Tung Le “Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing on a multi-drug resistance plasmid”

Long-range gene regulation is rare in bacteria, and it remains unknown whether other mechanisms, beyond classical DNA looping, are involved. Here, we use a range of approaches, including crystallography and single-molecule analysis, to report that long-range gene silencing on the plasmid RK2, a source of multidrug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We show that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters. We resolved the tripartite crystal structure of a KorB-KorA-DNA co-complex, finding that KorA latches KorB into a closed-clamp state. We argue that KorA-KorB interaction stalls KorB sliding at target core promoter elements to occlude RNA polymerase holoenzymes and thereby repress transcription. KorA-KorB interaction also enhances the residence time of the KorAB repressome at the target promoter, prolonging repression. Overall, our data uncovers the mechanism by which the clamp-locking protein KorA promotes a KorB functional switch between DNA sliding, which is important for plasmid segregation, and stalling, which is essential for KorB to mediate long-range repression