Fragmentation of Escherichia coli mRNA by MazF and MqsR.

MazEF and MqsRA are toxin-antitoxin systems, where the toxins MazF and MqsR sequence-specifically cleave single-stranded RNA, thereby shutting down protein synthesis and cell growth. However, it has been proposed that MazF functions in a highly specific pathway, where it truncates the 5' ends of a set of E. coli transcripts (the MazF regulon), which are then translated under stress conditions by specialized ribosomes. We mapped the cleavage sites of MazF and MqsR throughout the E. coli transcriptome. Our results show that both toxins cleave mRNA independently of the recognition site position and MazF freely cleaves transcripts of the proposed MazF regulon within coding sequences. Proteome analysis indicated that MazF expression leads to overall inhibition of protein synthesis and the putative MazF regulon proteins are not selectively synthesized in response to the toxin. Our results support a simpler role for endoribonuclease TA systems as indifferent destroyers of unstructured RNA.