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The mechanism responsible for the compaction of the genomic DNA of bacteriainside a structure called the nucleoid is a longstanding but still livelydebated question. Most puzzling is the fact that the nucleoid occupies only asmall fraction of the cell, although it is not separated from the rest of thecytoplasm by any membrane and would occupy a volume about thousand times largeroutside from the cell. Here, by performing numerical simulations withcoarse-grained models, we elaborate on the conjecture that the formation of thenucleoid may result from a segregative phase separation mechanism driven by thedemixing of the DNA coil and non-binding globular macromolecules present in thecytoplasm, presumably functional ribosomes. Simulations performed with crowdershaving spherical, dumbbell or octahedral geometry highlight the sensitivedependence of the level of DNA compaction on the dissymmetry of DNA/DNA,DNA/crowder, and crowder/crowder repulsive interactions, thereby supporting thesegregative phase separation scenario. Simulations also consistently predictmuch stronger DNA compaction close to the jamming threshold. Moreover,simulations performed with crowders of different sizes suggest that the finaldensity distribution of each species results from the competition betweenthermodynamic forces and steric hindrance, so that bigger crowders are expelledselectively from the nucleoid only at moderate total crowder concentrations.This work leads to several predictions, which may eventually be testedexperimentally.

Segregative phase separation scenario of the formation of the bacterial nucleoid