The DPS protein compacts the eubacterial chromosome during stress
When an E. coli cell enters into stationary phase, transcription and cell division cease completely. In such cells, the normal chromatin components, such as those described above, are replaced by a negatively charged protein called DPS. The interaction between DPS and DNA appears to be a specialised bacterial adaptation to survive starvation. In normal conditions of growth, the DNA within the bacterial cell is distributed evenly throughout the entire cytoplasm. In stationary cells, however, the DNA undergoes a dramatic change in its properties. Rather than being distributed evenly, it becomes localised as a tightly packaged, almost crystal-like structure associated with the DPS protein. This DNA, when examined in vitro, is protected from both enzymatic digestion by DNAases and from oxidative damage by hydrogen peroxide.
What is apparently contradictory in the interaction between the negatively charged DPS protein and DNA?
As discussed earlier, DNA carries a negatively charged backbone and yet it interacts with the negatively charged DPS protein.
The transition to this highly protected and condensed state is believed to be signalled by a reduction in the environmental concentration of divalent cations (e.g. Mg2+), which the bacterium uses as an indicator of the availability of nutrients. At a critical cation concentration, the remaining cations within the cell are thought to form cationic bridges between the DPS protein and the DNA helix. Importantly, no energy expenditure is required to form or maintain the DPS–cation–DNA complex within the cell. In times of decreased nutrient availability and limited energy supply, the purely chemical nature of this transition provides obvious advantages. This DNA structure persists until environmental conditions alter, leading to reversal of the tight packaging.
Similar strategies are adopted in other organisms, including plant seeds and spores, in which the cell cannot use energy-dependent repair processes to protect its genetic material. Under extreme conditions, such tight protein–DNA interactions serve to protect genomic DNA from damage.