Out-of-equilibrium control of the internal organization of bacteria

Caption: Left and center: Cartoon of an E. coli cell and its transcriptional-translational machinery. Blue coils of radius Rn represent mRNAs, the red coil of length L denotes the DNA, and ribosomes are shown in black. Right: Schematic of the components underlying the reaction-diffusion model, where the DNA plectoneme is represented by a set of disjoint cylinders, and polysomes and free ribosomes by spheres.

Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is condensed into a compact body---the nucleoid. We develop models that consider steric interactions among the components of the Escherichia coli transcriptional-translational machinery and out-of-equilibrium effects of mRNA transcription, translation, and degradation, in order to explain the observed features of the nucleoid.

We show that steric effects 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 is due to the out-of-equilibrium process of mRNA synthesis and degradation.