8PTG

Structure of the transcription termination factor Rho bound to RNA at the PBS and SBS

Summary for 8PTG

• Entry DOI: 10.2210/pdb8ptg/pdb
• EMDB information: 17870
• Descriptor: Transcription termination factor Rho, rut RNA, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: transcription termination factor rho inhibition of termination sm-like protein rof rho regulation, transcription rna binding pbs sbs, transcription
• Biological source: Escherichia coli; More
• Total number of polymer chains: 7
• Total formula weight: 317219.99

Authors

Said, N.,Hilal, T.,Wahl, M.C. (deposition date: 2023-07-14, release date: 2024-04-17, Last modification date: 2024-04-24)

Primary citation

Said, N.,Finazzo, M.,Hilal, T.,Wang, B.,Selinger, T.L.,Gjorgjevikj, D.,Artsimovitch, I.,Wahl, M.C.
Sm-like protein Rof inhibits transcription termination factor rho by binding site obstruction and conformational insulation.
Nat Commun, 15:3186-3186, 2024

PubMed Abstract: Transcription termination factor ρ 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 ρ-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 ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-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 ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.

PubMed: 38622114
DOI: 10.1038/s41467-024-47439-6

Experimental method

ELECTRON MICROSCOPY (2.9 Å)