Role of Molecular Crowding in Compacting Escherichia coli Nucleoid

Abstract

The physical conformation of bacterial nucleoids plays an essential role in a wide range of cellular processes, such as transcription, replication, chromosomal segregation, and DNA repair. Despite this broadly accepted recognition, we are yet to understand how DNA is organized within bacterial cells on the micrometer scale. Supercoiling, osmotic compaction by molecular crowders (molecular crowding), DNA-protein interactions, and attachments to the cell envelope have all been implicated in organizing and compacting DNA in the bacterial cell. However, how much impact each of these factors has on compacting DNA remains unclear. To address the role of molecular crowding in compacting the E. coli nucleoid, we combine experimental measurements with modeling. In experimental studies, we use either mechanical or chemical perturbations for cells to vary their water content, inevitably the volume fraction of crowders changes. We show that the nucleoid size decreases continuously as the volume fraction of crowders increases and reaches a compressibility limit when the volume fraction of crowders exceeds the physiological value by a factor of 1.3. We also show the compressibility values of nucleoids along the long and short axes of the cell are significantly anisotropic (ratio: 3 ∼ 4). Both of these findings are principally independent of growth conditions. Furthermore, we perform coarse-grained Brownian dynamical simulations that result in a good qualitative agreement with our experimental data. Nevertheless, at the quantitative level, the model predicts smaller anisotropy values (∼2). Altogether, our results lend further support to the idea that molecular crowding is the main factor compacting the bacterial DNA within the nucleoid.