Stationary phase KCl levels trigger changes in Dps conformation to facilitate its partitioning between reversibly-aggregated deposits and Dps-DNA condensates

Abstract

In E. coli populations subjected to starvation, the transition of cells into stationary-phase is characterized by reduced KCl levels, cytoplasmic acidification, and increased production of Dps, the DNA binding protein from starved cells. Here, we show that at KCl concentrations peculiar to the stationary-phase, Dps displays greater surface hydrophobicity, lower helical content, lower stability to denaturation, greater susceptibility to proteolysis, and an intriguing ability to undergo ‘reversible’ deposition into liquid-solid phase separated (LSPS) aggregates, when no DNA is present. Whereas we have already previously shown that, at growth-phase KCl concentrations, Dps either remains soluble or forms liquid-liquid phase separated (LLPS) condensates with DNA, when DNA is present, here we show that the coacervation of Dps with DNA is exacerbated by stationary-phase KCl concentrations. This leads us to suggest the following interesting possibilities: (i) newly-produced Dps is reversibly kinetically-partitioned between LSPS and LLPS states, at low KCl concentrations, depending on the availability of DNA; (ii) excess Dps that is not coacervated with DNA in the LSPS state, exists in the LSPS state at low KCl concentrations; and (iii) Dps in the LSPS state dissolves to become instantaneously available for the packaging of newly-produced DNA, once nutrition becomes available, growth resumes and cytoplasmic KCl concentrations rise, before there is any production of the growth-phase DNA-packaging protein, HU. Importance We demonstrate conformational behaviour with physiological implications involving Dps (DNA binding protein from starved cells). We have earlier shown that the highly-soluble Dps forms liquid-liquid phase separated (LLPS) condensates with DNA, at KCl concentrations peculiar to growth-phase E. coli. Here, we show that at KCl concentrations peculiar to stationary-phase E. coli, Dps undergoes conformational changes to either display heightened LLPS with DNA, or form liquid-solid phase separated (LSPS) aggregates. LSPS aggregates readily dissolve when KCl concentrations are restored to levels peculiar to growth-phase E. coli. We propose, therefore, that a dynamic kinetic partitioning of Dps between LSPS and LLPS states maintains excess (i.e., non-DNA-bound) Dps in the form of deposits that dissolve to support packaging of all newly-produced DNA while cells transition back into growth phase (and KCl levels rise), and while the nucleoid-associated protein (NAP) specific to the growth phase, known as HU, is not yet available.