Structural basis for transcript elongation control by NusG/RfaH universal regulators

Abstract

NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. In bacteria, NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and also coordinating {rho}-dependent termination and translation. RfaH is a specialized NusG paralog that engages the EC at ops sites and subsequently excludes NusG and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryo-EM to determine structures of ECs at ops with NusG or RfaH. Both factors chaperone base pairing of the EC upstream duplex DNA to suppress backtracking. RfaH loads onto the EC by specific recognition of an ops hairpin in the single-stranded nontemplate DNA. Binding of both NusG and RfaH is incompatible with the swiveled RNAP conformation necessary for hairpin-stabilized pausing, but only RfaH fully counteracts swiveling to suppress pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.