Structural Analysis of Late Intermediate Complex Formed between Plasmid ColIb-P9 Inc RNA and Its Target RNA

The antisense Inc RNA encoded by the IncIα ColIb-P9 plasmid replicon controls the translation of repZencoding the replication initiator and its leader peptiderepY at different rates with different mechanisms. The initial loop-loop base pairing between Inc RNA and the target in therepZ mRNA leader inhibits formation of a pseudoknot required for repZ translation. A subsequent base pairing at the 5′ leader of Inc RNA blocks repY translation. To delineate the molecular basis for the differential control, we analyzed the intermediate complexes formed between RepZ mRNA and Inc RNA54, a 5′-truncated Inc RNA derivative. We found that the initial base pairing at the loops transforms into a more stable intermediate complex by its propagation in both directions. The resulting extensive base pairing indicates that the inhibition of the pseudoknot formation is established at this stage. Furthermore, the region of extensive base pairing includes bases different in related plasmids showing different incompatibility. Thus, the observed extensive base pairing is important for determining the incompatibility of the low-copy-number plasmids. We discuss the evolution of replication control systems found in IncIα, IncB, and IncFII group plasmids.