritins have been solved, there is still no complete structure that shows both the trapped Fe-biomineral cluster and the nanocage. Furthermore, whereas the mechanism of iron trafficking has been explained using various approaches, structural details on the biomineralization process (i.e. the formation of the mineral itself) are generally lacking. Here, we report the cryo-electron microscopy (cryo-EM) structures of apoform and biomineral bound form (holoforms) of the Streptomyces coelicolor bacterioferritin (ScBfr) nanocage and the subunit crystal structure. The holoforms show different stages of Fe-biomineral accumulation inside the nanocage, in which the connections exist in two of the fourfold channels of the nanocage between the C-terminal of the ScBfr monomers and the Fe-biomineral cluster. The mutation and truncation of the bacterioferritin residues involved in these connections significantly reduced the iron and phosphate binding in comparison with those of the wild type and together explain the underlying mechanism. Collectively, our results represent a prototype for the bacterioferritin nanocage, which reveals insight into its biomineralization and the potential channel for bacterioferritin-associated iron trafficking.
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Affiliation(s)
| | - Tan Ying Chong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rajesh Rattinam
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yeu Khai Choong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Kannu Priya Pandey
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Tran Bich Ngoc
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jian Shi
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jayaraman Angayarkanni
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
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3
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Wang J, Wang Q, Tang YJ, Fu HM, Fang F, Guo JS, Yan P, Chen YP. Unraveling the structure and function of bacterioferritin in Candidatus Kuenenia stuttgartiensis: Iron storage sites maintain cellular iron homeostasis. WATER RESEARCH 2023; 238:120016. [PMID: 37146397 DOI: 10.1016/j.watres.2023.120016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 04/03/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Anammox bacteria rely heavily on iron and have many iron storage sites. However, the biological significance of these iron storage sites has not been clearly defined. In this study, we explored the properties and location of iron storage sites to better understand their cellular function. To do this, the Candidatus Kuenenia stuttgartiensis iron storage protein, bacterioferritin (K.S Bfr), was successfully expressed and purified. In vitro, correctly assembled globulins were observed by transmission electron microscopy. The self-assembled K.S Bfr has active redox and can bind Fe2+ and mineralize it in the protein cavity. In vivo, engineered bacteria with K.S Bfr showed good adaptability to Fe2+, with a survival rate of 78.9% when exposed to 5 mM Fe2+, compared with only 66.0% for wild-type bacteria lacking K.S Bfr. A potential iron regulatory strategy similar to that of Anammox was identified in transcriptomic analysis of engineered bacteria. This system may be controlled by the iron uptake regulator Furto transport Fe2+ via FeoB and store excess Fe2+ in K.S Bfr to maintain cellular homeostasis. K.S Bfr has superior iron storage capacity both intracellularly and in vitro. The discovery of K.S Bfr reveals the storage location of iron-rich nanoparticles, increases our understanding of the adaptability of iron-dependent bacteria to Fe2+, and suggests possible iron regulation strategies in Anammox bacteria.
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Affiliation(s)
- Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Yu-Jiao Tang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
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4
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Bacterioferritin nanocage: Structure, biological function, catalytic mechanism, self-assembly and potential applications. Biotechnol Adv 2022; 61:108057. [DOI: 10.1016/j.biotechadv.2022.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022]
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5
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Mohanty A, Parida A, Raut RK, Behera RK. Ferritin: A Promising Nanoreactor and Nanocarrier for Bionanotechnology. ACS BIO & MED CHEM AU 2022; 2:258-281. [PMID: 37101573 PMCID: PMC10114856 DOI: 10.1021/acsbiomedchemau.2c00003] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The essence of bionanotechnology lies in the application of nanotechnology/nanomaterials to solve the biological problems. Quantum dots and nanoparticles hold potential biomedical applications, but their inherent problems such as low solubility and associated toxicity due to their interactions at nonspecific target sites is a major concern. The self-assembled, thermostable, ferritin protein nanocages possessing natural iron scavenging ability have emerged as a potential solution to all the above-mentioned problems by acting as nanoreactor and nanocarrier. Ferritins, the cellular iron repositories, are hollow, spherical, symmetric multimeric protein nanocages, which sequester the excess of free Fe(II) and synthesize iron biominerals (Fe2O3·H2O) inside their ∼5-8 nm central cavity. The electrostatics and dynamics of the pore residues not only drives the natural substrate Fe2+ inside ferritin nanocages but also uptakes a set of other metals ions/counterions during in vitro synthesis of nanomaterial. The current review aims to report the recent developments/understanding on ferritin structure (self-assembly, surface/pores electrostatics, metal ion binding sites) and chemistry occurring inside these supramolecular protein cages (protein mediated metal ion uptake and mineralization/nanoparticle formation) along with its surface modification to exploit them for various nanobiotechnological applications. Furthermore, a better understanding of ferritin self-assembly would be highly useful for optimizing the incorporation of nanomaterials via the disassembly/reassembly approach. Several studies have reported the successful engineering of these ferritin protein nanocages in order to utilize them as potential nanoreactor for synthesizing/incorporating nanoparticles and as nanocarrier for delivering imaging agents/drugs at cell specific target sites. Therefore, the combination of nanoscience (nanomaterials) and bioscience (ferritin protein) projects several benefits for various applications ranging from electronics to medicine.
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6
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Gijsbers A, Zhang Y, Gao Y, Peters PJ, Ravelli RBG. Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development. Acta Crystallogr D Struct Biol 2021; 77:1077-1083. [PMID: 34342280 PMCID: PMC8329864 DOI: 10.1107/s2059798321007233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022] Open
Abstract
The use of cryo-EM continues to expand worldwide and calls for good-quality standard proteins with simple protocols for their production. Here, a straightforward expression and purification protocol is presented that provides an apoferritin, bacterioferritin B (BfrB), from Mycobacterium tuberculosis with high yield and purity. A 2.12 Å resolution cryo-EM structure of BfrB is reported, showing the typical cage-like oligomer constituting of 24 monomers related by 432 symmetry. However, it also contains a unique C-terminal extension (164-181), which loops into the cage region of the shell and provides extra stability to the protein. Part of this region was ambiguous in previous crystal structures but could be built within the cryo-EM map. These findings and this protocol could serve the growing cryo-EM community in characterizing and pushing the limits of their electron microscopes and workflows.
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Affiliation(s)
- Abril Gijsbers
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Yue Zhang
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Ye Gao
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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7
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Silva LSO, Matias PM, Romão CV, Saraiva LM. Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis. Front Microbiol 2021; 12:670681. [PMID: 33995335 PMCID: PMC8117158 DOI: 10.3389/fmicb.2021.670681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.
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Affiliation(s)
- Liliana S O Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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8
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Le Vay K, Carter BM, Watkins DW, Dora Tang TY, Ting VP, Cölfen H, Rambo RP, Smith AJ, Ross Anderson JL, Perriman AW. Controlling Protein Nanocage Assembly with Hydrostatic Pressure. J Am Chem Soc 2020; 142:20640-20650. [PMID: 33252237 DOI: 10.1021/jacs.0c07285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.
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Affiliation(s)
- Kristian Le Vay
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K
| | - Ben M Carter
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - T-Y Dora Tang
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Valeska P Ting
- Bristol Composites Institute (ACCIS), Department of Mechanical Engineering, University of Bristol, Queen's Building, Bristol BS8 1TR, U.K
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Robert P Rambo
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
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9
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Maity B, Hishikawa Y, Lu D, Ueno T. Recent progresses in the accumulation of metal ions into the apo-ferritin cage: Experimental and theoretical perspectives. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.03.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Punchi Hewage AND, Yao H, Nammalwar B, Gnanasekaran KK, Lovell S, Bunce RA, Eshelman K, Phaniraj SM, Lee MM, Peterson BR, Battaile KP, Reitz AB, Rivera M. Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J Am Chem Soc 2019; 141:8171-8184. [PMID: 31038945 PMCID: PMC6535718 DOI: 10.1021/jacs.9b00394] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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The iron storage
protein bacterioferritin (BfrB) is central to
bacterial iron homeostasis. The mobilization of iron from BfrB, which
requires binding by a cognate ferredoxin (Bfd), is essential to the
regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small
molecule inhibitors of the BfrB–Bfd protein–protein
interaction. The process was initiated by screening a fragment library
and followed by obtaining the structure of a fragment hit bound to
BfrB. The structural insights were used to develop a series of 4-(benzylamino)-
and 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively
bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent
growth phenotype. Further investigation determined that the analogs
elicit a pyoverdin hyperproduction phenotype that is consistent with
blockade of the BfrB–Bfd interaction and ensuing irreversible
accumulation of iron in BfrB, with concomitant depletion of iron in
the cytosol. The irreversible accumulation of iron in BfrB prompted
by the 4-substituted isoindoline analogs was confirmed by visualization
of BfrB-iron in P. aeruginosa cell lysates separated
on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial
fluoroquinolone and our isoindoline analogs results in significantly
lower cell survival relative to treatment with either antibiotic or
analog alone. Collectively, these findings furnish proof of concept
for the usefulness of small molecule probes designed to dysregulate
bacterial iron homeostasis by targeting a protein–protein interaction
pivotal for iron storage in the bacterial cell.
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Affiliation(s)
- Achala N D Punchi Hewage
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Baskar Nammalwar
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | | | - Scott Lovell
- Protein Structure Laboratory , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Richard A Bunce
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Kate Eshelman
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Sahishna M Phaniraj
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Molly M Lee
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Blake R Peterson
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc. , 3805 Old Easton Road , Doylestown , Pennsylvania 18902 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
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Eshelman K, Yao H, Punchi Hewage AND, Deay JJ, Chandler JR, Rivera M. Inhibiting the BfrB:Bfd interaction in Pseudomonas aeruginosa causes irreversible iron accumulation in bacterioferritin and iron deficiency in the bacterial cytosol. Metallomics 2018; 9:646-659. [PMID: 28318006 DOI: 10.1039/c7mt00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Iron is an essential nutrient for bacteria but the reactivity of Fe2+ and the insolubility of Fe3+ present significant challenges to bacterial cells. Iron storage proteins contribute to ameliorating these challenges by oxidizing Fe2+ using O2 and H2O2 as electron acceptors, and by compartmentalizing Fe3+. Two types of iron-storage proteins coexist in bacteria, the ferritins (Ftn) and the heme-containing bacterioferritins (Bfr), but the reasons for their coexistence are largely unknown. P. aeruginosa cells harbor two iron storage proteins (FtnA and BfrB), but nothing is known about their relative contributions to iron homeostasis. Prior studies in vitro have shown that iron mobilization from BfrB requires specific interactions with a ferredoxin (Bfd), but the relevance of the BfrB:Bfd interaction to iron homeostasis in P. aeruginosa is unknown. In this work we explore the repercussions of (i) deleting the bfrB gene, and (ii) perturbing the BfrB:Bfd interaction in P. aeruginosa cells by either deleting the bfd gene or by replacing the wild type bfrB gene with a L68A/E81A double mutant allele in the P. aeruginosa chromosome. The effects of the mutations were evaluated by following the accumulation of iron in BfrB, analyzing levels of free and total intracellular iron, and by characterizing the ensuing iron homeostasis dysregulation phenotypes. The results reveal that P. aeruginosa accumulates iron mainly in BfrB, and that the nutrient does not accumulate in FtnA to detectable levels, even after deletion of the bfrB gene. Perturbing the BfrB:Bfd interaction causes irreversible flow of iron into BfrB, which leads to the accumulation of unusable intracellular iron while severely depleting the levels of free intracellular iron, which drives the cells to an acute iron starvation response despite harboring "normal" levels of total intracellular iron. These results are discussed in the context of a dynamic equilibrium between free cytosolic Fe2+ and Fe3+ compartmentalized in BfrB, which functions as a buffer to oppose rapid changes of free cytosolic iron. Finally, we also show that P. aeruginosa cells utilize iron stored in BfrB for growth in iron-limiting conditions, and that the utilization of BfrB-iron requires a functional BfrB:Bfd interaction.
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Affiliation(s)
- Kate Eshelman
- Department of Chemistry and R. N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Multidisciplinary Research Building, 2030 Becker Dr, Lawrence, KS 66047, USA.
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12
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Sala D, Ciambellotti S, Giachetti A, Turano P, Rosato A. Investigation of the Iron(II) Release Mechanism of Human H-Ferritin as a Function of pH. J Chem Inf Model 2017; 57:2112-2118. [DOI: 10.1021/acs.jcim.7b00306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Davide Sala
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Silvia Ciambellotti
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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13
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Rivera M. Bacterioferritin: Structure, Dynamics, and Protein-Protein Interactions at Play in Iron Storage and Mobilization. Acc Chem Res 2017; 50:331-340. [PMID: 28177216 PMCID: PMC5358871 DOI: 10.1021/acs.accounts.6b00514] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite its essentiality to life, iron presents significant challenges to cells: the exceedingly low solubility of Fe3+ limits its bioavailability, and the reactivity of Fe2+ toward H2O2 is a source of the toxic hydroxyl radical (HO•). Consequently, cellular levels of free iron are highly regulated to ensure sufficiency while preventing iron-induced toxicity. Relatively little is known about the fate of iron in the bacterial cytosol or how cells balance the need for relatively high cytosolic iron concentrations with the potential toxicity of the nutrient. Iron storage proteins are integral to iron metabolism, and bacteria utilize two types of ferritin-like molecules to store iron, bacterial ferritin (Ftn) and bacterioferritin (Bfr). Ftn and Bfr compartmentalize iron at concentrations far above the solubility of Fe3+ and protect the reducing cell environment from unwanted Fe3+/Fe2+ redox cycling. This Account focuses on our laboratory's efforts to study iron storage proteins in the model bacterium Pseudomonas aeruginosa, an opportunistic pathogen. Prior to our studies, it was thought that P. aeruginosa cells relied on a single Bfr assembled from two distinct subunits coded by the bfrA and bfrB genes. It is now known that, like in most bacteria, two iron storage proteins coexist in P. aeruginosa cells, a bacterial Ftn (FtnA), coded by the ftnA (formerly bfrA) gene and a bacterioferritin (BfrB), coded by the bfrB gene. Studies with BfrB showed that Fe2+ oxidation occurs at ferroxidase centers (FCs), followed by gated translocation of Fe3+ to the interior cavity, a process that is, surprisingly, distinct from that observed with the extensively studied Bfr from Escherichia coli, where the FCs are stable and function only as a catalytic site for O2 reduction. Investigations with BfrB showed that the oxidation of Fe2+ at FCs and the internalization of Fe3+ depend on long-range cooperative motions, extending from 4-fold pores, via B-pores, into FCs. It remains to be seen whether similar studies with E. coli Bfr will reveal distinct cooperative motions contributing to the stability of its FCs. Mobilization of Fe3+ stored in BfrB requires interaction with a ferredoxin (Bfd), which transfers electrons to reduce Fe3+ in the internal cavity of BfrB for subsequent release of Fe2+. The structure of the BfrB/Bfd complex furnished the only known structure of a ferritin molecule in complex with a physiological protein partner. The BfrB/Bfd complex is stabilized by hot-spot residues in both proteins, which interweave into a highly complementary hot region. The hot-spot residues are conserved in the sequences of Bfr and Bfd proteins from a number of bacteria, indicating that the BfrB/Bfd interaction is of widespread significance in bacterial iron metabolism. The BfrB/Bfd structure also furnished the only known structure of a Bfd, which revealed a novel helix-turn-helix fold different from the β-strand and α-helix fold of plant and vertebrate [2Fe-2S]-ferredoxins. Bfds seem to be unique to bacteria; consequently, although mobilization of iron from eukaryotic ferritins may also be facilitated by protein-protein interactions, the nature of the protein that delivers electrons to the ferric core of eukaryotic ferritins remains unknown.
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Affiliation(s)
- Mario Rivera
- Department of Chemistry and Ralph N. Adams
Institute for Bioanalytical Chemistry, University of Kansas, 2030 Becker
Dr., Lawrence, Kansas 66047, United States
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Iron response regulator protein IrrB in Magnetospirillum gryphiswaldense MSR-1 helps control the iron/oxygen balance, oxidative stress tolerance, and magnetosome formation. Appl Environ Microbiol 2015; 81:8044-53. [PMID: 26386052 DOI: 10.1128/aem.02585-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Abstract
Magnetotactic bacteria are capable of forming nanosized, membrane-enclosed magnetosomes under iron-rich and oxygen-limited conditions. The complete genomic sequence of Magnetospirillum gryphiswaldense strain MSR-1 has been analyzed and found to contain five fur homologue genes whose protein products are predicted to be involved in iron homeostasis and the response to oxidative stress. Of these, only the MGMSRv2_3149 gene (irrB) was significantly downregulated under high-iron and low-oxygen conditions, during the transition of cell growth from the logarithmic to the stationary phase. The encoded protein, IrrB, containing the conserved HHH motif, was identified as an iron response regulator (Irr) protein belonging to the Fur superfamily. To investigate the function of IrrB, we constructed an irrB deletion mutant (ΔirrB). The levels of cell growth and magnetosome formation were lower in the ΔirrB strain than in the wild type (WT) under both high-iron and low-iron conditions. The ΔirrB strain also showed lower levels of iron uptake and H2O2 tolerance than the WT. Quantitative real-time reverse transcription-PCR analysis indicated that the irrB mutation reduced the expression of numerous genes involved in iron transport, iron storage, heme biosynthesis, and Fe-S cluster assembly. Transcription studies of the other fur homologue genes in the ΔirrB strain indicated complementary functions of the Fur proteins in MSR-1. IrrB appears to be directly responsible for iron metabolism and homeostasis and to be indirectly involved in magnetosome formation. We propose two IrrB-regulated networks (under high- and low-iron conditions) in MSR-1 cells that control the balance of iron and oxygen metabolism and account for the coexistence of five Fur homologues.
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15
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Mixotrophic growth of Pseudomonas sp. C27 at different C/N ratios: Quantitative proteomic analysis. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2015.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cunrath O, Geoffroy VA, Schalk IJ. Metallome of Pseudomonas aeruginosa: a role for siderophores. Environ Microbiol 2015; 18:3258-3267. [PMID: 26147433 DOI: 10.1111/1462-2920.12971] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/17/2015] [Accepted: 06/26/2015] [Indexed: 11/29/2022]
Abstract
In this paper, we describe the total metal composition (metallome) of Pseudomonas aeruginosa. Inductively coupled plasma atomic emission spectroscopy analyses showed that P. aeruginosa cells concentrate each metal of the metallome from the extracellular media with different efficiencies. Growth in nutrient-restricted media did not substantially affect the overall profile of the metallome; however, the uptake of some metals was strongly stimulated, showing the high potential of some metal acquisition pathways to adapt to changing growth conditions. We also investigated the role of the two major siderophores produced by P. aeruginosa, pyoverdine and pyochelin, in iron uptake and more generally in metallome homeostasis. In addition to their role in iron acquisition, siderophore production also significantly prevented the accumulation of toxic metals in P. aeruginosa cells, thus preserving the equilibrium of the metallome in a polluted environment.
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Affiliation(s)
- Olivier Cunrath
- Université de Strasbourg, ESBS, Blvd Sébastien Brant, Illkirch, F-67413, France.,CNRS, UMR7242, Blvd Sébastien Brant, Illkirch, F-67413, France
| | - Valérie A Geoffroy
- Université de Strasbourg, ESBS, Blvd Sébastien Brant, Illkirch, F-67413, France.,CNRS, UMR7242, Blvd Sébastien Brant, Illkirch, F-67413, France
| | - Isabelle J Schalk
- Université de Strasbourg, ESBS, Blvd Sébastien Brant, Illkirch, F-67413, France. .,CNRS, UMR7242, Blvd Sébastien Brant, Illkirch, F-67413, France.
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Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry 2015; 54:1611-27. [PMID: 25640193 DOI: 10.1021/bi501255r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, ‡Del Shankel Structural Biology Center, and §Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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Honarmand Ebrahimi K, Hagedoorn PL, Hagen WR. Unity in the Biochemistry of the Iron-Storage Proteins Ferritin and Bacterioferritin. Chem Rev 2014; 115:295-326. [DOI: 10.1021/cr5004908] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kourosh Honarmand Ebrahimi
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
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Ruvinsky AM, Vakser IA, Rivera M. Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins. J Chem Phys 2014; 140:115104. [PMID: 24655206 DOI: 10.1063/1.4868229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ferritin-like molecules show a remarkable combination of the evolutionary conserved activity of iron uptake and release that engage different pores in the conserved ferritin shell. It was hypothesized that pore selection and iron traffic depend on dynamic allostery with no conformational changes in the backbone. In this study, we detect the allosteric networks in Pseudomonas aeruginosa bacterioferritin (BfrB), bacterial ferritin (FtnA), and bullfrog M and L ferritins (Ftns) by a network-weaving algorithm (NWA) that passes threads of an allosteric network through highly correlated residues using hierarchical clustering. The residue-residue correlations are calculated in the packing-on elastic network model that introduces atom packing into the common packing-off model. Applying NWA revealed that each of the molecules has an extended allosteric network mostly buried inside the ferritin shell. The structure of the networks is consistent with experimental observations of iron transport: The allosteric networks in BfrB and FtnA connect the ferroxidase center with the 4-fold pores and B-pores, leaving the 3-fold pores unengaged. In contrast, the allosteric network directly links the 3-fold pores with the 4-fold pores in M and L Ftns. The majority of the network residues are either on the inner surface or buried inside the subunit fold or at the subunit interfaces. We hypothesize that the ferritin structures evolved in a way to limit the influence of functionally unrelated events in the cytoplasm on the allosteric network to maintain stability of the translocation mechanisms. We showed that the residue-residue correlations and the resultant long-range cooperativity depend on the ferritin shell packing, which, in turn, depends on protein sequence composition. Switching from the packing-on to the packing-off model reduces correlations by 35%-38% so that no allosteric network can be found. The influence of the side-chain packing on the allosteric networks explains the diversity in mechanisms of iron traffic suggested by experimental approaches.
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Affiliation(s)
- Anatoly M Ruvinsky
- Infection Innovative Medicine, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Ilya A Vakser
- Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Mario Rivera
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
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