Dissection of the core and auxiliary sequences in the vegetative replication origin of promiscuous plasmid RK2

The vegetative replication origin (oriV) of promiscuous IncP plasmid RK2 can function in many Gram-negative bacterial species when supplied with the plasmid-encoded replication protein TrfA and host-encoded replication proteins including DnaA. Nine TrfA binding sites (iterons) are known, and also two DnaA binding sites, box 1, between TrfA iterons 4 and 5, and box 2, downstream of repeat 9. The deletion analysis presented here shows that the core oriV requires DnaA box 1 for function in Escherichia coli and Pseudomonas putida. This DnA box is not essential in Pseudomonas aeruginosa, although its deletion does reduce plasmid copy number in this species. A putative IHF binding site is located upstream of DnaA box 1, but IHF deficiency in E. coli seems not to alter replication efficiency or copy number control. Cloned oriV can interfere with maintenance of an independent RK2 replicon. Analysis of replication inhibition functions associated with oriV showed that a short putative orf between TrfA iterons 1 and 2 is not necessary for replication inhibition, the presence of repeats 5 to 9 in target and inhibitor plasmid are not sufficient for efficient inhibition and inhibition does not correlate directly with the number of direct repeats present. Rather, the results showed that the isolated repeats 1 and 2 to 4, potentiate replication inhibition disproportionately to their effect on the number of TrfA binding sites. The results are consistent with the idea that repeats 1 to 4, arranged as a single copy and as an irregular group of three, potentiate the ability of the oriV region to form complexes which inhibit replication. We suggest that TrfA bound at these iterons may be more susceptible to forming pairs between oriV sequences on different plasmids.