Investigating the correlated dynamics of ribosomes and chromosomes in Escherichia coli

Segregation of chromosomal DNA is essential but a poorly understood process in prokaryotic cells. It has been proposed that two newly replicated DNA strands in a cylindrically confined volume segregate due to entropic force. Alternatively, it has also been proposed that a reaction-diffusion system involving ribosomal dynamics drives nucleoids apart. This study aims to test these ideas in Escherichia coli bacteria. We employed high throughput fluorescence microscopy in microfluidic devices, quantitative image analysis, and polymer physics-based modeling to understand how the segregation process unfolds during the DNA replication cycle and understand the role ribosomes play in this process. Our results show that nucleoid occupied volume in the cell is smaller by a fixed constant volume than the cell volume, irrespective of whether the replication is ongoing or not. We find that a broadly distributed ribosomal distribution peaks at midcell at the early stages of the replication cycle, as expected by a reaction-diffusion system involving ribosomes. However, unlike the model prediction, the midcell accumulation of ribosomes does not lead to the formation of distinct nucleoid lobes in the early stages of replication. Instead, we find that the density of chromosomal DNA starts to decrease at midcell/mid nucleoid when about 60% replication is complete. Our results experimentally confirm the importance of ribosomal dynamics in driving two daughter chromosomes apart. However, the existing model requires improvement to account for their limited effect in the early replication cycle.