The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions

Abstract

The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr’s salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed.

Green Synthesis of Co-Zn Spinel Ferrite Nanoparticles: Magnetic and Intrinsic Antimicrobial Properties

“…Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides. It was shown by X-ray absorption near edge structure (XANES) and Mössbauer spectroscopy presence of both trivalent and divalent iron ions in the Dps protein [40,41]. Thus, if iron-based MNPs penetrate the cell, then they should affect the metabolic processes involving Dps.…”

“…Although the importance of the magnetic structure of spinel MNPs is well investigated in catalysis [38,39], there is a lack of information about its influence on biological activity. Thus, all samples have been investigated using wild-type bacterial Escherichia coli (E.coli) K-12 MG1655 [40,41].…”

Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle

“…Each subunit contains 167 amino acids and has a molecular weight of 18.7 kDa [ 50 ]. Purified E. coli Dps molecules have been shown to self-aggregate in solution and upon addition of DNA, Dps dodecamers undergo extensive aggregation to rapidly form multi-layered plate-like crystals [ 51 ]. Co-crystallization of DNA and Dps is a defense strategy as DNA sequestration is a highly efficient means of protection against an array of environmental assaults.…”

“…Co-crystallization of DNA and Dps is a defense strategy as DNA sequestration is a highly efficient means of protection against an array of environmental assaults. Iron ions stabilize the dodecameric form of Dps [ 51 , 52 ]. In E. coli , the N-terminal tails with positively charged lysine residues are responsible for interaction with DNA, self-aggregation and DNA condensation.…”

Dps protein localization studies in nanostructured silicon matrix by scanning electron microscopy

“…Белковая часть включает 12 одинаковых субъединиц со структурой гомо-додекамера [5,6]. Молекулы белка Dps способны осуществлять накопление (депонирование) неорганических наночастиц системы железо-кислород [7] внутри полой части диаметром до 5 нм [7,8]. Таким образом, ферритин Dps является потенциальным контейнером природного происхождения, который может служить для накопления, хранения и адресной доставки наноматериалов.…”