Specificity determinants of the P1 and P7 plasmid centromere analogs

The cis-acting parS sites of P1 and P7 are similar in sequence and promote active partition of their respective plasmid prophages to daughter cells when the cognate Par proteins are supplied. Forty of the 94 relevant bases differ between the P1 and P7 parS sites, and the protein-site interactions show complete species specificity. A method was developed to predict which subset of the differing parS bases is responsible. When the four P1 bases thus identified were substituted into the P7 parS site, a complete switch to P1 specificity was observed. The P1-specific bases constitute two CG dinucleotide elements situated 66 bp apart. They lie within repeats of the TCGCCA sequence implicated in secondary contacts with the P1 ParB protein. The equivalent TC dinucleotides in the P7 site were found to be involved in P7 specificity. However, three other P7 bases can also contribute, including two in the heptamer repeats primarily responsible for ParB binding, and the P7-specific information shows some redundancy. The motifs containing the specificity dinucleotides and the primary ParB binding (heptamer) sites bear no obvious relationship of spacing or orientation to each other. For the ParB protein to contact both types of motif at the same time, the topology of the interaction must be complex.