Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

Abstract

Two independent, complementary methods of structural analysis were used to elucidate the effect of divalent magnesium and iron cations on the structure of the protective Dps-DNA complex. Small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM) demonstrate that Mg2+ ions block the N-terminals of the Dps protein preventing its interaction with DNA. Non-interacting macromolecules of Dps and DNA remain in the solution in this case. The subsequent addition of the chelating agent (EDTA) leads to a complete restoration of the structure of the complex. Different effect was observed when Fe cations were added to the Dps-DNA complex; the presence of Fe2+ in solution leads to the total complex destruction and aggregation without possibility of the complex restoration with the chelating agent. Here, we discuss these different responses of the Dps-DNA complex on the presence of additional free metal cations, investigating the structure of the Dps protein with and without cations using SAXS and cryo-EM. Additionally, the single particle analysis of Dps with accumulated iron performed by cryo-EM shows localization of iron nanoparticles inside the Dps cavity next to the acidic (hydrophobic) pore, near three glutamate residues.

Cryo-EM reveals the mechanism of DNA compaction byMycobacterium smegmatisDps2

“…MsDps2 is a DNA-binding protein from Mycobacterium smegmatis starved cells, which protects its genome during hostile environmental conditions like starvation, oxidative stress, or antibiotic stress (Roy et al ., 2008, Saraswathi et al ., 2009). The structural insights of DNA binding motifs of Dps protein has been under investigation by many scientific groups (Tereshkin et al ., 2019, Dadinova et al ., 2021, Dubrovin et al ., 2021). Few studies utilized AFM and negative staining TEM to visualize the DNA-Dps complexes.…”

“…Some studies showed that Dps can form a 2D array in the presence of DNA which was imaged using cryoelectron tomography to characterize the 3D structure of the Dps-DNA complex. However, none of these studies could determine the atomic resolution structure of Dps molecules during the interaction with DNA (Tereshkin et al ., 2019, Dadinova et al ., 2021, Dubrovin et al ., 2021). In this study, we applied single particle cryo-EM to determine the high-resolution structures of the MsDps2-DNA complex.…”

“…The role played by the multiplicity of positively charged residues and by the N- or C-terminus mobility in determining the strength and pH dependence of the interaction was evaluated in later studies (Dubrovin et al ., 2021, Kamyshinsky et al ., 2019). Various techniques, namely electrophoretic mobility shift assays and atomic force microscopy, negative staining TEM and cryo-EM tomography, were used to probe the interaction of Dps–DNA (Tereshkin et al ., 2019, Dadinova et al ., 2021, Dubrovin et al ., 2021, Kamyshinsky et al ., 2019).…”

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

“…Two metabolites, d -glucoronate and d -galacturonate, have been shown to provoke the dissociation of Dps dodecamers [ 56 ]. Further, Mg 2+ ions (MgCl 2 ) block the interaction of the Dps N-terminals with DNA, while the addition of Fe 2+ (FeSO 4 ) provokes complex destruction and aggregation as well as the formation of iron-containing clusters in the central cavity next to the acidic pore [ 57 ].…”

Controlled modulation of the dynamics of the Deinococcus grandisDps N‐terminal tails by divalent metals

“…Dps homologues with shorter, neutral, and/or spatially inaccessible N‐ or C‐terminal tails are generally unable to bind and compact DNA (Bozzi et al 1997 ; Papinutto et al 2002 ). The chemical composition of the solvent (namely pH, concentration of NaCl or Mg 2+ ) is a key factor in the regulation of the DNA binding process, that also affects the conformation of the N‐terminal tails (Huergo et al 2013 ; Lee et al 2015 ; Dadinova et al 2021 ; Soshinskaya et al 2020 ).…”