Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF. (23rd June 2017)

• Record Type: Journal Article
• Authors: Khusainov, Iskander; Vicens, Quentin; Ayupov, Rustam; Usachev, Konstantin; Myasnikov, Alexander; Simonetti, Angelita; Validov, Shamil; Kieffer, Bruno; Yusupova, Gulnara; Yusupov, Marat; Hashem, Yaser
• Is Part Of: EMBO journal. Volume 36:Number 14(2017)
• Page Start: 2073
• Page End: 2087
• Publication Date: 2017-06-23
• Subjects: cryo‐electron microscopy -- hibernation -- pathogen -- ribosome; Molecular biology -- Periodicals; 572.805
• DOI: 10.15252/embj.201696105
• Languages: English
• ISSNs: 0261-4189

Abstract

Abstract: In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress‐induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation‐promoting factor (SaHPF) that we solved using cryo‐electron microscopy. Our reconstructions reveal that the N‐terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C‐terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD‐dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA. We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials. Synopsis: The controlled formation of ribosome dimers reduces translation as part of the bacterial stress response. This study reveals the structural basis for how hibernation factor HPF bridges two inactive ribosomes in a 100S disome. Structures of hibernating ribosomes from Staphylococcus aureus were solved using a combination of cryo‐EM and NMR. Ribosome dimerization is promoted by binding of a protein hibernation factor (SaHPF) SaHPF binds the 30S subunit via its N‐terminal domain and brings two ribosomes together by C‐terminal homodimer formation. An NMR structure of the C‐terminal domain of SaHPF reveals the residues involved in dimerization. Ribosome association into disomes is stabilized by helix 26 of the 16S ribosomal RNA. Ribosomes within dimers adopt both rotated and unrotated conformations. Abstract : By combining cryoEM and NMR, this study illustrates how bacterial ribosomes are stored in an inactive dimeric 100S (disome) state during stress responses.