DNA-polymer architecture orchestrates the segregation and spatio-temporal organization of E. coli chromosomes during replication in slow growth

TL;DR

This study uses polymer physics and simulations to reveal how DNA architecture influences chromosome segregation and organization in E. coli during slow growth, aligning with experimental observations.

Contribution

It demonstrates that specific DNA-polymer topology and entropic forces drive chromosome segregation and organization, supported by simulation results matching experimental data.

Findings

Polymer architecture enhances segregation dynamics.

Chromosomal loci localize along the cell axis during segregation.

Contact maps reproduce experimental Hi-C macro-domains.

Abstract

The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder, we use Monte carlo simulations to show that the segregation dynamics is spontaneously enhanced by the adoption of a certain DNA-polymer architecture as replication progresses. Secondly, the chosen polymer-topology ensures its self-organization along the cell axis while segregation is in progress, such that various chromosomal loci get spatially localized. The time evolution of loci positions quantitatively match the corresponding experimentally reported results, including observation of the cohesion time and the ter-transition. Additionally, the contact map generated using our bead-spring model reproduces the four macro-domains of the experimental Hi-C maps. Lastly, the proposed mechanism reproduces the observed universal dynamics as the sister loci separate during segregation. It was already hypothesized and expected that SMC proteins, e.g. MukBEF contribute over and above entropic repulsion between bacterial-DNA ring-polymers to aid the segregation of daughter DNAs in the E.coli cell cycle. We propose that cross-links (plausibly induced by SMC proteins) at crucial positions along the contour is enough to provide sufficient forces for segregation within reasonable time scales. A mapping between Monte Carlo diffusive dynamics time scales and real time units helps us use experimentally relevant numbers for our modeling.