sRNA-mediated control of transcription termination in E. coli

Bacterial small RNAs (sRNAs) have been implicated in various aspects of post-transcriptional gene regulation. Here we demonstrate that sRNAs also act at the level of transcription termination. We use the rpoS gene, which encodes a general stress sigma, as a model system, and show that sRNAs (DsrA, ArcZ, and RprA) bind the factor σS rpoS 5’UTR to suppress premature Rho-dependent transcription termination, both in vitro and in vivo. sRNA-mediated antitermination markedly stimulates transcription of rpoS during the transition to the stationary phase of growth, thereby facilitating a rapid adjustment of bacteria to global metabolic changes. Next generation RNA sequencing and bioinformatic analysis indicate that Rho functions as a global “attenuator” of transcription, acting at the 5’UTR of hundreds of bacterial genes, and that its suppression by sRNAs is a widespread mode of bacterial gene regulation.