A new family of bacterial ribosome hibernation factors

Karla Helena-Bueno, Mariia Yu. Rybak, Chinenye L. Ekemezie, Rudi Sullivan, Charlotte R. Brown, Charlotte Dingwall, Arnaud Baslé, Claudia Schneider, James P. R. Connolly, James N. Blaza, Bálint Csörgő, Patrick J. Moynihan, Matthieu G. Gagnon (), Chris H. Hill () and Sergey V. Melnikov ()
Additional contact information
Karla Helena-Bueno: Newcastle University
Mariia Yu. Rybak: University of Texas Medical Branch
Chinenye L. Ekemezie: Newcastle University
Rudi Sullivan: University of Birmingham
Charlotte R. Brown: Newcastle University
Charlotte Dingwall: Newcastle University
Arnaud Baslé: Newcastle University
Claudia Schneider: Newcastle University
James P. R. Connolly: Newcastle University
James N. Blaza: University of York
Bálint Csörgő: HUN-REN Biological Research Centre
Patrick J. Moynihan: University of Birmingham
Matthieu G. Gagnon: University of Texas Medical Branch
Chris H. Hill: University of York
Sergey V. Melnikov: Newcastle University

Nature, 2024, vol. 626, issue 8001, 1125-1132

Abstract: Abstract To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3–6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon–EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.

Date: 2024
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DOI: 10.1038/s41586-024-07041-8

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