The Dps Protein of Agrobacterium tumefaciens Does Not Bind to DNA but Protects It toward Oxidative Cleavage

Abstract

Agrobacterium tumefaciens Dps (DNA-binding proteins from starved cells), encoded by the dps gene located on the circular chromosome of this plant pathogen, was cloned, and its structural and functional properties were determined in vitro. In Escherichia coli Dps, the family prototype, the DNA binding properties are thought to be associated with the presence of the lysine-containing N-terminal tail that extends from the protein surface into the solvent. The x-ray crystal structure of A. tumefaciens Dps shows that the positively charged N-terminal tail, which is 11 amino acids shorter than in the E. coli protein, is blocked onto the protein surface. This feature accounts for the lack of interaction with DNA. The intersubunit ferroxidase center characteristic of Dps proteins is conserved and confers to the A. tumefaciens protein a ferritin-like activity that manifests itself in the capacity to oxidize and incorporate iron in the internal cavity and to release it after reduction. In turn, sequestration of Fe(II) correlates with the capacity of A. tumefaciens Dps to reduce the production of hydroxyl radicals from H 2 O 2 through Fenton chemistry. These data demonstrate conclusively that DNA protection from oxidative damage in vitro does not require formation of a Dps-DNA complex. In vivo, the hydroxyl radical scavenging activity of A. tumefaciens Dps may be envisaged to act in concert with catalase A to counteract the toxic effect of H 2 O 2 , the major component of the plant defense system when challenged by the bacterium.

A proteomic study of Methylobacterium extorquens reveals a response regulator essential for epiphytic growth

“…Because the detoxification of ROS becomes particularly important under starvation conditions (32), the observed induction of ROS-removing enzymes in M. extorquens AM1 might thus be a reaction to endogenously formed ROS. On the other hand, it is well known that plant cells challenge bacteria by means of an oxidative burst (33) and superoxide dismutase (SOD), and Kat and Dps have been shown to counteract the toxic effects of ROS produced by plants (34,35). All of the stress proteins that we identified appeared to be epiphytic-specific rather than phyllosphere-specific.…”

Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold

“…Additional residues, histidine and tryptophan, provide another coordinated sites to make an iron center. 26,27 Histidine plays a role in the redox process in the iron binding. 27 Based on this concept, the corresponding residues and the possible binding environment were examined in HP0242.…”

Ferritin reactions: Direct identification of the site for the diferric peroxide reaction intermediate

“…Ferritin nanocavities form during the spontaneous assembly of ellipsoidal, polypeptide subunits (1-3), 24 in maxiferritins (Ϸ480 kDa) and 12 in miniferritins (240 kDa), also called DNA protection during starvation proteins. The biological importance of ferritin is emphasized by the lethality of ferritin gene deletion in mammals (4), defects in the CNS from mutations in humans (5), and oxidant sensitivity after deletions of the multiple ferritins in bacteria (6)(7)(8). Reactions of iron and oxygen catalyzed by maxiferritins, in cells of higher plants, animals including humans, and microorganisms, stabilize iron with oxygen at 10 14 times above the K s to match cellular iron concentrations, whereas miniferritins protect DNA by trapping oxidants with iron in the hydrated ferric oxide mineral.…”

“…The location of F ox sites in ferritin has been inferred to be in the center of each active subunit for maxiferritins and at junctions of subunit dimers in miniferritins, based on models of protein cocrystals with Fe 2ϩ analogues such as Mg 2ϩ or Ca 2ϩ (7)(8)(9)(10)(11)(12)(13). Such models are reasonable for the ferrous substrate, but not for ferric intermediates such as the diferric peroxo (DFP) complex or products such as diferric oxo͞hydroxo mineral precursors.…”