Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Abstract

Noncoding small RNAs regulate gene expression in all organisms, in some cases through direct association with RNA polymerase (RNAP). Here we report that the mechanism of 6 S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding. In fact, the DNA-dependent RNAP uses bound 6 S RNA as a template for RNA synthesis, producing 14-to 20-nucleotide RNA products (pRNA). These results demonstrate that 6 S RNA is functionally engaged in the active site of RNAP. Synthesis of pRNA destabilizes 6 S RNA–RNAP complexes leading to release of the pRNA-6 S RNA hybrid. In vivo, 6 S RNA–directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6 S RNA in response to nutrient availability.