Bacterial chromosome organization: few special cross-links, cell confinement, and molecular crowders play the pivotal roles.

Using a coarse-grained bead-spring model of bacterial chromosomes of C. crescentus and E. coli we show that just 33 and 38 effective cross-links in 4017 and 4642 monomer chain at special positions along the chain contour can lead to the large length-scale organization of the DNA polymer, where confinement effects of the cell walls play a crucial role in the organization. The positions of the 33/38 cross-links along the chain contour are chosen from the Hi-C contact map of bacteria C. crescentus and E. coli. We represent 1000 base pairs as a coarse-grained monomer in our bead-spring flexible ring polymer model of the DNA. Thus 4017/4642 beads on a flexible ring polymer represent the C. crescentus/ E. coli DNA polymer with ~4 million base pairs. Choosing suitable parameters from our preceding study, we also incorporate the role of molecular crowders and the ability of the chain to release topological constraints. We also validate our prediction of the organization of the bacterial chromosomes with available experimental data.
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