Plasmid and chromosome partitioning: surprises from phylogeny

Plasmids encode partitioning genes (par) that are required for faithful pla smid segregation at cell division. Initially, par loci were identified on p lasmids, but more recently they were also found on bacterial chromosomes, W e present here a phylogenetic analysis of par loci from plasmids and chromo somes from prokaryotic organisms. All known plasmid-encoded par loci specif y three components: a cis-acting centromere-like site and two trans-acting proteins that form a nucleoprotein complex at the centromere (i.e. the part ition complex), The proteins are encoded by two genes in an operon that is autoregulated by the par-encoded proteins. In all cases, the upstream gene encodes an ATPase that is essential for partitioning. Recent cytological an alyses indicate that the ATPases function as adaptors between a host-encode d component and the partition complex and thereby tether plasmids and chrom osomal origin regions to specific subcellular sites (i.e. the poles or quar ter-cell positions). Two types of partitioning ATPases are known: the Walke r-type ATPases encoded by the par/sop gene family (type I partitioning loci ) and the actin-like ATPase encoded by the par locus of plasmid R1 (type II partitioning locus), A phylogenetic analysis of the large family of Walker type of partitioning ATPases yielded a surprising pattern: most of the pla smid-encoded ATPases clustered into distinct subgroups, Surprisingly, howev er, the par loci encoding these distinct subgroups have different genetic o rganizations and thus divide the type I loci into types la and Ib. A second surprise was that almost all chromosome-encoded ATPases, including members from both Gram-negative and Gram-positive Bacteria and Archaea, clustered into one distinct subgroup. The phylogenetic tree is consistent with latera l gene transfer between Bacteria and Archaea, Using database mining with th e ParM ATPase of plasmid R1, we identified a new par gene family from enter ic bacteria, These type II loci, which encode ATPases of the actin type, ha ve a genetic organization similar to that of type Ib loci.