Preferential localization of the bacterial nucleoid

TL;DR

This study uses simulations to explore why bacterial nucleoids are centrally located, suggesting that compaction and physical interactions, rather than specific tethering mechanisms, drive their preferential positioning.

Contribution

The paper demonstrates through coarse-grained simulations that DNA compaction near the jamming threshold naturally leads to nucleoid localization at cell centers, implying physical interactions are sufficient.

Findings

DNA compaction correlates with nucleoid central localization.

Localization arises from physical interactions near the jamming threshold.

Supports the idea of anchoring or dynamical mechanisms for nucleoid positioning.

Abstract

Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show that such spherical nucleoids are invariably positioned at the center of mononucleoid cells. The present work aims to determine whether such preferential localization results from generic (entropic) interactions between the nucleoid and the cell membrane or instead requires some specific mechanism, like the tethering of DNA at mid-cell or periodic fluctuations of the concentration gradient of given chemical species. To this end, we performed numerical simulations using a coarse-grained model based on the assumption that the formation of the nucleoid results from a segregative phase separation mechanism driven by the de-mixing of the DNA and non-binding globular macromolecules. These simulations show that the abrupt compaction of the DNA coil, which takes place at large crowder density, close to the jamming threshold, is accompanied by the re-localization of the DNA coil close to the regions of the bounding wall with the largest curvature, like the hemispherical caps of rod-like cells, as if the DNA coil were suddenly acquiring the localization properties of a solid sphere. This work therefore supports the hypothesis that the localization of compact nucleoids at regular cell positions involves either some anchoring of the DNA to the cell membrane or some dynamical localization mechanism.