Experiments on movement of DNA regions in Escherichia coli evaluated by computer simulation

During the cell cycle of Escherichia coli DNA is replicated and segregated over two prospective daughter cells. Nucleoids as a whole separate gradually in line with cell elongation, but sub-nucleoid DNA regions may behave differently, separating non-gradually. We tested the ability of three models to predict the outcome of a fluorescent in situ hybridisation (FISH) experiment. We did this by comparing computer-simulated data with experimental data. The first model predicts gradual separation in line with cell elongation. The second model predicts that origins stick together for some time after duplication before one copy jumps to the other side of the cell (non-gradual separation). The simulated data of these models are very similar, indicating that FISH is not a suitable method to distinguish between these two models. The third model predicts that origins may be anywhere within the nucleoid(s). We found that simulated data using the third model resemble the experimental data most. However, DNA regions are not randomly localised in the cell, although their localisation is fuzzy. We propose that movement of DNA regions is the result of a combination of factors. Nucleoid segregation (or the forces behind it) dictates the overall direction of movement. Other factors, of which we show that diffusion could be an important one, move DNA in other directions giving rise to non-gradual movement in individual cells and contributing to variation in intracellular position per cell length in a population of cells.