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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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Guerra JPL, Blanchet CE, Vieira BJC, Waerenborgh JC, Jones NC, Hoffmann SV, Pereira AS, Tavares P. Controlled modulation of the dynamics of the Deinococcus grandis Dps N-terminal tails by divalent metals. Protein Sci 2023; 32:e4567. [PMID: 36658780 PMCID: PMC9885476 DOI: 10.1002/pro.4567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation-induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA-binding properties of most Dps proteins studied so far are related to their unordered, flexible, N- and C-terminal extensions. In a previous work, we revealed that the N-terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high-spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal-binding properties of the wild-type protein with a binding site-impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small-angle X-ray scattering. The N-terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N-terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA-binding properties of Dps proteins through metal binding to their N- and/or C-terminal extensions.
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Affiliation(s)
- João P. L. Guerra
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
| | | | - Bruno J. C. Vieira
- Centro de Ciências e Tecnologias Nucleares, DECN, Instituto Superior TécnicoUniversidade de LisboaBobadela LRSPortugal
| | - João C. Waerenborgh
- Centro de Ciências e Tecnologias Nucleares, DECN, Instituto Superior TécnicoUniversidade de LisboaBobadela LRSPortugal
| | - Nykola C. Jones
- ISA, Department of Physics and AstronomyAarhus UniversityAarhusDenmark
| | | | - Alice S. Pereira
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
| | - Pedro Tavares
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology | FCT NOVAUniversidade NOVA de LisboaCaparicaPortugal
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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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4
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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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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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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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8
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Li X, Mustila H, Magnuson A, Stensjö K. Homologous overexpression of NpDps2 and NpDps5 increases the tolerance for oxidative stress in the multicellular cyanobacterium Nostoc punctiforme. FEMS Microbiol Lett 2019; 365:5071947. [PMID: 30107525 PMCID: PMC6116882 DOI: 10.1093/femsle/fny198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
The filamentous cyanobacterium Nostoc punctiforme has several oxidative stress-managing systems, including Dps proteins. Dps proteins belong to the ferritin superfamily and are involved in abiotic stress management in prokaryotes. Previously, we found that one of the five Dps proteins in N. punctiforme, NpDps2, was critical for H2O2 tolerance. Stress induced by high light intensities is aggravated in N. punctiforme strains deficient of either NpDps2, or the bacterioferritin-like NpDps5. Here, we have investigated the capacity of NpDps2 and NpDps5 to enhance stress tolerance by homologous overexpression of these two proteins in N. punctiforme. Both overexpression strains were found to tolerate twice as high concentrations of added H2O2 as the control strain, indicating that overexpression of either NpDps2 or NpDps5 will enhance the capacity for H2O2 tolerance. Under high light intensities, the overexpression of the two NpDps did not enhance the tolerance against general light-induced stress. However, overexpression of the heterocyst-specific NpDps5 in all cells of the filament led to a higher amount of chlorophyll-binding proteins per cell during diazotrophic growth. The OENpDps5 strain also showed an increased tolerance to ammonium-induced oxidative stress. Our results provide information of how Dps proteins may be utilised for engineering of cyanobacteria with enhanced stress tolerance.
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Affiliation(s)
- Xin Li
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Henna Mustila
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Ann Magnuson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
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9
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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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10
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Structural diffusion properties of two atypical Dps from the cyanobacterium Nostoc punctiforme disclose interactions with ferredoxins and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148063. [PMID: 31419396 DOI: 10.1016/j.bbabio.2019.148063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Ferritin-like proteins, Dps (DNA-binding protein from starved cells), store iron and play a key role in the iron homeostasis in bacteria, yet their iron releasing machinery remains largely unexplored. The electron donor proteins that may interact with Dps and promote the mobilization of the stored iron have hitherto not been identified. Here, we investigate the binding capacity of the two atypical Dps proteins NpDps4 and NpDps5 from Nostoc punctiforme to isolated ferredoxins. We report NpDps-ferredoxin interactions by fluorescence correlation spectroscopy (FCS) and fluorescence resonance energy transfer (FRET) methods. Dynamic light scattering, size exclusion chromatography and native gel electrophoresis results show that NpDps4 forms a dodecamer at both pH 6.0 and pH 8.0, while NpDps5 forms a dodecamer only at pH 6.0. In addition, FCS data clearly reveal that the non-canonical NpDps5 interacts with DNA at pH 6.0. Our spectroscopic analysis shows that [FeS] centers of the three recombinantly expressed and isolated ferredoxins are properly incorporated and are consistent with their respective native states. The results support our hypothesis that ferredoxins could be involved in cellular iron homeostasis by interacting with Dps and assisting the release of stored iron.
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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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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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13
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The two Dps proteins, NpDps2 and NpDps5, are involved in light-induced oxidative stress tolerance in the N 2-fixing cyanobacterium Nostoc punctiforme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1766-1776. [PMID: 27528559 DOI: 10.1016/j.bbabio.2016.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/23/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are considered biotechnologically prominent organisms for production of high-value compounds. Cyanobacteria are subject to high-light intensities, which is a challenge that needs to be addressed in design of efficient bio-engineered photosynthetic organisms. Dps proteins are members of the ferritin superfamily and are omnipresent in prokaryotes. They play a major role in oxidative stress protection and iron homeostasis. The filamentous, heterocyst-forming Nostoc punctiforme, has five Dps proteins. In this study we elucidated the role of these Dps proteins in acclimation to high light intensity, the gene loci organization and the transcriptional regulation of all five dps genes in N. punctiforme was revealed, and dps-deletion mutant strains were used in physiological characterization. Two mutants defective in Dps2 and Dps5 activity displayed a reduced fitness under increased illumination, as well as a differential Photosystem (PS) stoichiometry, with an elevated Photosystem II to Photosystem I ratio in the dps5 deletion strain. This work establishes a Dps-mediated link between light tolerance, H2O2 detoxification, and iron homeostasis, and provides further evidence on the non-redundant role of multiple Dps proteins in this multicellular cyanobacterium.
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Li X, Sandh G, Nenninger A, Muro-Pastor AM, Stensjö K. Differential transcriptional regulation of orthologous dps genes from two closely related heterocyst-forming cyanobacteria. FEMS Microbiol Lett 2015; 362:fnv017. [PMID: 25663155 DOI: 10.1093/femsle/fnv017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In cyanobacteria, DNA-binding proteins from starved cells (Dps) play an important role in the cellular response to oxidative and nutritional stresses. In this study, we have characterized the cell-type specificity and the promoter regions of two orthologous dps genes, Npun_R5799 in Nostoc punctiforme and alr3808 in Anabaena sp. PCC 7120. A transcriptional start site (TSS), identical in location to the previously identified proximal TSS of alr3808, was identified for Npun_R5799 under both combined nitrogen supplemented and N2-fixing growth conditions. However, only alr3808 was also transcribed from a second distal TSS. Sequence homologies suggest that the promoter region containing the distal TSS is not conserved upstream of orthologous genes among heterocyst-forming cyanobacteria. The analysis of promoter GFP-reporter strains showed a different role in governing cell-type specificity between the proximal and distal promoter of alr3808. We here confirmed the heterocyst specificity of the distal promoter of alr3808 and described a very early induction of its expression during proheterocyst differentiation. In contrast, the complete promoters of both genes were active in all cells. Even though Npun_R5799 and alr3808 are orthologs, the regulation of their respective expression differs, indicating distinctions in the function of these cyanobacterial Dps proteins depending on the strain and cell type.
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Affiliation(s)
- Xin Li
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Gustaf Sandh
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Anja Nenninger
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, E-41092 Seville, Spain
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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Ekman M, Sandh G, Nenninger A, Oliveira P, Stensjö K. Cellular and functional specificity among ferritin-like proteins in the multicellular cyanobacterium Nostoc punctiforme. Environ Microbiol 2013; 16:829-44. [PMID: 23992552 DOI: 10.1111/1462-2920.12233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/28/2013] [Indexed: 01/26/2023]
Abstract
Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. In the present paper, we report a multidimensional characterization of these proteins. Our phylogenetic and bioinformatics analyses suggest both structural and physiological differences among the ferritin-like proteins. The expression of these five genes responded differently to hydrogen peroxide treatment, with a significantly higher rise in transcript level for Npun_F3730 as compared with the other four genes. A specific role for Npun_F3730 in the cells tolerance against hydrogen peroxide was also supported by the inactivation of Npun_F3730, Npun_R5701 and Npun_R6212; among these, only the ΔNpun_F3730 strain showed an increased sensitivity to hydrogen peroxide compared with wild type. Analysis of promoter-GFP reporter fusions of the ferritin-like genes indicated that Npun_F3730 and Npun_R5701 were expressed in all cell types of a diazotrophic culture, while Npun_F6212 was expressed specifically in heterocysts. Our study provides the first comprehensive analysis combining functional differentiation and cellular specificity within this important group of proteins in a multicellular cyanobacterium.
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Affiliation(s)
- Martin Ekman
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
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Ardini M, Fiorillo A, Fittipaldi M, Stefanini S, Gatteschi D, Ilari A, Chiancone E. Kineococcus radiotolerans Dps forms a heteronuclear Mn-Fe ferroxidase center that may explain the Mn-dependent protection against oxidative stress. Biochim Biophys Acta Gen Subj 2013; 1830:3745-55. [PMID: 23396000 DOI: 10.1016/j.bbagen.2013.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 01/14/2013] [Accepted: 02/04/2013] [Indexed: 01/30/2023]
Abstract
BACKGROUND The ferroxidase center of DNA-binding protein from starved cells (Dps) is a major player in the iron oxidation/detoxification process that leads to a decreased reactive oxygen species production. The possible Mn(II) participation in this process has been studied in Dps from Kineococcus radiotolerans, a radiation-resistant bacterium with a high cytosolic Mn/Fe ratio and a high capacity to survive ionizing and stress conditions. METHODS The X-ray structure of recombinant K. radiotolerans Dps loaded with Mn(II) has been solved at 2.0Å resolution. Mn(II) binding to K. radiotolerans Dps and its effect on Fe(II) oxidation have been characterized in spectroscopic measurements. RESULTS In K. radiotolerans Dps, the Fe-Fe ferroxidase center can have a Mn-Fe composition. Mn(II) binds only at the high affinity, so-called A site, whereas Fe(II) binds also at the low affinity, so-called B site. The Mn-Fe and Fe-Fe centers behave distinctly upon iron oxidation by O2. A site-bound Mn(II) or Fe(II) plays a catalytic role, while B site-bound Fe(II) behaves like a substrate and can be replaced by another Fe(II) after oxidation. When H2O2 is the Fe(II) oxidant, single electrons are transferred to aromatic residues near the ferroxidase center and give rise to intra-protein radicals thereby limiting OH release in solution. The presence of the Mn-Fe center results in significant differences in the development of such intra-protein radicals. CONCLUSIONS Mn(II) bound at the Dps ferroxidase center A site undergoes redox cycling provided the B site contains Fe. GENERAL SIGNIFICANCE The results provide a likely molecular mechanism for the protective role of Mn(II) under oxidative stress conditions as it participates in redox cycling in the hetero-binuclear ferroxidase center.
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Affiliation(s)
- Matteo Ardini
- Department of Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Italy
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Sato N, Moriyama T, Toyoshima M, Mizusawa M, Tajima N. The all0458/lti46.2 gene encodes a low temperature-induced Dps protein homologue in the cyanobacteria Anabaena sp. PCC 7120 and Anabaena variabilis M3. MICROBIOLOGY-SGM 2012; 158:2527-2536. [PMID: 22837304 DOI: 10.1099/mic.0.060657-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA-binding proteins from starved cells (Dps), which are encoded by many bacterial genomes, protect genomic DNA via non-specific DNA binding, as well as inhibition of free radical formation by chelating Fe(II). In the filamentous cyanobacterium Anabaena, the second gene (lti46.2) in the low temperature-induced gene operon lti46 in strain M3 was found to encode a homologue of Dps, but for a long time this gene remained poorly characterized. A gene cluster, all0459-all0458-all0457, was found later to be 100% identical to the lti46 gene cluster in a closely related strain, PCC 7120. In the present study, we detected ferroxidase activity of the Lti46.2/All0458 protein, which formed a dodecamer, as found in other Dps proteins. In addition, three homologues of all0458 were found in strain PCC 7120, namely, all1173, alr3808 and all4145. We analysed expression of the lti46 or all0459-8-7 gene cluster in both strains, M3 and PCC 7120, and confirmed its induction by low temperature. We found that the All0458-GFP fusion protein and the All1173-GFP fusion protein were localized to the nucleoids. In the all0458 null mutant, the transcript of the alr3808 gene accumulated. These results suggest that there might be complex cooperation of various members of the dps family in protecting the genome from environmental stresses such as changing temperature.
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Affiliation(s)
- Naoki Sato
- JST, CREST, K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Takashi Moriyama
- JST, CREST, K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Masakazu Toyoshima
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Mika Mizusawa
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Naoyuki Tajima
- JST, CREST, K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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Abstract
Dps proteins are the structural relatives of bacterioferritins and ferritins ubiquitously present in the bacterial and archaeal kingdoms. The ball-shaped enzymes play important roles in the detoxification of ROS (reactive oxygen species), in iron scavenging to prevent Fenton reactions and in the mechanical protection of DNA. Detoxification of ROS and iron chaperoning represent the most archetypical functions of dodecameric Dps enzymes. Recent crystallographic studies of these dodecameric complexes have unravelled species-dependent mechanisms of iron uptake into the hollow spheres. Subsequent functions in iron oxidation at ferroxidase centres are highly conserved among bacteria. Final nucleation of iron as iron oxide nanoparticles has been demonstrated to originate at acidic residues located on the inner surface. Some Dps enzymes are also implicated in newly observed catalytic functions related to the formation of molecules playing roles in bacterium–host cell communication. Most recently, Dps complexes are attracting attention in semiconductor science as biomimetic tools for the technical production of the smallest metal-based quantum nanodots used in nanotechnological approaches, such as memory storage or solar cell development.
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Haikarainen T, Thanassoulas A, Stavros P, Nounesis G, Haataja S, Papageorgiou AC. Structural and thermodynamic characterization of metal ion binding in Streptococcus suis Dpr. J Mol Biol 2010; 405:448-60. [PMID: 21056572 DOI: 10.1016/j.jmb.2010.10.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 10/27/2010] [Indexed: 02/04/2023]
Abstract
The use of protein cages for the creation of novel inorganic nanomaterials has attracted considerable attention in recent years. Ferritins are among the most commonly used protein cages in nanoscience. Accordingly, the binding of various metals to ferritins has been studied extensively. Dps (DNA-binding protein from starved cells)-like proteins belong to the ferritin superfamily. In contrast to ferritins, Dps-like proteins form 12-mers instead of 24-mers, have a different ferroxidase center, and are able to store a smaller amount of iron atoms in a hollow cavity (up to ∼500, instead of the ∼4500 iron atoms found in ferritins). With the exception of iron, the binding of other metal cations to Dps proteins has not been studied in detail. Here, the binding of six divalent metal ions (Zn(2+), Mn(2+), Ni(2+), Co(2+), Cu(2+), and Mg(2+)) to Streptococcus suisDps-like peroxide resistance protein (SsDpr) was characterized by X-ray crystallography and isothermal titration calorimetry (ITC). All metal cations, except for Mg(2+), were found to bind to the ferroxidase center similarly to Fe(2+), with moderate affinity (binding constants between 0.1×10(5) M(-1) and 5×10(5) M(-1)). The stoichiometry of binding, as deduced by ITC data, suggested the presence of a dication ferroxidase site. No other metal binding sites were identified in the protein. The results presented here demonstrate the ability of SsDpr to bind various metals as substitutes for iron and will help in better understanding protein-metal interactions in the Dps family of proteins as potential metal nanocontainers.
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Affiliation(s)
- Teemu Haikarainen
- Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521, Finland
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Structural characterization and biological implications of di-zinc binding in the ferroxidase center of Streptococcus pyogenes Dpr. Biochem Biophys Res Commun 2010; 398:361-5. [DOI: 10.1016/j.bbrc.2010.06.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 06/16/2010] [Indexed: 11/17/2022]
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