Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation

Nelly Said, Mark Finazzo, Tarek Hilal, Bing Wang, Tim Luca Selinger, Daniela Gjorgjevikj, Irina Artsimovitch () and Markus C. Wahl ()
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Nelly Said: Institute of Chemistry and Biochemistry, Freie Universität Berlin
Mark Finazzo: The Ohio State University
Tarek Hilal: Institute of Chemistry and Biochemistry, Freie Universität Berlin
Bing Wang: The Ohio State University
Tim Luca Selinger: Institute of Chemistry and Biochemistry, Freie Universität Berlin
Daniela Gjorgjevikj: Institute of Chemistry and Biochemistry, Freie Universität Berlin
Irina Artsimovitch: The Ohio State University
Markus C. Wahl: Institute of Chemistry and Biochemistry, Freie Universität Berlin

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-47439-6

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