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How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis

Science  18 May 2012:
Vol. 336, Issue 6083, pp. 915-918
DOI: 10.1126/science.1218538

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The Hibernating Ribosome

When bacteria enter stationary phase, their ribosomes are inactivated. In Escherichia coli, ribosome modulation factor (RMF) causes dimerization of the 70S ribosome and the dimer is stabilized by, hibernation promotion factor (HPF). Alternately, the stationary phase protein, YfiA, inactivates 70S ribosomes. Polikanov et al. (p. 915) present high-resolution structures of the Thermus thermophilus 70S ribosome bound to each of these three factors. The structures suggest that RMF binding inhibits protein synthesis by preventing initial messenger RNA (mRNA) binding and that HPF and YfiA have overlapping binding sites and would both interfere with binding of mRNA, transfer RNA, and initiation factors.

Abstract

Eubacteria inactivate their ribosomes as 100S dimers or 70S monomers upon entry into stationary phase. In Escherichia coli, 100S dimer formation is mediated by ribosome modulation factor (RMF) and hibernation promoting factor (HPF), or alternatively, the YfiA protein inactivates ribosomes as 70S monomers. Here, we present high-resolution crystal structures of the Thermus thermophilus 70S ribosome in complex with each of these stationary-phase factors. The binding site of RMF overlaps with that of the messenger RNA (mRNA) Shine-Dalgarno sequence, which prevents the interaction between the mRNA and the 16S ribosomal RNA. The nearly identical binding sites of HPF and YfiA overlap with those of the mRNA, transfer RNA, and initiation factors, which prevents translation initiation. The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation.

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