DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus

Abstract

Escherichia coli Dps (DNA-binding proteins from starved cells) is the prototype of a DNA-protecting protein family expressed by bacteria under nutritional and oxidative stress. The role of the lysine-rich and highly mobile Dps N-terminus in DNA protection has been investigated by comparing the self-aggregation and DNA-condensation capacity of wild-type Dps and two N-terminal deletion mutants, DpsDelta8 and DpsDelta18, lacking two or all three lysine residues, respectively. Gel mobility and atomic force microscopy imaging showed that at pH 6.3, both wild type and DpsDelta8 self-aggregate, leading to formation of oligomers of variable size, and condense DNA with formation of large Dps-DNA complexes. Conversely, DpsDelta18 does not self-aggregate and binds DNA without causing condensation. At pH 8.2, DpsDelta8 and DpsDelta18 neither self-aggregate nor cause DNA condensation, a behavior also displayed by wild-type Dps at pH 8.7. Thus, Dps self-aggregation and Dps-driven DNA condensation are parallel phenomena that reflect the properties of the N-terminus. DNA protection against the toxic action of Fe(II) and H2O2 is not affected by the N-terminal deletions either in vitro or in vivo, in accordance with the different structural basis of this property.

Substantial DNA damage from submicromolar intracellular hydrogen peroxide detected in Hpx - mutants of Escherichia coli

“…At present, the ability of Dpr to complement dps mutants suggests that iron sequestration is sufficient to protect the DNA under the log-phase conditions of our experiments. A similar result was recently reported for a mutant form of Dps that could not form oligomers but nevertheless could sequester iron and protect DNA from oxidants (45).…”

An archaeal antioxidant: Characterization of a Dps-like protein from Sulfolobus solfataricus

“…For example, extension of the N-terminal E. coli Dps subunit or in the C-terminal extension of the Mycobacterium smegmatis Dps subunit have been implicated in DNA binding (33,36,37). These suggestions have recently been corroborated by N-terminal deletion mutants of E. coli Dps that do not bind DNA (38). Multiple sequence alignments identify basic residues in extended N-terminal domains of both the SsDps and in the Dps-like protein from H. salinarum, suggesting their role in DNA association (35,39,40).…”

Identification and biochemical properties of Dps (starvation‐induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120

“…Similar phenomena has ever been observed from very few Dps homologues (2), notwithstanding they are all denominated for DNA binding features. In E. coli Dps, the family prototype, positive charged lysine-rich N-terminal tail was proposed to tightly correlate with the formation of DNA-Dps complex (21), because the lysine residues could help Dps incorporate negatively charged groups at the surface of DNA molecules by electrostatic interaction. However, N-terminus of Dps1173, which is 4 amino acids shorter than that of E. coli protein, shows the absence of positive charged residues.…”