From local motor protein activity to global chromosome order in bacteria

Bacterial chromosomes are highly compressed polymers that exhibit dynamic, large-scale order throughout the cell cycle. This order plays a functional role during chromosome segregation, a vital process for cell division. Here, we present two disctinct ways in which bacteria use loop-extruding motor proteins to organize their chromosomes at cellular scales. Loop extrusion is an active process, during which a motor protein stochastically binds to DNA, reels in a loop, and unbinds again. Using a combination of polymer theory and simulations, we show how two distinct patterns of loop-extruder binding and unbinding give rise to different kinds of chromosomal order across bacterial species. First, we discuss the canonical case of loop extruders that specifically bind at the origin of replication, as seen in most bacteria. We show that this binding pattern facilitates chromosome segregation by altering the effective topology of the bacterial chromosome. Second, we discuss how aspecific binding of loop-extruders effectively stiffens a part of the Escherichia coli chromosome, thereby giving rise to a strikingly different chromosome orientation within the cell. Together, these examples illustrate how regulation of loop extruders at the protein-level can give rise to robust, large-scale chromosome organization.