Subdiffusive movement of chromosomal loci in bacteria explained by DNA bridging

Abstract

Chromosomal loci in bacterial cells show a robust subdiffusive scaling of the mean square displacement, $\text{MSD}(\ensuremath{\tau})\ensuremath{\sim}{\ensuremath{\tau}}^{\ensuremath{\alpha}}$, with $\ensuremath{\alpha}<0.5$. On the other hand, recent experiments have also shown that DNA-bridging nucleoid associated proteins (NAPs) play an important role in chromosome organization and compaction. Here, using polymer simulations we investigate the role of DNA bridging in determining the dynamics of chromosomal loci. We find that bridging compacts the polymer and reproduces the subdiffusive elastic dynamics of monomers at timescales shorter than the bridge lifetime. Consistent with this prediction, we measure a higher exponent in a NAP mutant compared to the wild type. Furthermore, bridging can reproduce the rare but ubiquitous rapid movements of chromosomal loci that have been observed in experiments. In our model the scaling exponent defines a relationship between the abundance of bridges and their lifetime. Using this and the observed mobility of chromosomal loci, we predict a lower bound on the average bridge lifetime of around five seconds.