(A) In ΔtruA strains, hypomodified tRNAs are susceptible to nuclease, leading to tRNA fragment accumulation. RtcA converts the ends of the 5′ fragments to 2′, 3′-cyclic phosphate (cP).
(B) In ΔruvA strains and after treatment with DNA damaging agents, a RecA-regulated endonuclease cleaves tRNAs, resulting in 5′ halves ending in cyclic phosphate.
(C–E) We propose that 5′ tRNA halves ending in cyclic phosphate can be degraded by PNPase (C); bind the CARF domain of a RtcR dimer, resulting in oligomerization and operon activation (D); and may also be repaired by RtcB (E).