Crystal Structure of Shigella flexneri SF173 Reveals a Dimeric Helical Bundle Conformation

Kim, Ji-Hun; Won, Hyung‐Sik; Yoon, Won-Su; Seok, Seung-Hyeon; Jung, Bong-Jun; Lee, Seu-Na; Sim, Dae-Won; Seo, Min‐Duk

doi:10.3390/cryst8020097

Cited by 2 publications

(1 citation statement)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…NlpE is an outer membrane lipoprotein that activates the Cpx pathway in response to envelope stress (43). Rof is expressed from a divergent promoter in tandem with a small conserved protein of unknown function, YaeP (44).…”

Section: Resultsmentioning

confidence: 99%

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

Said,

Finazzo,

Hilal

et al. 2023

Preprint

View full text Add to dashboard Cite

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. Our electron microscopic 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 confirmed that the observed Rho-Rof interface is required for Rof-mediated inhibition of cell growth and Rho-termination in vitro. Bioinformatic analyses revealed 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 would be lethal.

show abstract

Section: Resultsmentioning

confidence: 99%

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

Said,

Finazzo,

Hilal

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

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

Said,

Finazzo,

Hilal

et al. 2024

Nat Commun

View full text Add to dashboard Cite

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.

show abstract

Crystal Structure of Shigella flexneri SF173 Reveals a Dimeric Helical Bundle Conformation

Cited by 2 publications

References 31 publications

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

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

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

Contact Info

Product

Resources

About