Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria.

摘要: INTRODUCTION Riboswitches and attenuators are cis-regulatory RNA elements (ribo-regulators), which in most cases control bacterial gene expression via ligand-mediated, premature transcription termination. Depending on the presence or absence of specific ligand, formation a terminator upstream causes to abort prematurely, generating short unproductive transcripts. In response changes metabolite concentrations, structure ribo-regulator is altered, destabilizing allowing read-through into gene, thus resulting full-length mRNA. These ribo-regulators play central roles physiology virulence have been used for synthetic biology applications as well recognized therapeutic targets antibiotics. RATIONALE Despite importance riboswitches attenuators, there currently no experimental high-throughput method discovery such across genomes. Furthermore, given ligand interest, until now was efficient approach identify natural that sense respond it. RESULTS We developed term-seq, enables quantitative mapping all exposed 3′ ends bacteria allows unbiased, genome-wide identification genes regulated by This quantitatively measures vivo activities expressed genome simultaneously under physiological conditions, enabling interest. Application term-seq model Bacillus subtilis, Listeria monocytogenes, Enterococcus faecalis detected vast majority known multiple previously unidentified regulators function conditional demonstrate utility our screening specifically small antibiotic molecules. found numerous antibiotics resistance genes, both pathogenic human microbiome, termination-based allow when present cell. Focusing lmo0919, one antibiotic-regulated we revealed this locus confers translation-inhibiting lincomycin. antibiotic, terminated prematurely ribo-regulator. However, upon exposure lincomycin, drug-inhibited ribosomes stall over conserved three-amino-acid open reading frame within ribo-regulator, triggering conformational change transcriptional inducing mRNA encodes gene. CONCLUSION results describe either monocultures complex communities microbiome. they reveal broad role termination regulating classes microbiome provide general tool discovering metabolites choice.