Distinct 30S subunit dimerization architecture facilitated by a novel ribosome dimerization factor in archaea

Ahmed Hassan1, Matyas Pinkas1, Kosuke Ito2, Toshio Uchiumi2, Gabriel Demo1

1Central European Institute of Technology, Masaryk University, Brno, Czech Republic

2Department of Biology, Niigata University, Niigata, Japan

gabriel.demo@ceitec.muni.cz

 

Protein synthesis utilizes a significant portion of the cell's available resources. In the face of unfavourable conditions, specialized mechanisms come into play to reduce the overall costly protein synthesis. Several ribosome-associated factors play a role in this regulation in bacteria. Some induce an inactive, hibernating state in the ribosome, forming 70S monomers (such as RaiA)1 or 100S dimers (RMF and HPF)2-4. Other factors hinder translation at various stages in the translation cycle acting as anti-association factors not allowing the formation of 70S ribosome (such as RsfS)5. Therefore, ribosome dimerization and anti-association are important regulatory events to inactivate the protein synthesis in bacteria and enable their survival under various stress conditions.

While the hibernation and anti-association mechanisms have been extensively studied in various bacterial species, the ribosomal response to adverse conditions causing growth arrest is not well understood in archaea and eukaryotes.

Here, we describe the first single particle cryo-electron microscopy structures of archaeal 30S dimers bound to a novel archaeal ribosome dimerization factor (aRDF)6. The overall arrangement of the 30S-30S dimer exhibits a head-to-body orientation connected by two homodimers of aRDF. aRDF forms a direct interaction with the L41e ribosomal protein, a key player in the establishment of a ribosomal bridge during subunit association. Therefore, the binding mode of aRDF illustrates its anti-association capability, preventing the formation of archaeal 70S ribosomes. Thus, the comprehensive structural architecture of aRDF-mediated 30S subunit dimerization provides unprecedented insights into the mechanism of ribosome shutdown in archaea.

 

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5.         Khusainov, I., Fatkhullin, B., Pellegrino, S., et al. Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach. Nat Commun. 11(1), 1656 (2020).

6.         Chiaki, Y., Natsumi, M., Sonoko, I., et al. A novel ribosome-dimerization protein found in the hyperthermophilic archaeon Pyrococcus furiosus using ribosome-associated proteomics. Biochem Biophys Res Comm. 593, 116-121 (2022).

 

 

This study was supported by the project National Institute of virology and bacteriology (Programme EXCELES, ID Project No. LX22NPO5103) - Funded by the European Union - Next Generation EU.