BPS2026 – Simulating loop-extrusion-driven chromosome segregation in a minimal bacterial cell

Minimal bacterial cells provide a powerful system for uncovering the essential mechanisms of chromosome organization and segregation. Lacking canonical systems such as Min and ParABS, these organisms rely primarily on structural maintenance of chromosomes (SMC) proteins for partitioning. Here, we present a 4D (3D + time) polymer-based model of the JCVI-syn3A chromosome (543 kbp) that captures replication and partitioning dynamics across the full cell cycle. The model incorporates realistic cell geometries inspired by fluorescence imaging, ribosome distributions from cryo-ET, and polymer physics with energy minimization and equilibration steps. We implement experimentally informed rates for SMC translocation and DNA replication, enabling direct visualization of chromosome dynamics in dividing cell volumes. Our simulations reproduce efficient chromosome partitioning mediated solely by SMC-driven loop extrusion and reveal how segregation depends on parameters such as SMC dwell time and SMC-SMC interactions. Furthermore, we compute contact maps for replicating chromosomes over the entire cell cycle, providing a direct link between simulation and experimental observables. Our results demonstrate that SMC proteins alone are sufficient to drive robust chromosome partitioning in minimal cells and highlight the minimal requirements for bacterial chromosome management and division.