IF3 licenses newly made 30S subunits for translation during stress

Sharma, Indra Mani; Woodson, Sarah A.

doi:10.1101/655696

Cited by 2 publications

(1 citation statement)

References 66 publications

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“…Proteins enriched in ribosomes obtained from Δ hpf and hpf Δ dimer strains include the ribosome maturation factors RimM and RimP as well as RbfA that binds the 30S subunit in a position that overlaps with the A and P site tRNA binding sites similar to HPF (38). RbfA prevents initiation by a 30S subunit that has not fully matured (39, 40). Since S2 and S3 are late-binding proteins, the association of RbfA with ribosomes isolated from Δ hpf further indicates that the 30S may be structurally similar to a small subunit that has not completed assembly and which should be prevented from initiation.…”

Section: Discussionmentioning

confidence: 99%

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Feaga

Kopylov

Kim³

et al. 2019

Preprint

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18The formation of ribosome dimers during periods of quiescence is widespread among bacteria 19 and some higher eukaryotes. However, the mechanistic importance of dimerization is not well 20 understood. In bacteria ribosome dimerization is mediated by the Hibernation Promoting Factor 21 (HPF). Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves 22 active ribosomes by preventing the loss of essential ribosomal proteins. Ribosomes isolated from 23 strains either lacking HPF (∆hpf) or encoding a mutant allele of HPF that binds the ribosome but 24 does not mediate dimerization were substantially depleted of the small subunit proteins S2 and 25 S3. Strikingly, these proteins are located at the ribosome dimer interface. We used single particle 26 cryo-EM to further characterize ribosomes isolated from a ∆hpf mutant strain and observed that 27 many were missing S2, S3, or both. These data support a model in which the ribosome 28 dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome 29 function. 31 Significance Statement 32When nutrients become scarce, many bacterial species enter an extended state of quiescence. 33 A major challenge of this state is how to attenuate protein synthesis, the most energy consuming 34 cellular process, while preserving ribosomes for the return to favorable conditions. Here, we show 35 that the ribosome-binding protein HPF which dimerizes ribosomes functions to protect essential 36 ribosomal proteins at the dimer interface. HPF is almost universally conserved in bacteria and 37 HPF deletions in diverse species exhibit decreased viability under nutrient limitation. Our data 38 provide mechanistic insight into this phenotype and establish a role for HPF in maintaining 39 translationally competent ribosomes during quiescence. 40 \body 41 42 51 Ribosomes in quiescent cells ranging from bacteria (3, 7, 8) to some mammalian cells (9, 10) 52 form dimers. However, the functional consequences of dimerization remain mysterious. In 53 bacteria, ribosome dimerization is mediated by the protein HPF. Two monomers of HPF bind two 54 70S ribosomes and interact at their C-termini to form 100S ribosome dimers (11). Most bacteria 55 encode an HPF homolog, and mutants lacking HPF exhibit pleiotropic phenotypes, including 56 decreased viability during extended stationary phase (12), increased antibiotic sensitivity (13), 57 decreased virulence (14), and a reduction in protein synthesis and growth after nutrient limitation 58 (15, 16). Ribosome dimerization may inhibit protein synthesis (17, 18) and bacteria lacking HPF 59 exhibit increased polysomes, indicative of increased protein synthesis (19). However, phenotypes 60 associated with HPF deletion may also be explained by ribosome instability as ribosomal RNA 61 has been shown to be degraded in some mutants lacking HPF (15, 20, 21). 62 Recent structures of 100S ribosome dimers from Escherichia coli, Staphylococcus aureus, 63 and B. subtilis reveal that HPF binding to the ...

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Section: Discussionmentioning

confidence: 99%

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Feaga

Kopylov

Kim³

et al. 2019

Preprint

View full text Add to dashboard Cite

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Ribosome Dimerization Protects the Small Subunit

et al. 2020

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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 hibernation-promoting factor (HPF) functions to protect essential ribosomal proteins. Ribosomes isolated from strains lacking HPF (Δhpf) 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-electron microscopy (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. IMPORTANCE The 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 rRNA. 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 the loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with the 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.

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IF3 licenses newly made 30S subunits for translation during stress

Cited by 2 publications

References 66 publications

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Ribosome Dimerization Protects the Small Subunit

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