Modulation of DNA entanglements by Nucleoid Associated Proteins

The bacterial genome can be up to ~mm-long when stretched and yet is packaged within a ~um-size cell. Its correct folding and organization are vital as entanglements between DNA segments are detrimental and may lead to cell death. Much of this organization is due to abundant Nucleoid Associated Proteins (NAPs). In spite of our understanding of the detailed molecular details through which NAPs bend, kink, coat, stiffen and bridge bacterial genomes, the precise mechanisms through which they organize bacterial genomes in dense and crowded environments remains elusive. The Integration Host Factor (IHF) and Histone-like Nucleoid-Structuring (HNS) proteins are examples of abundant NAPs that organize the bacterial genome. While the former kinks DNA at extreme angles, the latter can either stiffen or bridge DNA depending on pH, temperature, or concentration of divalent ions. In this talk, I will report on recent results we obtained using particle tracking microrheology on entangled solutions of large lambda-DNA functionalized by IHF/HNS proteins. We show that IHF can strongly reduce entanglements and even remove elastic components ultimately fluidizing the solution of entangled DNA. At the same time, we observe that in spite of its role to stiffen and bridge DNA molecules, HNS has only a moderate impact in increasing the fluid viscosity and elasticity. Taken together our results suggest that while IHF may be essential to "fluidize" the bacterial genome, HNS may be employed to silence genes locally without introducing long-lived entanglements which may negatively impact cell health.