A New Mechanism for Ribosome Rescue Can Recruit RF1 or RF2 to Nonstop Ribosomes
ABSTRACTBacterial ribosomes frequently translate to the 3′ end of an mRNA without terminating at an in-frame stop codon. In all bacteria studied to date, these “nonstop” ribosomes are rescued usingtrans-translation. Genes required fortrans-translation are essential in some species, but other species can survive withouttrans-translation because they express an alternative ribosome rescue factor, ArfA or ArfB.Francisella tularensiscells lackingtrans-translation are viable, butF. tularensisdoes not encode ArfA or ArfB. Transposon mutagenesis followed by deep sequencing (Tn-seq) identified a new alternative ribosome rescue factor, now named ArfT.arfTcan be deleted in wild-type (wt) cells but not in cells that lacktrans-translation activity. Overexpression of ArfT suppresses the slow-growth phenotype in cells lackingtrans-translation and counteracts growth arrest caused bytrans-translation inhibitors, indicating that ArfT rescues nonstop ribosomesin vivo. Ribosome rescue assaysin vitroshow that ArfT promotes hydrolysis of peptidyl-tRNA on nonstop ribosomes in conjunction withF. tularensisrelease factors. Unlike ArfA, which requires RF2 for activity, ArfT can function with either RF1 or RF2. Overall, these results indicate that ArfT is a new alternative ribosome rescue factor with a distinct mechanism from ArfA and ArfB.IMPORTANCEFrancisella tularensisis a highly infectious intracellular pathogen that kills more than half of infected humans if left untreated.F. tularensishas also been classified as a potential bioterrorism agent with a great risk for deliberate misuse. Recently, compounds that inhibit ribosome rescue have been shown to have antibiotic activity againstF. tularensisand other important pathogens. Like all bacteria that have been studied,F. tularensisusestrans-translation as the main pathway to rescue stalled ribosomes. However, unlike most bacteria,F. tularensiscan survive without any of the known factors for ribosome rescue. Our work identified aF. tularensisprotein, ArfT, that rescues stalled ribosomes in the absence oftrans-translation using a new mechanism. These results indicate that ribosome rescue activity is essential inF. tularensisand suggest that ribosome rescue activity might be essential in all bacteria.