  Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is
typically condensed into a compact body - the nucleoid. This compaction
influences the localization and dynamics of many cellular processes including
transcription, translation, and cell division. Here, we develop a model that
takes into account steric interactions among the components of the Escherichia
coli transcriptional-translational machinery (TTM) and out-of-equilibrium
effects of mRNA transcription, translation, and degradation, in order to
explain many observed features of the nucleoid. We show that steric effects,
due to the different molecular shapes of the TTM components, are sufficient to
drive equilibrium phase separation of the DNA, explaining the formation and
size of the nucleoid. In addition, we show that the observed positioning of the
nucleoid at midcell is due to the out-of-equilibrium process of messenger RNA
(mRNA) synthesis and degradation: mRNAs apply a pressure on both sides of the
nucleoid, localizing it to midcell. We demonstrate that, as the cell grows, the
production of these mRNAs is responsible for the nucleoid splitting into two
lobes, and for their well-known positioning to 1/4 and 3/4 positions on the
long cell axis. Finally, our model quantitatively accounts for the observed
expansion of the nucleoid when the pool of cytoplasmic mRNAs is depleted.
Overall, our study suggests that steric interactions and out-of-equilibrium
effects of the TTM are key drivers of the internal spatial organization of
bacterial cells.
