Modeling the Effects of HU Proteomic Interactions in the Genome Configuration of a Minimal Cell

The genetic material inside cells is encoded in DNA molecules, which contain the necessary information to produce proteins and other key molecules. Currently, new models have been developed from a physico-chemical perspective where the dynamics of cell constituents is governed by physical and thermodynamic forces. To this end, small-genome cells, such as the synthetic JCVI-Syn3A minimal cell, which only contains 452 protein-coding genes, provides a good framework to investigate the physics underlying key cellular processes. To properly characterize the kinetics of such processes, it is important to study the physical organization of the genome. In this work, we investigate the effect of the HU proteomic interactions on chromosomal configuration. To model the circular bacterial chromosome, we develop a mesoscale bead-spring model where medium-sized gene blocks are represented by coarse-grained beads. The physical-chemical properties of specific beads depend on the genome sequence of JCVI-Syn3A. The presence of HU proteins affects the chromosomal distribution, including coiling and the compactification of the genetic material, leading to nucleoid formation, which can potentially affect transcription kinetics and gene expression.