On the Spatial Positioning of Ribosomes around chromosome in E. coli Cytoplasm

The organization of the E. coli chromosome is a topic of ongoing research, encompassing the effects of nucleoid-associated proteins, supercoiling, and the surrounding cytoplasmic environment. Ribosomes, being highly abundant in the cytoplasm, have been observed to be excluded from the nucleoid, functioning as macromolecular crowders and creating an environment that hinders chromosome function. Previous modeling studies have predominantly treated ribosomes as passive crowders within the nucleoid. In this study, we present a refined model that incorporates multiple experimental data to investigate the three-dimensional distribution of ribosomes in vivo, surpassing the assumption of their inertness. Our findings unveil the existence of a central void within the nucleoid, which is populated by ribosomes. Through our model, we determine the size of the chromosome mesh and analyze the characteristic conformation of bound ribosomes. Our results demonstrate that bound ribosomes can navigate the chromosome mesh via a worm-like motion, allowing them to reach the central void. Furthermore, we quantitatively illustrate the differential exclusion of free and bound ribosomes from the nucleoid using three-dimensional density analysis. Lastly, we propose that this segregation is crucial for maximizing the utilization of synthesized mRNA and facilitating efficient translation into proteins, which are essential for bacterial survival. ### Competing Interest Statement The authors have declared no competing interest.