Topological scanning of the P1 plasmid partition site

The parS site of the P1 plasmid promotes active partition of P1 to daughter cells when the P1 ParA and ParB proteins are provided. The structure of parS was modified by substituting portions of the sequence with synthetic oligonucleotides and testing partition activity of the resulting mutants in an in vivo assay. The boundaries of the site were defined. They enclose a 74 bp region with a central integration host factor (IHF) binding region flanked by two arms containing heptamer and hexamer ParB binding motifs. The IHF binding region was shown to be important for partition activity but could be replaced by sequences containing A tracts that induce static bends in the DNA. The properties of sites with spacer sequences of different lengths inserted at one of five different locations led to the following conclusions. (1) The spacing between the heptamer and hexamer ParB binding motifs in both arms is critical for function. (2) Optimum partition activity requires that the parS site arms are bent toward each other with specific faces of the two helices facing each other. (3) Both arms show torsional rigidity in the active complex. (4) The left arm is laterally inflexible and activity is lost when it is extended unless the right arm is similarly extended. (5) The right arm is laterally flexible so that, when it is extended by an integral number of turns of the helix, it can still align properly with a left arm of wild-type length. The results suggest that right-arm flexibility is promoted by an A + T-rich region that is essential for IHF binding and lies adjacent to the IHF binding consensus motif. Inherent flexibility of this A + T-rich region also appears to account for the residual activity of parS sites in which the IHF binding consensus has been destroyed by multiple point mutations. The results are consistent with a proposed structure in which specific alignment of the parS site arms by an IHF-promoted bend allows them to be linked by bifunctional ParB protein binding. We suggest that such a structure might be involved in the specific pairing and unpairing of daughter plasmids during partition by an isomerization reaction.