Synergistic role of DNA-binding protein and macromolecular crowding on DNA condensation. An experimental and theoretical approach

Abstract

Genome packaging in prokaryotic cells is believed to be carried out by a combination of DNA-binding proteins, crowding effects, and DNA supercoiling. Much is known about DNA–protein interaction as well as the condensation of DNA due to excluded volume effects however, and to our knowledge, few studies have targeted the potential synergistic role of DNA-binding proteins and crowding agents on DNA condensation.This work aims at assessing the effect of crowding, induced by polyethylene glycol (PEG), on DNA–H-NS binding, with H-NS a histone-like nucleoid structuring protein that is believed to play a crucial role in gene regulation.A non-monotonic behavior was found upon the addition of PEG to DNA–H-NS complexes; 100mgmL−1 of PEG leads to the expansion of the DNA, while 200mgmL−1 of PEG to a stronger DNA condensation, when compared to complexes in the absence of PEG. Such behavior was found at intermediate concentrations of H-NS. Spermine (Spm) was additionally studied, to assess the importance of the specificity of the DNA-binding agent. The synergistic effect of Spm and PEG on DNA condensation was very clear and especially large for the higher studied concentration of PEG. The effect of ionic strength was additionally looked upon. Two regimes were found; at low Spm concentrations, DNA ψ-condensation dominates and systems with higher ionic strength show a larger DNA condensation. At large Spm concentrations, on the other hand, a larger ionic strength leads to a more moderate DNA condensation. Synergism effects were found to be larger at low DNA–Spm concentrations and high ionic strengths.Results from Monte Carlo simulations, using a very simple model to mimic the experimental studies, also indicate a synergistic effect of the DNA-binding and crowding agents on DNA condensation for intermediate concentrations of the DNA-binding agents. Since H-NS proteins are known to self-assemble in the presence of DNA, an attractive potential was also used in the protein model. It was found that such self-association is needed to induce DNA condensation and that strong synergism occurred solely for intermediate attractive potentials. It is suggested that crowding agents act to reduce the critical association concentration of the proteins.