The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain.

CRISPR-associated Rossmann fold (CARF) domain signaling underpins modula-tion of CRISPR-Cas nucleases; however, the RtcR CARF domain controls expres-sion of two conserved RNA repair enzymes, cyclase RtcA and ligase RtcB. Here, we demonstrate that RtcAB are required for RtcR-dependent transcription acti-vation and directly bind to RtcR CARF. RtcAB catalytic activity is not required for complex formation with CARF, but is essential yet not sufficient for RtcRAB-dependent transcription activation, implying the need for an additional RNA repair-dependent activating signal. This signal differs from oligoadenylates, a known ligand of CARF domains, and instead appears to originate from the trans-lation apparatus: RtcB repairs a tmRNA that rescues stalled ribosomes and in-creases translation elongation speed. Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mecha-nism to regulate RNA repair required for a functioning translation apparatus.