Identification of factors that prevent ribosome stalling during early elongation

Protein synthesis is catalyzed by the ribosome and a host of highly conserved elongation factors. Most elongation factors that are conserved in all domains of life are essential, such as EF-Tu (e/aEF1A) and EF-G (e/aEF2). In contrast, the universally conserved elongation factor P (EF-P/eIF5A) is essential in eukaryotes but is dispensable in most bacteria. EF-P prevents ribosome stalling at difficult-to translate sequences, especially polyprolines. Since efp deletion phenotypes range from modest to lethal in different bacterial species, we hypothesized that some bacteria encode an uncharacterized elongation factor with compensatory functions. To identify this factor, we used Tn-seq to screen for genes that are essential in the absence of EF-P in Bacillus subtilis. This screen identified YfmR, a member of the ABCF family of ATPases, as a translation factor that is essential when efp is deleted. We find that depleting YfmR from Δefp cells decreases actively translating ribosomes and increases free ribosomal subunits bound to initiator tRNA, suggesting that ribosomes stall in early elongation. We also find that deleting efp from the spore-forming pathogen Bacillus anthracis causes a severe survival defect in liquid culture and in the presence of macrophages. B. anthracis Δefp also does not produce detectable spores. We find that heterologous expression of B. subtilis YfmR in B. anthracis Δefp cells partially rescues the severe growth and sporulation defects of this mutant. Our results therefore identify YfmR as an important translation factor that becomes essential in the absence of EF-P, and suggest that the essential function of YfmR and EF-P is to assist translation during early elongation.