Three novel plasmid R6K proteins act in concert to distort DNA within the alpha and beta origins of DNA replication

Three novel R6K genes which are responsible for expression of DNA distortion polypeptides (DDP) were identified. The DDPs act in vivo in concert to induce similar stepwise DNA helix distortions within two long inverted repeats (alpha LIR and beta LIR), which are essential elements for the two distally located R6K alpha and beta DNA replication origins. DDP1 and DDP2 are encoded by two tandem genes located at the 5' end of alpha LIR, whereas a gene coding for DDP3 is located at the 3' end of beta LIR. DDP1 and DDP2 are required for primary DNA distortion within alpha LIR or beta LIR, while DDP3 is essential for generation of secondary DNA distortion in these LIR sequences. Creation of DNA distortion within alpha LIR depends on its specific interaction with DDP1 and on the presence of the R6K primase DNA-binding site. The possible relevance of these findings to R6K replication is discussed.