Prophage excision switches the primary ribosome rescue pathway and rescue‐associated gene regulations in Escherichia coli

Escherichia coli has multiple pathways to release nonproductive ribosome complexes stalled at the 3′ end of nonstop mRNA: tmRNA (SsrA RNA)‐mediated trans‐translation and stop codon‐independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and its expression is repressed by trans‐translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans‐translation, but the physiological situations in which ArfA is expressed have not been elucidated. Here, we found that the excision of CP4‐57 prophage adjacent to E. coli ssrA leads to the inactivation of tmRNA and switches the primary rescue pathway from trans‐translation to ArfA/RF2. This “rescue‐switching” rearranges not only the proteome landscape in E. coli but also the phenotype such as motility. Furthermore, among the proteins with significantly increased abundance in the ArfA(+) cells, we found ZntR, whose mRNA is transcribed together as the upstream part of nonstop arfA mRNA. Repression of ZntR and reconstituted model genes depends on the translation of the downstream nonstop ORFs that trigger the trans‐translation‐coupled exonucleolytic degradation by polynucleotide phosphorylase (PNPase). Namely, our studies provide a novel example of trans‐translation‐dependent regulation and re‐define the physiological roles of prophage excision.