The Rtc RNA repair system, comprising of the RNA cyclase RtcA, the RNA ligase RtcB and the transcriptional activator RtcR, is present in many bacterial species causing human diseases, including the model organisms and putative pathogens Escherichia coli and Salmonella enterica, and has been suggested to play a role in the development of antibiotic resistance. Here we explore the events underlying Rtc activation via RtcR and its CRISPR-associated Rossmann fold (CARF) domain as well as its physiological role during infection. In vitro transcription and ATPase assays showcased the inherent inhibition exerted by the RtcR CARF domain towards RtcR activation as well as its recognition of 2’,3’cP RNA termini – known to act as substrates for the system’s ligase, RtcB – as inducing ligands. End-labelling as well as adapter ligation with RtcB of in vivo bound RNA extracts derived from wildtype or N-terminal truncated RtcR provides evidence for the in vivo association of 2’,3’cP-RNA molecules with RtcR. Β-galactosidase assays demonstrated more prominent rtcBA expression in the rtc-inducing ΔhisT and Δrna E. coli mutants when compared to the wildtype, regardless of nutrient abundance. rtcBA expression appears at least partly RtcR-dependent, relying on certain inverted repeats, possibly carrying RtcR binding sites, located at specific positions in the rtcBA promoter. Pathogenicity assays using the infection model G. mellonella demonstrated that wildtype E. coli K12 MG1655 cells are more virulent in vivo compared to variants lacking any of the Rtc components or the functionally important RtcR CARF domain. Complementation of rtc gene deletions with wildtype Rtc proteins, but not functionally catalytic mutants, reverses the infection phenotype to that of wildtype. Post-infection treatment of larvae with the ribosome-targeting antibiotics chloramphenicol and tetracycline fails at affecting the survival rates of larvae infected with wildtype E. coli, suggesting a link between the Rtc system and antibiotic tolerance in vivo.