Bacteria adapt nutrient deprivation by reducing vacant 70S ribosomes via the silencing factor RsfS

Abstract

Bacteria rapidly remodel protein synthesis to survive nutrient limitation, yet how inactive ribosomes are selectively regulated remains incompletely understood. Ribosome silencing factor S (RsfS) is the only known bacterial factor that selectively dissociates vacant 70S ribosomes, but its physiological function in bacterial adaptation has remained elusive. Here, we demonstrate that RsfS promotes bacterial survival during nutrient starvation by selectively dismantling non-translating vacant 70S ribosomes while sparing translating ribosomes. Biochemical analyses show that RsfS efficiently dissociates vacant 70S ribosomes but has little effect on programmed ribosomes in the pre-translocation or post-translocation states, thereby preserving ongoing protein synthesis. Ribosome profiling further reveals that loss of RsfS results in a global reduction in translational efficiency and widespread translational reprogramming during starvation. Mechanistically, dissociation of vacant ribosomes by RsfS suppresses futile EF-G-dependent GTP hydrolysis and prevents unnecessary energy expenditure associated with inactive ribosome cycling. Consistent with this mechanism, RsfS enhances bacterial adaptation to nutrient deprivation without compromising active translation. Together, our findings identify RsfS as a unique regulator of bacterial ribosome homeostasis that conserves cellular energy through selective dissociation of vacant 70S ribosomes, revealing a previously unrecognized strategy by which bacteria optimize translation under nutrient-limited conditions.