Computational study of bacterial chromosome organization by H-NS-mediated cross-linking and molecular crowding

Abstract

Chromosomes are organized by nucleoid-associated proteins within a densely packed cellular environment crowded with freely diffusing macromolecules, often referred to as crowders. Using a coarse-grained computational model, we examine the physical effects of the protein H-NS and molecular crowders on bacterial chromosome organization. In our model, an H-NS dimer with two binding sites cross-links a coarse-grained DNA polymer with a ring topology. Our simulations reveal the complex organizational behavior of the polymer. At low crowder volume fractions (≲0.2), the polymer adopts a heterogeneous organization, with some regions arranged in parallel, while others remain extended—an effect that becomes more pronounced as the polymer backbone stiffens. At higher crowder volume fractions (≳0.2), the polymer adopts a circular organization, with multiple turns of the chain aligned in parallel. This organization correlates with enhanced clustering of H-NS at high crowding levels, facilitated by the parallel alignment of DNA segments. Furthermore, H-NS clustering strengthens with increasing backbone stiffness, suggesting cooperative H-NS binding. We also find that chain stiffness enhances the synergistic action of crowders and H-NS. In contrast, H-NS alone induces a more heterogeneous and irregular chain collapse.