Effects of central dogma processes on the compaction and segregation of bacterial nucleoids

The bacterial cytoplasm is characterized by a distinctive membrane-less organelle, the nucleoid, which harbors chromosomal DNA. We investigate the effects of dynamic processes associated with transcription and translation on the structure of this organelle, using coarse-grained molecular dynamics (MD) simulations implemented with out-of-equilibrium reactions. Our model captures the scale of the entire cell and incorporates a reaction-diffusion system for ribosomes and polyribosomes, combining their out-of-equilibrium dynamics with excluded volume interactions with DNA. Our findings demonstrate that out-of-equilibrium reactions increase the size of the nucleoid. In addition, we show that the nucleoid size increase is proportional to transcriptional activity. Our model reproduces the time-dependent change in nucleoid size observed in rifampicin treatment experiments, where the pool of polyribosomes is depleted. Furthermore, we find these active processes are essential for complete sister chromosome separation and correct nucleoid positioning within the cell. Overall, our study reveals the effects of the central dogma processes on the internal organization and localization of bacterial nucleoids.