Examples of long-range gene regulation in bacteria are rare and generally thought to involve DNA looping. Here, using a combination of biophysical approaches including X-ray crystallography and single-molecule analysis for the KorB–KorA system in Escherichia coli, we show that long-range gene silencing on the plasmid RK2, a source of multi-drug 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 up to 1.5 kb away. We resolved the tripartite crystal structure of a KorB–KorA–DNA co-complex, revealing that KorA latches KorB into a closed clamp state. DNA-bound KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Together, our findings explain the mechanistic basis for KorB role switching from a DNA-sliding clamp to a co-repressor and provide an alternative mechanism for long-range regulation of gene expression in bacteria.

细菌中长程基因调控的例子很少见，通常被认为涉及 DNA 循环。在这里，使用生物物理方法的组合，包括 X 射线晶体学和大肠杆菌中 KorB-KorA 系统的单分子分析，我们表明质粒 RK2 上的远程基因沉默是多种革兰氏阴性细菌的多药耐药来源，是通过 DNA 滑动夹 KorB 和夹锁定蛋白 KorA 合作实现的。我们表明 KorB 是一种 CTPase 夹，可以捕获并沿 DNA 滑动以到达最远 1.5 kb 外的远端靶启动子。我们解析了 KorB-KorA-DNA 共复合物的三方晶体结构，揭示了 KorA 将 KorB 锁定到闭合夹持状态。因此，DNA 结合的 KorA 通过阻止 KorB 在靶启动子处滑动以阻挡 RNA 聚合酶全酶来刺激抑制。总之，我们的研究结果解释了 KorB 角色从 DNA 滑动夹切换到共阻遏因子的机制基础，并为细菌中基因表达的远程调节提供了另一种机制。