Dynamics of Chromosome Organization During the Cell Cycle of a Minimal Bacterial Cell

The minimal bacterial cell, JCVI-syn3A, is the result of synthetic genome minimization cycles, ending with a 543 kbp genome with 493 genes. Genome-scale gene essentiality and proteomics, along with the essential metabolism of Syn3A were previously determined (Breuer et al., eLife 2019). Whole-cell kinetic models (WCKMs) of Syn3A are being developed by combining a kinetic model of the metabolism with a model of genetic information processing (Thornburg et al., Frontiers in Molecular Biosciences 2019). In previous work, we reconstructed cell geometries of Syn3A, including the ribosome distribution, from cryo-electron tomography and generated ensembles of self-avoiding circular chromosome configurations on a lattice, which were constrained by the cell geometry and ribosomes (Gilbert et al., Frontiers in Molecular Biosciences 2021). Initially, these configurations of the DNA were static within any WCKM simulations and their heterogeneous crowding influenced the diffusion of biological macromolecules, such as RNA polymerases (RNAP) and mRNA, throughout the course of the simulations. A continuum model of Syn3A’s chromosome is now being developed to model the dynamics of the chromosome’s organization over the course of a complete cell cycle, which will include both DNA replication and cell division. Within the continuum model, the DNA is modeled as a stiff homopolymer with a torsional stiffness at a resolution of 10 bp per monomer. A hybrid methodology is being used to couple the spatially-resolved WCKM to a Brownian dynamics simulation of the DNA polymer and ribosomes. This allows for changes in the accessibility of genes to RNAPs, kinetics-based replication to govern the processive motion of replication forks, and segregation of daughter chromosomes during cell division. As was confirmed by 3C-seq, Syn3A lacks systems governing chromosome organization, leaving the fundamental processes common to all bacteria as the sole factors influencing chromosome organization.