Transcription termination factor Rho and its interaction with RNA. (A) Diagram of the primary structure of Rho. (B) Structure of the closed Rho hexamer from Escherichia coli bound to λtR1 RNA (PDBs 8E3H and 8E6W). RNA is in red, with dinucleotides in YC-binding pockets shown in green. The YC-binding clefts (PBS) are in magenta, and the SBS residues in orange. (C) Consensus RNA binding motifs deduced from (top) the alignment of the λtR1 RNA segments bound to the Rho hexamer shown in B, or (bottom) differential MEME enrichment of the 2511 E. coli putative Rut peaks consistently detected by Helicase-SELEX versus 3000 Rut-less control sequences (1315 sites; E-value: 5.8 × 10−30) (Delaleau et al. 2022). (D) Diagram depicting the trajectory of RNA along the crown-like PBS site of Rho, its entry in the central Rho channel, and its interaction with the SBS loops, which triggers the closure and catalytic activation of the Rho hexamer. (E) Helicase-SELEX with Rho revealed putative Rut sites along the E. coli genome, visualized as discrete sequence enrichment peaks (blue) in this representative region of the (+) strand. Approximately one-third of the putative Rut sites are located upstream of or within genes (Delaleau et al. 2022), representing primary candidate sites for conditional RDTT.
