The genomic DNA of bacteria occupies only a fraction of the cell called the
nucleoid, although it is not bounded by any membrane and would occupy a volume
hundreds of times larger than the cell in the absence of constraints. The two
most important contributions to the compaction of the DNA coil are the
cross-linking of the DNA by nucleoid proteins (like H-NS and StpA) and the
demixing of DNA and other abundant globular macromolecules which do not bind to
the DNA (like ribosomes). The present work deals with the interplay of
DNA-bridging proteins and globular macromolecular crowders, with the goal of
determining the extent to which they collaborate in organizing the nucleoid. In
order to answer this question, a coarse-grained model was developed and its
properties were investigated through Brownian dynamics simulations. These
simulations reveal that the radius of gyration of the DNA coil decreases
linearly with the effective volume ratio of globular crowders and the number of
DNA bridges formed by nucleoid proteins in the whole range of physiological
values. Moreover, simulations highlight the fact that the number of DNA bridges
formed by nucleoid proteins depends crucially on their ability to
self-associate (oligomerize). An explanation for this result is proposed in
terms of the mean distance between DNA segments and the capacity of proteins to
maintain DNA--bridging in spite of the thermal fluctuations of the DNA network.
Finally, simulations indicate that non-associating proteins preserve a high
mobility inside the nucleoid while contributing to its compaction, leading to a
DNA/protein complex which looks like a liquid droplet. In contrast,
self-associating proteins form a little deformable network which cross-links
the DNA chain, with the consequence that the DNA/protein complex looks more
like a gel