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 coarsegrained 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. SignificanceUnderstanding how bacteria organize their chromosomes is fundamental to cell biology. Through our coarse-grained molecular dynamics simulations incorporating out-of-equilibrium processes of transcription and translation, we are able to capture the effects of these central dogma processes on DNA organization and demonstrate that these active biological processes expand the nucleoid and facilitate the separation of daughter chromosomes. Our simulations are compared to experimental measurements and highlight the impact of the out-of-equilibrium conditions of the living cell. These findings point out the crucial interplay between physical forces and biological activity in cellular organization, suggesting that cellular structure depends on non-equilibrium processes.