Vibrio cholerae YaeO is a Structural Homologue of RNA Chaperone Hfq that Inhibits Rho-dependent Transcription Termination by Dissociating its Hexameric State

Pal, Kamalendu; Yadav, Malti; Jain, Sakshi; Ghosh, Biplab; Sen, Ranjan; Sen, U.

doi:10.1016/j.jmb.2019.09.019

Cited by 11 publications

(16 citation statements)

References 39 publications

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“…The peptides that we have reported here define another class of Rho inhibitors that target the PBS of Rho. In this regard, these peptides functionally resemble the other two PBS-binding Rho antagonists, YaeO and Hfq (24)(25)(26). Hence, both the ATP-binding pocket in the central channel and the N-terminal RNA-binding sites offer target areas for designing novel Rho inhibitors.…”

Section: Discussionmentioning

confidence: 96%

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Ghosh

Sharma

Kumar

et al. 2021

Journal of Biological Chemistry

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The transcription terminator Rho regulates many physiological processes in bacteria, such as antibiotic sensitivity, DNA repair, RNA remodeling, and so forth, and hence, is a potential antimicrobial target, which is unexplored. The bacteriophage P4 capsid protein, Psu, moonlights as a natural Rho antagonist. Here, we report the design of novel peptides based on the C-terminal region of Psu using phenotypic screening methods. The resultant 38-mer peptides, in addition to containing mutagenized Psu sequences, also contained plasmid sequences, fused to their C termini. Expression of these peptides inhibited the growth of Escherichia coli and specifically inhibited Rhodependent termination in vivo. Peptides 16 and 33 exhibited the best Rho-inhibitory properties in vivo. Direct high-affinity binding of these two peptides to Rho also inhibited the latter's RNA-dependent ATPase and transcription termination functions in vitro. These two peptides remained functional even if eight to ten amino acids were deleted from their C termini. In silico modeling and genetic and biochemical evidence revealed that these two peptides bind to the primary RNA-binding site of the Rho hexamer near its subunit interfaces. In addition, the gene expression profiles of these peptides and Psu overlapped significantly. These peptides also inhibited the growth of Mycobacteria and inhibited the activities of Rho proteins from Mycobacterium tuberculosis, Xanthomonas, Vibrio cholerae, and Salmonella enterica. Our results showed that these novel anti-Rho peptides mimic the Rho-inhibition function of the 42-kDa dimeric bacteriophage P4 capsid protein, Psu. We conclude that these peptides and their C-terminal deletion derivatives could provide a basis on which to design novel antimicrobial peptides.

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Section: Discussionmentioning

confidence: 96%

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Ghosh

Sharma

Kumar

et al. 2021

Journal of Biological Chemistry

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“…1 D ) suggests a common mechanism of ρ inhibition. However, recombinant V. cholerae Rof ( vc Rof) has been observed to form higher-order oligomers in vitro , of which the dimer state could be stabilized by treatment with iodoacetamide/TCEP; furthermore, vc Rof seems to disassemble ρ hexamers in vitro (22). ρ-bound E. coli Rof ( ec Rof) and a vc Rof monomer (PDB ID: 6JIE) (22) exhibit similar structures that superimpose with a root-mean-square deviation (rmsd) of 1.05 Å for 58 pairs of Cα atoms (2.65 Å for all 72 pairs of Cα atoms).…”

Section: Resultsmentioning

confidence: 99%

“…However, recombinant V. cholerae Rof ( vc Rof) has been observed to form higher-order oligomers in vitro , of which the dimer state could be stabilized by treatment with iodoacetamide/TCEP; furthermore, vc Rof seems to disassemble ρ hexamers in vitro (22). ρ-bound E. coli Rof ( ec Rof) and a vc Rof monomer (PDB ID: 6JIE) (22) exhibit similar structures that superimpose with a root-mean-square deviation (rmsd) of 1.05 Å for 58 pairs of Cα atoms (2.65 Å for all 72 pairs of Cα atoms). Similar to isolated ec Rof, isolated vc Rof differs from ρ-bound ec Rof in the orientation of the N-terminal region, which is diverted from the OB-fold; furthermore, helix α1 in isolated vc Rof is shortened by one turn compared to ec Rof (Fig.…”

Section: Resultsmentioning

confidence: 99%

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

Said,

Finazzo,

Hilal

et al. 2023

Preprint

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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.

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“… 50 Several binding partners of Rho, including NusG, NusA, Hfq, YaeO, and Psu, regulate Rho-dependent transcription termination. 51 , 52 As Rho-dependent termination function is essential in bacteria, further study of the regulation of Rho by binding proteins is important.…”

Section: Discussionmentioning

confidence: 99%

YihE is a novel binding partner of Rho and regulates Rho-dependent transcription termination in the Cpx stress response

Wang

Pei

et al. 2022

iScience

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Vibrio cholerae YaeO is a Structural Homologue of RNA Chaperone Hfq that Inhibits Rho-dependent Transcription Termination by Dissociating its Hexameric State

Cited by 11 publications

References 39 publications

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

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

YihE is a novel binding partner of Rho and regulates Rho-dependent transcription termination in the Cpx stress response

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