Abstract
Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPFlong. The N-terminal domain of HPFlong binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPFlong binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPFlong, and the Shine–Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPFlong due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPFlong-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.
Highlights
Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes
Rmf may be specific for γ-proteobacteria[14], most bacteria and some plant plastids[15, 16] carry a gene homologous to hpf short, here referred to as hpf long, and form 100S particles through a different mechanism, which we describe in this paper
We present a second mechanism of ribosome dimerization that may be widely used in the bacterial kingdom and is distinctly different from the one proposed for E. coli
Summary
Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. The mechanism in E. coli is mediated by the ribosome modulation factor (RMF)[10], which binds to a site in the 30S and interferes with the Shine–Dalgarno (SD) sequence This prevents the interaction between mRNA and the 16S rRNA and leads to the formation of 90S dimers[11]. Using the recently published structure of the 70S ribosome of the Gram-positive bacterium Bacillus subtilis (PDB-code 3J9W21) as a starting model, as well as the highest resolution E. coli 70S structure (PDB-code 4YBB22), we were able to model the structure of the L. lactis 70S ribosome We located both the N- and C-terminal domains of HPFlong in the 100S ribosome as well as the interaction sites of the 70S particles within the dimer. We present a second mechanism of ribosome dimerization that may be widely used in the bacterial kingdom and is distinctly different from the one proposed for E. coli
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