RtcB is the RNA ligase component of an Escherichia coli RNA repair operon

Abstract

RNA 2′,3′-cyclic phosphate ends play important roles in RNA metabolism as substrates for RNA ligases during tRNA restriction-repair and tRNA splicing. Diverse bacteria from multiple phyla encode a two-component RNA repair cassette, comprising Pnkp (polynucleotide kinase-phosphatase-ligase) and Hen1 (RNA 3′-terminal ribose 2′-O-methyltransferase), that heals and then seals broken tRNAs with 2′,3′-cyclic phosphate and 5′-OH ends. The Pnkp-Hen1 repair operon is absent in the majority of bacterial species, thereby raising the prospect that other RNA repair systems might be extant. A candidate component is RNA 3′-phosphate cyclase, a widely distributed enzyme that transforms RNA 3′-monophosphate termini into 2′,3′-cyclic phosphates but cannot seal the ends it produces. Escherichia coli RNA cyclase (RtcA) is encoded in a σ54- regulated operon with RtcB, a protein of unknown function. Taking a cue from Pnkp-Hen1, we purified E. coli RtcB and tested it for RNA ligase activity. We report that RtcB per se seals broken tRNA-like stem-loop structures with 2′,3′-cyclic phosphate and 5′-OH ends to form a splice junction with a 2′-OH, 3′,5′-phosphodiester. We speculate that: (i) RtcB might afford bacteria a means to recover from stress-induced RNA damage; and (ii) RtcB homologs might catalyze tRNA repair or splicing reactions in archaea and eukarya. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.