Differential Localization and Functional Specialization of Centromere-Like Sites in Replicons of .

Partitioning systems ensure the stable inheritance of bacterial low-copy-number replicons, such as chromosomes, chromids, and megaplasmids. These loci consist of two genes encoding partition proteins A and B, and at least one centromere-like sequence. In chromids and megaplasmids, partitioning systems are often located in the vicinity of replication systems. An extreme example of this co-localization are alphaproteobacterial replicons, where the partition () and replication () genes form a single operon, with sequences usually positioned in close proximity to these genes. In this study, we characterized a more complex system found in Paracoccus aminophilus () megaplasmid pAMI4 (438 kb). Besides the operon with a single site, this replicon has a 2-kb non-coding locus positioned 11.5 kb downstream of , which contains three additional repeats (). We demonstrated that is bound by partition protein B and is essential for proper pAMI4 partitioning . In search of similar loci, we conducted a comparative analysis of distribution in other replicons. This revealed different patterns of localization in and . However, in both these taxonomic orders, sites are almost always located inside or close to the operon. No other -like loci were found in the closest relatives of pAMI4. Another evolutionarily-independent example of such a locus was identified as a conserved feature in chromosome 2 of Allorhizobium vitis and related replicons. The replication/partitioning loci are widespread in extrachromosomal replicons of . They are evolutionarily diverse, subject to multi-layer self-regulation, and are responsible for the maintenance of different types of replicons, such as plasmids (e.g., pTi and pRi tumorigenic and rhizogenic plasmids), megaplasmids (e.g., pSymA and pSymB) and essential chromids (e.g., secondary chromosomes of , Brucella and ). In this study, we functionally analyzed an atypical partition-related component of systems, the locus, found in the megaplasmid pAMI4. We also identified centromere-like site distribution patterns in different groups of replicons and found other unrelated -like loci, which had been overlooked. Our findings raise questions concerning the biological reasons for differential distribution, which may reflect variations in operon regulation as well as different replication and partition modes of replicons belonging to the family.