Ribosome dimerization protects the small subunit

When nutrients become scarce, bacteria can enter an extended state of quiescence. A major challenge of this state is how to preserve ribosomes for the return to favorable conditions. Here, we show that the ribosome-dimerization protein HPF functions to protect essential ribosomal proteins. Ribosomes isolated from strains lacking HPF (Deltahpf), or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization, were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located directly at the ribosome dimer interface. We used single particle cryo-EM to further characterize these ribosomes and observed that a high percentage of ribosomes were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function. HPF is almost universally conserved in bacteria and HPF deletions in diverse species exhibit decreased viability during starvation. Our data provide mechanistic insight into this phenotype and establish a mechanism for how HPF protects ribosomes during quiescence.ImportanceThe formation of ribosome dimers during periods of dormancy is widespread among bacteria. Dimerization is typically mediated by a single protein, Hibernation Promoting Factor (HPF). Bacteria lacking HPF exhibit strong defects in viability and pathogenesis and in some species, extreme loss of ribosomal RNA. The mechanistic basis of these phenotypes has not been determined. Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves ribosomes by preventing loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with loss of HPF since ribosome protection would aid survival during nutrient limitation and impart a strong selective advantage when the bacterial cell rapidly reinitiates growth in the presence of sufficient nutrients.