Science http://dx.doi.org/10.1126/science.aad9822 (2016)

Credit: SCIENCE

Cis-acting RNA elements in bacterial genes, such as riboswitches and attenuators, regulate gene expression in response to metabolite binding. To date, most riboregulators and their ligands have been discovered by comparative genomic analysis calibrated with metabolic logic. Dar et al. now report an approach, called term-seq, for the experimental identification of riboregulators and their modes of gene regulation. Term-seq maps the 3′-termini of RNA transcripts on a genome-wide scale and, when used in combination with other genomic methods, identifies genes that contain putative riboregulator motifs and undergo conditional transcriptional termination in response to the presence of a metabolite or drug. In Bacillus subtilis and other bacteria, the method successfully identified known riboregulators and revealed previously unknown small-molecule-dependent regulatory RNA motifs. For example, in the pathogenic bacterium Listeria monocytogenes, a small RNA, rli53, was identified as a regulator of the bacterial response to the antibiotic lincomycin: in the presence of drug, this riboregulator facilitated transcription of lmo0919, an ABC transporter that acts as an antibiotic efflux pump. A meta-transcriptomic analysis of human microbiome samples demonstrated the utility of term-seq for profiling antibiotic-responsive riboregulator activity within microbial communities, greatly expanding the scope of this tool for RNA motif discovery and antimicrobial research.