DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli

When DNA is transcribed to RNA, the DNA double helix is constantly unwound and rewound to provide access for RNA polymerase (RNAP). This induces DNA supercoiling as a function of transcript length due to over- and under-twisting of the DNA downstream and upstream of RNAP, respectively. Using single-particle cryo-EM and in vivo assays we investigated the relationship between bacterial RNAP and DNA Topoisomerase I (TopoI), which removes negative supercoils accumulating upstream of RNAP. TopoI binds to relaxed DNA upstream of RNAP in a manner suggesting a sensory role awaiting the formation of negative supercoils and involving a conformational switch in the functional domains of TopoI. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage while binding the complementary strand with an auxiliary domain. We propose a comprehensive model for DNA relaxation in the context of a transcribing RNAP.