Bacterial nucleoid: Interplay of DNA demixing and supercoiling

TL;DR

This study uses a computational model to explore how DNA demixing and supercoiling interact to influence bacterial DNA compaction, revealing different regimes and thresholds affecting DNA structure.

Contribution

The paper introduces a coarse-grained simulation model to analyze the combined effects of DNA demixing and supercoiling on bacterial nucleoid organization.

Findings

DNA demixing and supercoiling effects can add up to DNA compaction under certain conditions.

Beyond moderate supercoiling, the DNA coil's radius may stop decreasing or increase.

The DNA coil may become non-spherical near the jamming threshold due to energetic trade-offs.

Abstract

This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this paper, we investigate the interplay of these two mechanisms, with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime where the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold, as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.