Sm-like protein Rof inhibits transcription termination factor rho by binding site obstruction and conformational insulation
N. Said, M. Finazzo, T. Hilal, B. Wang, T. L. Selinger, D. Gjorgjevikj, I. Artsimovitch, M. C. Wahl – 2024
Transcription termination factor rho is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits rho-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of rho-Rof and rho-RNA complexes show that Rof undergoes pronounced conformational changes to bind rho at the protomer interfaces, undercutting rho conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between rho and RNA polymerase. Consistently, Rof impedes rho ring closure, rho-RNA interactions and rho association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed rho-Rof interface is required for Rof-mediated inhibition of cell growth and rho-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the rho-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence rho under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by rho may be detrimental.