A replication initiator protein enhances the rate of hybrid formation between a silencer RNA and an activator RNA.

The replication origin gamma of plasmid R6K in certain miniplasmids is kept silent by a silencer RNA. We have identified a major and three minor transcripts that are synthesized in a direction antiparallel and complementary to the silencer RNA. The major RNA, called the activator, is essential for replication from ori gamma. The complementary nature of the activator and silencer RNAs strongly suggests that the former is a target of the latter. We have also discovered that the initiator protein is a sequence-specific double-stranded RNA-binding protein that accelerates the rate of activator-silencer hybrid formation. Thus the efficient silencing of ori gamma can be explained by silencer RNA-activator RNA hybrid formation that is driven to completion by the initiator protein.