On the Spatial Positioning of Ribosomes around chromosome inE. coliCytoplasm

Abstract

AbstractThe spatial organization of ribosomes in the cytoplasm of Escherichia coli (E. coli) bacteria has been a subject of longstanding intrigue. Previous investigations suggested that ribosomes remain completely excluded from the chromosome-rich nucleoid region in a “poor solvent” like cytoplasm. Here, we present an integrated model of the bacterial cytoplasm, informed by experimental data, which updates this prevailing narrative. We demonstrate that ribosomes maintain a delicate balance of both attractive and repulsive interactions with the chromosome, contrary to the conventional notion of it acting as an inert crowder in cytoplasm. The multi-dimensional spatial distribution of free ribosomes (30S and 50S) and bound ribosomes (70S polysome) inside the cytoplasm reveals that the extent of mutual ribosome-chromosome segregation is relatively less pronounced due to the presence of non-negligible amount of ribosomes within the inner core of the cytoplasm. In particular, we identify a central void within the inner-most core of the nucleoid that lacks chromosomal DNA but can accommodate finite proportion of both free (11 %) and bound (18 %) ribosomes. Furthermore, our analysis of the chromosome mesh size and the conformation of bound ribosomes suggests that bound ribosomes remain elongated and would be able to navigate past the chromosome mesh to access the central void. Together by highlighting the dynamic nature of ribosome localization in E. coli, this investigation proposes that this segregation is crucial for maximizing the utilization of synthesized mRNA and facilitating efficient translation into proteins, which are essential for bacterial survival.