Structural characterization of hibernating ribosomes in four Gram-negative pathogenic bacteria
Abstract
Ribosome hibernation is a conserved bacterial stress-response mechanism that promotes translational shutdown and enhances survival under adverse conditions, contributing to persistence and tolerance to ribosome-targeting antibiotics. Here, we report high-resolution cryo-electron microscopy (cryo-EM) structures (2.5–2.8 Å) of hibernating 70S ribosomes from four clinically important ESKAPE pathogens: Pseudomonas aeruginosa , Enterobacter hormaechei , Klebsiella quasipneumoniae , and Acinetobacter baumannii . Structural analyses identified the bound hibernation factors as HPF in P. aeruginosa and E. hormaechei , and YfiA in K. quasipneumoniae and A. baumannii . Despite sequence divergence, HPF and YfiA adopt a conserved fold and occupy the same ribosomal binding site, interacting primarily with 16S rRNA and ribosomal proteins uS7 and uS9 and occupying the A- and P-sites while extending toward the E-site. Comparative analyses revealed a conserved core interaction network, including contacts with functionally important modified 16S rRNA nucleotides, alongside species-specific adaptations that preserve overall ribosome-binding architecture. Analysis of hibernating ribosome populations uncovered substantial heterogeneity in E-site tRNA occupancy, bS21 association, and mRNA binding among species, suggesting that these features are species-dependent rather than determined solely by the identity of the hibernation factor. Together, these structures provide a comprehensive comparative view of HPF- and YfiA-mediated ribosome hibernation across major Gram-negative pathogens, revealing conserved molecular principles and species-specific adaptations that expand our understanding of bacterial translational dormancy and establish a structural framework for future antibacterial strategies targeting ribosome hibernation.
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BibTeX
@article{balasubramaniam2026structural,
title = {{Structural characterization of hibernating ribosomes in four Gram-negative pathogenic bacteria}},
author = {Vasanthakrishnan Radhakrishnan Balasubramaniam and Olivier Delalande and Yann Lefrançois Copy and Sophie Chat and Sylvie Georgeault-Daguenet and Mohamed Sassi and Emmanuel Giudice and Reynald Gillet},
journal = {Communications Biology},
year = {2026},
month = oct,
doi = {10.1038/s42003-026-11002-4},
url = {https://hal.science/hal-05778509v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Structural characterization of hibernating ribosomes in four Gram-negative pathogenic bacteria
AU - Vasanthakrishnan Radhakrishnan Balasubramaniam
AU - Olivier Delalande
AU - Yann Lefrançois Copy
AU - Sophie Chat
AU - Sylvie Georgeault-Daguenet
AU - Mohamed Sassi
AU - Emmanuel Giudice
AU - Reynald Gillet
PY - 2026
DA - 2026/10/05
JO - Communications Biology
DO - 10.1038/s42003-026-11002-4
UR - https://hal.science/hal-05778509v1
AB - Ribosome hibernation is a conserved bacterial stress-response mechanism that promotes translational shutdown and enhances survival under adverse conditions, contributing to persistence and tolerance to ribosome-targeting antibiotics. Here, we report high-resolution cryo-electron microscopy (cryo-EM) structures (2.5–2.8 Å) of hibernating 70S ribosomes from four clinically important ESKAPE pathogens: Pseudomonas aeruginosa , Enterobacter hormaechei , Klebsiella quasipneumoniae , and Acinetobacter baumannii . Structural analyses identified the bound hibernation factors as HPF in P. aeruginosa and E. hormaechei , and YfiA in K. quasipneumoniae and A. baumannii . Despite sequence divergence, HPF and YfiA adopt a conserved fold and occupy the same ribosomal binding site, interacting primarily with 16S rRNA and ribosomal proteins uS7 and uS9 and occupying the A- and P-sites while extending toward the E-site. Comparative analyses revealed a conserved core interaction network, including contacts with functionally important modified 16S rRNA nucleotides, alongside species-specific adaptations that preserve overall ribosome-binding architecture. Analysis of hibernating ribosome populations uncovered substantial heterogeneity in E-site tRNA occupancy, bS21 association, and mRNA binding among species, suggesting that these features are species-dependent rather than determined solely by the identity of the hibernation factor. Together, these structures provide a comprehensive comparative view of HPF- and YfiA-mediated ribosome hibernation across major Gram-negative pathogens, revealing conserved molecular principles and species-specific adaptations that expand our understanding of bacterial translational dormancy and establish a structural framework for future antibacterial strategies targeting ribosome hibernation.
SN - 2399-3642
ER -