Fig. 5: Schematic diagrams of roles of tmRNA·SmpB and ArfA in rescue of antibiotic-dependent stalled ribosomes in E. coli.

A The stalled-ribosome rescue process in the presence of the aminoglycosides. Upper: tmRNA·SmpB rescues stalled ribosomes caused by the aminoglycosides by adding the tag peptide to the nascent polypeptides (indicated by a wide blue arrow). Tag-dependent proteolysis of the resultant aberrant proteins rapidly occurs so that ROS generation can be suppressed. Lower: in the absence of tmRNA·SmpB, ArfA is expressed; however, it does not help to rescue ribosomes exposed to aminoglycosides. Misreading of mRNA and/or stop codon read thorough occurs, and consequently, aberrant proteins accumulate in cells (see the text). This results in an increase in intracellular ROS levels that may lead to severe growth reduction or cell death. B The stalled-ribosome rescue process in the presence of tetracyclines and amphenicols. Red and blue vertical arrows indicate increase and decrease in mRNA induced by the antibiotics, respectively. A dotted T-shaped lines indicate a weakening of inhibition. When ArfA begins to increase in cells, this causes a positive feedback mechanisms where ArfA further increases itself (indicated by a rotated arrow). Although full-length ArfA protein that is produced when arfA mRNA is not cleaved by RNase III may also be more expressed, it is unstable and degraded immediately, as it possesses an extremely hydrophobic C-terminal tail that leads to aggregation and degradation of the full-length protein²³. ArfA can rescue stalled ribosomes caused by the bacteriostatic antibiotics even more efficiently (a blue arrow) than can tmRNA·SmpB (a light blue arrow). Note that neither tetracyclines nor amphenicols induce ROS generation.