Alladi Ramakrishnan Hall

Bacterial chromosome organization: special crosslinks, confinement effects and molecular crowders play the pivotal roles

Apratim Chatterji

IISER Pune

Using a bead-spring model of bacterial DNA polymers of C. crescentus we show that just 33 effective cross-links at special positions along the chain contour of the DNA of bacteria C. crescentus can lead to the large scale organization of the DNA-polymer with 4.017×10^6 base pairs, where confinement effects play a key role in the organization. The positions of the the 33 cross-links are chosen from the contact map data of C. crescentus. The DNA is modeled as flexible bead-spring ring polymer with 4017 beads, i.e. each bead represents 1000 base pairs.

We further investigate the pivotal role played by the ability of DNA molecule to release topological constraints by chain crossing to get organized at micron length scales. We observe that chain compaction induced by the crowded environment in the bacterial cytoplasm contributes to the organization the bead-spring model of the DNA-polymer. Using Monte-Carlo simulations we show that the release of topological constraints and the crowding environment is necessary for the polymer to obtain a unique organization. We have also compared our results with the organization of a ring polymer with an equal number of cross-links but at random positions along the chain.

These studies are repeated for the chromosome of E.coli and we arrive at similar conclusions. This assures us of the robustness of our findings.