The mechanism of transcription antitermination by RfaH

Abstract

RfaH is a bacterial antitermination factor whose function depends on a 12‐nt ops element located in the leader regions of several operons; the ops element both induces RNA polymerase (RNAP) pausing and serves as a recognition site for RfaH. During recruitment, RfaH establishes transient contacts with the ops bases in the non‐template DNA strand exposed on the RNAP surface. After recruitment, RfaH remains bound to RNAP throughout transcription of the entire operon and switches RNAP into a processive state using four mechanisms. First, RfaH competes with σ and prevents σ‐dependent arrest during elongation. Second, RfaH competes with NusG and thus indirectly reduces Rho‐dependent termination. Third, RfaH induces forward translocation of RNAP, thereby inhibiting isomerization into an off‐pathway state that occurs from a pre‐translocated conformation. Fourth, RfaH establishes simultaneous contacts with the β’ clamp and the β lobe, the two elements that maintain the RNAP grip on the nucleic acid chains, thereby preventing the clamp opening that is thought to occur during pausing. While the first three mechanisms are specific to the RfaH‐like proteins, the last mechanism is likely broadly conserved. We propose that structurally diverse antiterminators from bacteria to humans solidify the transcription elongation complex to inhibit conformational transitions that underlie pausing and termination.