1
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Guerra JPL, Penas D, Tavares P, Pereira AS. Influence of Cupric (Cu 2+) Ions on the Iron Oxidation Mechanism by DNA-Binding Protein from Starved Cells (Dps) from Marinobacter nauticus. Int J Mol Sci 2023; 24:10256. [PMID: 37373403 DOI: 10.3390/ijms241210256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by oxidizing and storing ferrous ions within their cavity, using either hydrogen peroxide or molecular oxygen as the co-substrate, thus reducing the toxic effects of Fenton reactions. Interestingly, the interaction between Dps and transition metals (other than iron) is a known but relatively uncharacterized phenomenon. The impact of non-iron metals on the structure and function of Dps proteins is a current topic of research. This work focuses on the interaction between the Dps from Marinobacter nauticus (a marine facultative anaerobe bacterium capable of degrading petroleum hydrocarbons) and the cupric ion (Cu2+), one of the transition metals of greater biological relevance. Results obtained using electron paramagnetic resonance (EPR), Mössbauer and UV/Visible spectroscopies revealed that Cu2+ ions bind to specific binding sites in Dps, exerting a rate-enhancing effect on the ferroxidation reaction in the presence of molecular oxygen and directly oxidizing ferrous ions when no other co-substrate is present, in a yet uncharacterized redox reaction. This prompts additional research on the catalytic properties of Dps proteins.
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Affiliation(s)
- João P L Guerra
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Daniela Penas
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro Tavares
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alice S Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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2
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Chesnokov Y, Mozhaev A, Kamyshinsky R, Gordienko A, Dadinova L. Structural Insights into Iron Ions Accumulation in Dps Nanocage. Int J Mol Sci 2022; 23:ijms23105313. [PMID: 35628121 PMCID: PMC9140674 DOI: 10.3390/ijms23105313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 02/05/2023] Open
Abstract
Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of ferric ions in its nanocages, thus providing the bacterium with physical and chemical protection. Here, cryo-electron microscopy was used to study the accumulation of iron ions in the nanocage of a Dps protein from Escherichia coli. We demonstrate that Fe2+ concentration in the solution and incubation time have an insignificant effect on the volume and the morphology of iron minerals formed in Dps nanocages. However, an increase in the Fe2+ level leads to an increase in the proportion of larger clusters and the clusters themselves are composed of discrete ~1-1.5 nm subunits.
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Affiliation(s)
- Yury Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Myasnitskaya Str. 20, 101000 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia
| | - Roman Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky Lane 9, 141700 Dolgoprudny, Russia
| | - Alexander Gordienko
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Correspondence: ; Tel.: +7-(499)-135-62-00
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3
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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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4
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Pajarillo EAB, Lee E, Kang DK. Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2021; 7:750-761. [PMID: 34466679 PMCID: PMC8379138 DOI: 10.1016/j.aninu.2021.03.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/27/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Metals such as iron, manganese, copper, and zinc are recognized as essential trace elements. These trace metals play critical roles in development, growth, and metabolism, participating in various metabolic processes by acting as cofactors of enzymes or providing structural support to proteins. Deficiency or toxicity of these metals can impact human and animal health, giving rise to a number of metabolic and neurological disorders. Proper breakdown, absorption, and elimination of these trace metals is a tightly regulated process that requires crosstalk between the host and these micronutrients. The gut is a complex system that serves as the interface between these components, but other factors that contribute to this delicate interaction are not well understood. The gut is home to trillions of microorganisms and microbial genes (the gut microbiome) that can regulate the metabolism and transport of micronutrients and contribute to the bioavailability of trace metals through their assimilation from food sources or by competing with the host. Furthermore, deficiency or toxicity of these metals can modulate the gut microenvironment, including microbiota, nutrient availability, stress, and immunity. Thus, understanding the role of the gut microbiota in the metabolism of manganese, iron, copper, and zinc, as well as in heavy metal deficiencies and toxicities, and vice versa, may provide insight into developing improved or alternative therapeutic strategies to address emerging health concerns. This review describes the current understanding of how the gut microbiome and trace metals interact and affect host health, particularly in pigs.
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Affiliation(s)
- Edward Alain B. Pajarillo
- Department of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee 32307, FL, USA
| | - Eunsook Lee
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
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5
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Ardini M, Bellelli A, Williams DL, Di Leandro L, Giansanti F, Cimini A, Ippoliti R, Angelucci F. Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology. Bioconjug Chem 2021; 32:43-62. [PMID: 33411522 PMCID: PMC8023583 DOI: 10.1021/acs.bioconjchem.0c00621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Morpheeins
are proteins that reversibly assemble into different
oligomers, whose architectures are governed by conformational changes
of the subunits. This property could be utilized in bionanotechnology
where the building of nanometric and new high-ordered structures is
required. By capitalizing on the adaptability of morpheeins to create
patterned structures and exploiting their inborn affinity toward inorganic
and living matter, “bottom-up” creation of nanostructures
could be achieved using a single protein building block, which may
be useful as such or as scaffolds for more complex materials. Peroxiredoxins
represent the paradigm of a morpheein that can be applied to bionanotechnology.
This review describes the structural and functional transitions that
peroxiredoxins undergo to form high-order oligomers, e.g., rings,
tubes, particles, and catenanes, and reports on the chemical and genetic
engineering approaches to employ them in the generation of responsive
nanostructures and nanodevices. The usefulness of the morpheeins’
behavior is emphasized, supporting their use in future applications.
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Affiliation(s)
- Matteo Ardini
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Roma "Sapienza", Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - David L Williams
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Luana Di Leandro
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Francesco Giansanti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Annamaria Cimini
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
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6
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Williams SM, Chatterji D. An Overview of Dps: Dual Acting Nanovehicles in Prokaryotes with DNA Binding and Ferroxidation Properties. Subcell Biochem 2021; 96:177-216. [PMID: 33252729 DOI: 10.1007/978-3-030-58971-4_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA binding proteins under starvation (Dps) are proteins belonging to the ferritin family with the capacity for DNA binding, in addition to iron storage and ferroxidation. Present only in the prokaryotes, these multifaceted proteins have been assigned with a number of roles, from pathogenesis to nucleoid condensation and protection. They have a significant role in protecting the cells from free radical assaults, indirectly by sequestration of iron and by directly binding to the DNA. Due to their symmetry, stability and biomineralization capacity, these proteins have ever increasing potential applications in biotechnology and drug delivery. This chapter tries to bring together all these aspects of Dps in the view of current understanding and older perspectives by studies of our group as well as other experts in the field.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, United Kingdom.
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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7
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A ring-shaped protein clusters gold nanoparticles acting as molecular scaffold for plasmonic surfaces. Biochim Biophys Acta Gen Subj 2020; 1864:129617. [DOI: 10.1016/j.bbagen.2020.129617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 12/18/2022]
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8
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Minato T, Teramoto T, Kakuta Y, Ogo S, Yoon KS. Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites. FEBS Open Bio 2020; 10:1219-1229. [PMID: 32170832 PMCID: PMC7327923 DOI: 10.1002/2211-5463.12837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The DNA‐binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.
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Affiliation(s)
- Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.,Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, Fukuoka, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan.,Center for Small Molecule Energy, Kyushu University, Fukuoka, Japan
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan.,Center for Small Molecule Energy, Kyushu University, Fukuoka, Japan
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9
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Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Högbom M, Shafaat HS. Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. J Am Chem Soc 2020; 142:5338-5354. [PMID: 32062969 DOI: 10.1021/jacs.0c00333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater MnII affinity than FeII affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
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Affiliation(s)
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, SE-171 21 Solna, Sweden
| | | | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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10
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Zeth K, Sancho-Vaello E, Okuda M. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps. Inorg Chem 2019; 58:11351-11363. [PMID: 31433627 DOI: 10.1021/acs.inorgchem.9b00301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron storage in biology is carried out by cage-shaped proteins of the ferritin superfamily, one of which is the dodecameric protein Dps. In Dps, four distinct steps lead to the formation of metal nanoparticles: attraction of ion-aquo complexes to the protein matrix, passage of these complexes through translocation pores, oxidation of these complexes at ferroxidase centers, and, ultimately, nanoparticle formation. In this study, we investigated Dps from Listeria innocua to structurally characterize these steps for Co2+, Zn2+, and La3+ ions. The structures reveal that differences in their ion coordination chemistry determine alternative metal ion-binding sites on the areas of the surface surrounding the translocation pore that captures nine La3+, three Co2+, or three Zn2+ ions as aquo clusters and passes them on for translocation. Inside these pores, ion-selective conformational changes at key residues occur before a gating residue to actively move ions through the constriction zone. Ions upstream of the Asp130 gate residue are typically hydrated, while ions downstream directly interact with the protein matrix. Inside the cavity, ions move along negatively charged residues to the ferroxidase center, where seven main residues adapt to the three different ions by dynamically changing their conformations. In total, we observed more than 20 metal-binding sites per Dps monomer, which clearly highlights the metal-binding capacity of this protein family. Collectively, our results provide a detailed structural description of the preparative steps for amino acid-assisted biomineralization in Dps proteins, demonstrating unexpected protein matrix plasticity.
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Affiliation(s)
- Kornelius Zeth
- Roskilde University , Department of Science and Environment , Universitetsvej 1 , 4000 Roskilde , Denmark.,Universidad del Pais Vasco (UPV/EHU) , 48940 Leioa , Basque Country , Spain
| | - Enea Sancho-Vaello
- Unidad de Biofisica, Consejo Superior de Investigaciones Científicas , Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU) , Barrio Sarriena s/n, Leioa , 48940 Leioa , Basque Country , Spain
| | - Mitsuhiro Okuda
- Unidad de Biofisica, Consejo Superior de Investigaciones Científicas , Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU) , Barrio Sarriena s/n, Leioa , 48940 Leioa , Basque Country , Spain.,CIC nanoGUNE , 20018 Donostia-San Sebastian , Basque Country , Spain.,IKERBASQUE , Basque Foundation for Science , 48011 Bilbao , Basque Country , Spain
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11
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Howe C, Moparthi VK, Ho FM, Persson K, Stensjö K. The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria. PLoS One 2019; 14:e0218300. [PMID: 31369577 PMCID: PMC6675082 DOI: 10.1371/journal.pone.0218300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 11/18/2022] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) have been found to detoxify H2O2. At their catalytic centers, the ferroxidase center (FOC), Dps proteins utilize Fe2+ to reduce H2O2 and therefore play an essential role in the protection against oxidative stress and maintaining iron homeostasis. Whereas most bacteria accommodate one or two Dps, there are five different Dps proteins in Nostoc punctiforme, a phototrophic and filamentous cyanobacterium. This uncommonly high number of Dps proteins implies a sophisticated machinery for maintaining complex iron homeostasis and for protection against oxidative stress. Functional analyses and structural information on cyanobacterial Dps proteins are rare, but essential for understanding the function of each of the NpDps proteins. In this study, we present the crystal structure of NpDps4 in its metal-free, iron- and zinc-bound forms. The FOC coordinates either two iron atoms or one zinc atom. Spectroscopic analyses revealed that NpDps4 could oxidize Fe2+ utilizing O2, but no evidence for its use of the oxidant H2O2 could be found. We identified Zn2+ to be an effective inhibitor of the O2-mediated Fe2+ oxidation in NpDps4. NpDps4 exhibits a FOC that is very different from canonical Dps, but structurally similar to the atypical one from DpsA of Thermosynechococcus elongatus. Sequence comparisons among Dps protein homologs to NpDps4 within the cyanobacterial phylum led us to classify a novel FOC class: the His-type FOC. The features of this special FOC have not been identified in Dps proteins from other bacterial phyla and it might be unique to cyanobacterial Dps proteins.
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Affiliation(s)
- Christoph Howe
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Vamsi K. Moparthi
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Felix M. Ho
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karina Persson
- Department of Chemistry, Umeå University, Umeå, Sweden
- * E-mail: (KS); (KP)
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail: (KS); (KP)
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12
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Shuryak I. Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2019; 196:50-63. [PMID: 30388428 DOI: 10.1016/j.jenvrad.2018.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, 630 West 168(th) street, VC-11-234/5, New York, NY, 10032, USA.
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13
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Howe C, Ho F, Nenninger A, Raleiras P, Stensjö K. Differential biochemical properties of three canonical Dps proteins from the cyanobacterium Nostoc punctiforme suggest distinct cellular functions. J Biol Chem 2018; 293:16635-16646. [PMID: 30171072 DOI: 10.1074/jbc.ra118.002425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/29/2018] [Indexed: 11/06/2022] Open
Abstract
DNA-binding proteins from starved cells (Dps, EC: 1.16.3.1) have a variety of different biochemical activities such as DNA-binding, iron sequestration, and H2O2 detoxification. Most bacteria commonly feature one or two Dps enzymes, whereas the cyanobacterium Nostoc punctiforme displays an unusually high number of five Dps proteins (NpDps1-5). Our previous studies have indicated physiological differences, as well as cell-specific expression, among these five proteins. Three of the five NpDps proteins, NpDps1, -2, and -3, were classified as canonical Dps proteins. To further investigate their properties and possible importance for physiological function, here we characterized and compared them in vitro Nondenaturing PAGE, gel filtration, and dynamic light-scattering experiments disclosed that the three NpDps proteins exist as multimeric protein species in the bacterial cell. We also demonstrate Dps-mediated iron oxidation catalysis in the presence of H2O2 However, no iron oxidation with O2 as the electron acceptor was detected under our experimental conditions. In modeled structures of NpDps1, -2, and -3, protein channels were identified that could serve as the entrance for ferrous iron into the dodecameric structures. Furthermore, we could demonstrate pH-dependent DNA-binding properties for NpDps2 and -3. This study adds critical insights into the functions and stabilities of the three canonical Dps proteins from N. punctiforme and suggests that each of the Dps proteins within this bacterium has a specific biochemical property and function.
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Affiliation(s)
- Christoph Howe
- From the Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Felix Ho
- From the Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Anja Nenninger
- From the Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Patrícia Raleiras
- From the Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Karin Stensjö
- From the Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
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14
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Ardini M, Howes BD, Fiorillo A, Falvo E, Sottini S, Rovai D, Lantieri M, Ilari A, Gatteschi D, Spina G, Chiancone E, Stefanini S, Fittipaldi M. Study of manganese binding to the ferroxidase centre of human H-type ferritin. J Inorg Biochem 2018; 182:103-112. [PMID: 29454149 DOI: 10.1016/j.jinorgbio.2018.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/11/2018] [Accepted: 02/04/2018] [Indexed: 01/15/2023]
Abstract
Ferritins are ubiquitous and conserved proteins endowed with enzymatic ferroxidase activity, that oxidize Fe(II) ions at the dimetal ferroxidase centre to form a mineralized Fe(III) oxide core deposited within the apo-protein shell. Herein, the in vitro formation of a heterodimetal cofactor constituted by Fe and Mn ions has been investigated in human H ferritin (hHFt). Namely, Mn and Fe binding at the hHFt ferroxidase centre and its effects on Fe(II) oxidation have been investigated by UV-Vis ferroxidation kinetics, fluorimetric titrations, multifrequency EPR, and preliminary Mössbauer spectroscopy. Our results show that in hHFt, both Fe(II) and Mn(II) bind the ferroxidase centre forming a Fe-Mn cofactor. Moreover, molecular oxygen seems to favour Mn(II) binding and increases the ferroxidation activity of the Mn-loaded protein. The data suggest that Mn influences the Fe binding and the efficiency of the ferroxidation reaction. The higher efficiency of the Mn-Fe heterometallic centre may have a physiological relevance in specific cell types (i.e. glia cells), where the concentration of Mn is the same order of magnitude as iron.
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Affiliation(s)
- Matteo Ardini
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Barry D Howes
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Elisabetta Falvo
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Silvia Sottini
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Donella Rovai
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Lantieri
- ISC-CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Dante Gatteschi
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Gabriele Spina
- INSTM, Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Emilia Chiancone
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Simonetta Stefanini
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.
| | - Maria Fittipaldi
- INSTM, Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Florence, Italy.
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15
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Huta BP, Miller NH, Robertson EL, Doyle RP. Metal-citrate complex transport in Kineococcus radiotolerans. J Basic Microbiol 2017; 58:209-216. [PMID: 29226973 DOI: 10.1002/jobm.201700427] [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: 08/07/2017] [Revised: 10/23/2017] [Accepted: 11/19/2017] [Indexed: 11/07/2022]
Abstract
The growth of an organism is highly dependent on the acquisition of carbon and metals, and availability of these nutrients in the environment affects its survival. Organisms can obtain both nutrients simultaneously through proteins of the CitMHS superfamily. Bioinformatic studies suggested a CitMHS gene (Accession number ABS03965.1) in Kineococcus radiotolerans. Radio flux assays following 14-C radiolabelled citrate, either free or complexed to a variety of metal ions, in K. radiotolerans demonstrated internalization of the citrate when bound to select metal ions only, primarily in the form of calcium-citrate. A pH response was also observed, consistent with a permease (ATP independent) mechanism as noted for other CitMHS family members, with greater uptake at pH 7 compared to pH 10. These results confirm the ability of K. radiotolerans to transport complexed citrate.
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Affiliation(s)
- Brian P Huta
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | - Nigel H Miller
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Robert P Doyle
- Department of Chemistry, Syracuse University, Syracuse, New York, USA.,Department of Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
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16
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Peana M, Medici S, Pangburn HA, Lamkin TJ, Ostrowska M, Gumienna-Kontecka E, Zoroddu MA. Manganese binding to antioxidant peptides involved in extreme radiation resistance in Deinococcus radiodurans. J Inorg Biochem 2016; 164:49-58. [DOI: 10.1016/j.jinorgbio.2016.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 12/13/2022]
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17
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Arnold AR, Zhou A, Barton JK. Characterization of the DNA-Mediated Oxidation of Dps, A Bacterial Ferritin. J Am Chem Soc 2016; 138:11290-8. [PMID: 27571139 DOI: 10.1021/jacs.6b06507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dps proteins are bacterial ferritins that protect DNA from oxidative stress and have been implicated in bacterial survival and virulence. In addition to direct oxidation of the Dps iron sites by diffusing oxidants, oxidation from a distance via DNA charge transport (CT), where electrons and electron holes are rapidly transported through the base-pair π-stack, could represent an efficient DNA protection mechanism utilized by Dps. Here, we spectroscopically characterize the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation using an intercalating ruthenium photooxidant and the flash-quench technique. Upon irradiation with poly(dGdC)2, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)2 is substituted with poly(dAdT)2, the yield of Dps oxidation is decreased significantly, consistent with guanine radical intermediates facilitating Dps oxidation. We have also explored possible protein electron transfer (ET) intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the iron-binding ferroxidase site (W52 in E. coli Dps). In EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, a W52A Dps mutant was significantly deficient compared to WT Dps in forming the characteristic EPR signal at g = 4.3, consistent with W52 acting as an ET hopping intermediate. This effect is mirrored in vivo in E. coli survival in response to hydrogen peroxide, where mutation of W52 leads to decreased survival under oxidative stress.
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Affiliation(s)
- Anna R Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Andy Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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18
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Sanchuki HBS, Valdameri G, Moure VR, Rodriguez JA, Pedrosa FO, Souza EM, Korolik V, Ribeiro RR, Huergo LF. Conserved histidine residues at the ferroxidase centre of the Campylobacter jejuni Dps protein are not strictly required for metal binding and oxidation. MICROBIOLOGY-SGM 2015; 162:156-163. [PMID: 26555736 DOI: 10.1099/mic.0.000210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Iron is an essential micronutrient for living organisms as it is involved in a broad variety of important biological processes. However, free iron inside the cell could be potentially toxic, generating hydroxyl radicals through the Fenton reaction. Dps (DNA-binding protein from starved cells) belongs to a subfamily of ferritins and can store iron atoms inside the dodecamer. The presence of a ferroxidase centre, composed of highly conserved residues, is a signature of this protein family. In this study, we analysed the role of two conserved histidine residues (H25 and H37) located at the ferroxidase centre of the Campylobacter jejuni Dps protein by replacing them with glycine residues. The C. jejuni H25G/H37G substituted variant showed reduced iron binding and ferroxidase activities in comparison with wt Dps, while DNA-binding activity remained unaffected. We also found that both CjDps wt and CjDps H25G/H37G were able to bind manganese atoms. These results indicate that the H25 and H37 residues at the ferroxidase centre of C. jejuni Dps are not strictly required for metal binding and oxidation.
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Affiliation(s)
- Heloisa B S Sanchuki
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Glaucio Valdameri
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Vivian R Moure
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Jorge A Rodriguez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Guadalajara, Mexico
| | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | | | - Luciano F Huergo
- Setor Litoral, UFPR, Matinhos, PR, Brazil.,Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
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19
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Santos SP, Mitchell EP, Franquelim HG, Castanho MARB, Abreu IA, Romão CV. Dps fromDeinococcus radiodurans: oligomeric forms of Dps1 with distinct cellular functions and Dps2 involved in metal storage. FEBS J 2015; 282:4307-27. [DOI: 10.1111/febs.13420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/30/2015] [Accepted: 08/14/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sandra P. Santos
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | | | - Henri G. Franquelim
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Portugal
| | | | - Isabel A. Abreu
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- 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
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20
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Juttukonda LJ, Skaar EP. Manganese homeostasis and utilization in pathogenic bacteria. Mol Microbiol 2015; 97:216-28. [PMID: 25898914 DOI: 10.1111/mmi.13034] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2015] [Indexed: 01/08/2023]
Abstract
Manganese (Mn) is a required cofactor for all forms of life. Given the importance of Mn to bacteria, the host has devised strategies to sequester Mn from invaders. In the macrophage phagosome, NRAMP1 removes Mn and other essential metals to starve intracellular pathogens; in the extracellular space, calprotectin chelates Mn and Zn. Calprotectin-mediated Mn sequestration is a newly appreciated host defense mechanism, and recent findings are highlighted herein. In order to acquire Mn when extracellular concentrations are low, bacteria have evolved efficient Mn acquisition systems that are under elegant transcriptional control. To counteract Mn overload, some bacteria possess Mn-specific export systems that are important in vivo, presumably for control of intracellular Mn levels. Mn transporters, their transcriptional regulators and some Mn-requiring enzymes are necessary for virulence of certain bacterial pathogens, as revealed by animal models of infection. Furthermore, Mn is an important facet of the cellular response to oxidative stress, a host antibacterial strategy. The battle for Mn between host and pathogen is now appreciated to be a major determinant of the outcome of infection. In this MicroReview, the contribution of Mn to the host-pathogen interaction is reviewed, and key questions are proposed for future study.
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Affiliation(s)
- Lillian J Juttukonda
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
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21
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22
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Lisher JP, Giedroc DP. Manganese acquisition and homeostasis at the host-pathogen interface. Front Cell Infect Microbiol 2013; 3:91. [PMID: 24367765 PMCID: PMC3851752 DOI: 10.3389/fcimb.2013.00091] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/18/2013] [Indexed: 11/21/2022] Open
Abstract
Pathogenic bacteria acquire transition metals for cell viability and persistence of infection in competition with host nutritional defenses. The human host employs a variety of mechanisms to stress the invading pathogen with both cytotoxic metal ions and oxidative and nitrosative insults while withholding essential transition metals from the bacterium. For example, the S100 family protein calprotectin (CP) found in neutrophils is a calcium-activated chelator of extracellular Mn and Zn and is found in tissue abscesses at sites of infection by Staphylococcus aureus. In an adaptive response, bacteria have evolved systems to acquire the metals in the face of this competition while effluxing excess or toxic metals to maintain a bioavailability of transition metals that is consistent with a particular inorganic "fingerprint" under the prevailing conditions. This review highlights recent biological, chemical and structural studies focused on manganese (Mn) acquisition and homeostasis and connects this process to oxidative stress resistance and iron (Fe) availability that operates at the human host-pathogen interface.
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Affiliation(s)
- John P. Lisher
- Graduate Program in Biochemistry, Indiana UniversityBloomington, IN, USA
| | - David P. Giedroc
- Graduate Program in Biochemistry, Indiana UniversityBloomington, IN, USA
- Department of Chemistry, Indiana UniversityBloomington, IN, USA
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