Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid

Low copy number plasmids in bacteria require segregation for stable inheritance through cell division. This is often achieved by a parABC locus, comprising an ATPase ParA, DNA-binding protein ParB and a parC region, encoding ParB-binding sites. These minimal components space plasmids equally over the nucleoid, yet the underlying mechanism is not understood. Here we investigate a model where ParA-ATP can dynamically associate to the nucleoid and is hydrolyzed by plasmid-associated ParB, thereby creating nucleoid-bound, self-organizing ParA concentration gradients. We show mathematically that differences between competing ParA concentrations on either side of a plasmid can specify regular plasmid positioning. Such positioning can be achieved regardless of the exact mechanism of plasmid movement, including plasmid diffusion with ParA-mediated immobilization or directed plasmid motion induced by ParB/parC-stimulated ParA structure disassembly. However, we find experimentally that parABC from Escherichia coli plasmid pB171 increases plasmid mobility, inconsistent with diffusion/immobilization. Instead our observations favor directed plasmid motion. Our model predicts less oscillatory ParA dynamics than previously believed, a prediction we verify experimentally. We also show that ParA localization and plasmid positioning depend on the underlying nucleoid morphology, indicating that the chromosomal architecture constrains ParA structure formation. Our directed motion model unifies previously contradictory models for plasmid segregation and provides a robust mechanistic basis for self-organized plasmid spacing that may be widely applicable.Author Summary: How DNA is stably inherited through cell division is a fundamental question in cell biology. The most common system that mediates plasmid DNA inheritance in bacteria is through a parABC locus, encoding proteins ParA and ParB, and DNA sequence parC. These components can position plasmids at equally spaced positions throughout a cell to ensure plasmids are present in both daughter cells when the cell divides into two. Here we study the mechanism by which ParA structures achieve this precise positioning. We show that ParA can direct relatively immobile plasmids over the bacterial chromosome using self-organizing, competitive ParA structures, whose disassembly is induced by plasmid parC-bound ParB. More generally these findings will help us to understand transport and regular positioning of intracellular cargo.