Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

In bacteria, Hfq is a core RNA chaperone that catalyzes the interaction of mRNAs with regulatory small RNAs (sRNAs). To determine in vivo RNA sequence requirements for Hfq interactions, and to study riboregulation in a bacterial pathogen, Hfq was UV crosslinked to RNAs in enterohemorrhagic Escherichia coli (EHEC). Hfq bound repeated trinucleotide motifs of A-R-N (A-A/G-any nucleotide) often associated with the Shine-Dalgarno translation initiation sequence in mRNAs. These motifs overlapped or were adjacent to the mRNA sequences bound by sRNAs. In consequence, sRNA-mRNA duplex formation will displace Hfq, promoting recycling. Fifty-five sRNAs were identified within bacteriophage-derived regions of the EHEC genome, including some of the most abundant Hfq-interacting sRNAs. One of these (AgvB) antagonized the function of the core genome regulatory sRNA, GcvB, by mimicking its mRNA substrate sequence. This bacteriophage-encoded “anti-sRNA” provided EHEC with a growth advantage specifically in bovine rectal mucus recovered from its primary colonization site in cattle. [Display omitted] •Transcriptome-wide map of Hfq binding reveals targeting rules•Many sRNAs identified in pathogenicity islands•Pathogenicity-associated anti-sRNAs antagonize sRNAs encoded in core genome•Anti-sRNAs alter cell metabolism as part of niche colonization Hfq catalyzes the interaction of small RNAs (sRNA) with mRNAs. Tree et al. use UV-induced RNA-protein crosslinking to define Hfq substrates in pathogenic Escherichia coli, identifying abundant sRNAs derived from integrated bacteriophages, including “anti-sRNAs” that inhibit the activity of sRNAs.