RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

Abstract

The YbeB (DUF143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. While they have been shown to be associated with ribosomes, their molecular function remains unclear. Here we show that YbeB is a ribosomal silencing factor (RsfA) in the stationary growth phase and during the transition from rich to poor media. A knock-out of the rsfA gene shows two strong phenotypes: (i) the viability of the mutant cells are sharply impaired during stationary phase (as shown by viability competition assays), and (ii) during transition from rich to poor media the mutant cells adapt slowly and show a growth block of more than 10 hours (as shown by growth competition assays). RsfA silences translation by binding to the L14 protein of the large ribosomal subunit and, as a consequence, impairs subunit joining (as shown by molecular modeling, reporter gene analysis, in vitro translation assays, and sucrose gradient analysis). This particular interaction is conserved in all species tested, including Escherichia coli, Treponema pallidum, Streptococcus pneumoniae, Synechocystis PCC 6803 , as well as human mitochondria and maize chloroplasts (as demonstrated by yeast two-hybrid tests, pull-downs, and mutagenesis). RsfA is unrelated to the eukaryotic ribosomal anti-association/60S-assembly factor eIF6, which also binds to L14, and is the first such factor in bacteria and organelles. RsfA helps cells to adapt to slow-growth/stationary phase conditions by down-regulating protein synthesis, one of the most energy-consuming processes in both bacterial and eukaryotic cells.

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

“…S5. Some of these features may provide inhibitory mechanisms similar to that of the periphery binding site of RsfS that inhibits protein synthesis by interfering with the association of the two subunits (69,70).…”

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…88 Ribosomal inactivation is attributed to factors such as ribosome modulation factor (RMF), ribosome-associated inhibitor A (RaiA), and ribosomal silencing factor (RsfA), which are induced by the elevated level of ppGpp present during slow growth. 89-91 T. Hwa and collaborators 88 argue that ribosomal inactivation occurs without a concomitant decrease in the concentration of available ternary complexes (comprising aminoacylated tRNA, elongation factor TU and GTP), which would ensure the maintenance of a reasonable translation elongation rate. There is an apparent conflict between the latter argument and our demand-based model of tRNA degradation.…”

Molecular characterization and function analysis of the rice OsDUF946 family

“…The domain of unknown function (DUF) families in the Pfam database (http://pfam.xfam.org/family) includes many highly conserved DUFs presumably with important biological function, as well as DUFs whose functions have not been proved to be essential and have not been unravelled yet [1][2][3]. Some DUF-containing proteins have recently been reported to enhance the abiotic stress tolerance in plants [4][5][6][7][8].…”