[Paper Review] Topology mediated organization of E.coli chromosome in fast growth conditions

Shreerang Pande, Debarshi Mitra+1 more|arXiv (Cornell University)|Apr 5, 2023

Evolution and Genetic DynamicsBiochemistry, Genetics and Molecular Biology3 citations

TL;DR

The paper proposes that entropy-driven repulsion between topologically modified DNA loops organizes the *E. coli* chromosome in fast-growing conditions, where overlapping cell cycles lead to multi-fork replication. Using Monte Carlo simulations of a bead-spring polymer model in a cylindrical confinement, it reproduces experimentally observed spatial segregation of oriC, dif-ter, and replication forks, demonstrating that entropic forces alone can drive emergent chromosome organization without active motor proteins.

ABSTRACT

Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific polymer topology as it goes through its cell cycle. We establish that the emergent entropic forces between polymer segments of the DNA-polymer with modified topology, leads to chromosome organization as seen in-vivo. We employ computer simulations of a replicating bead spring model of a polymer in a cylinder to investigate the problem. Our simulation of the overlapping cell cycles not only show successful segregation, but also reproduces the evolution of the spatial organization of the chromosomes as observed in experiments. This manuscript in addition to our previous work on slowly growing bacterial cells, shows that our topology-based model can explain the organization of chromosomes in all growth conditions.

Motivation & Objective

• To understand the mechanism behind spatial chromosome organization in fast-growing *E. coli* with overlapping cell cycles and multi-fork replication.
• To test whether entropic forces arising from topological constraints in confined ring polymers can explain observed in vivo chromosome architecture.
• To unify the explanation of chromosome organization across both slow and fast growth conditions using a single polymer physics framework.
• To validate the hypothesis that replication fork dynamics are a consequence of spatial organization rather than its cause.

Proposed method

• A coarse-grained bead-spring model simulates the *E. coli* chromosome as a topologically modified ring polymer confined within a cylindrical cell-like volume.
• Cross-links are introduced at specific loci to emulate linker proteins, creating stable loops that alter the polymer’s topology and entropic interactions.
• Monte Carlo simulations enable local diffusion and relaxation of the polymer, allowing entropic forces to drive self-organization over time.
• The model incorporates overlapping cell cycles with defined C and D periods (55 min and 44 min), matching experimental growth conditions.
• Replication is modeled as a train-track process with two replication forks advancing along the chromosome, while topology and confinement guide spatial segregation.
• Topoisomerase-like actions are simulated by periodically reducing monomer diameters to relieve local topological stress.

Experimental results

Research questions

• RQ1 How does the *E. coli* chromosome achieve spatial organization when multiple rounds of replication occur simultaneously in fast-growing conditions?
• RQ2 Can entropic forces arising from topological constraints in confined ring polymers explain the observed segregation of oriC, dif-ter, and replication forks?
• RQ3 To what extent can a topology-based polymer model reproduce the radial and longitudinal organization seen in live-cell imaging experiments?
• RQ4 Is the spatial organization of the chromosome a cause or a consequence of replication fork positioning?
• RQ5 Can the same physical principles explain chromosome organization in both slow and fast growth conditions?

Key findings

• The model successfully reproduces the spatial segregation of oriC and dif-ter loci along the long axis of the cell, matching experimental observations.
• Introduction of cross-linked loops leads to bimodal radial distributions for certain loci, consistent with in vivo imaging data showing distinct positioning of chromosome arms.
• The simulation shows that replication forks localize at specific positions along the chromosome, emerging from the polymer’s topological architecture rather than being actively directed.
• The presence of smaller subloops within larger loops enhances the separation of chromosome arms along the short axis, mimicking experimental radial organization.
• The model reproduces the evolution of chromosome organization over time, including the dynamic positioning of replication forks during overlapping cell cycles.
• The results support the hypothesis that replication fork dynamics are a consequence of pre-existing spatial organization, not its driver.