Abstract
Many small regulatory noncoding RNAs act by base-pairing with their target RNAs and interfering with their translation and/or affecting their stability, but not all such RNAs act in this way. The highly conserved prokaryotic 6 S RNA interacts with and inhibits Escherichia coli σ70-containing RNA polymerase (RNAP). 6 S RNA contains a single-stranded RNA bulge structure that mimics a gene promoter "open complex" and suggests that it might compete with promoters for RNAP. Wassarman and Saecker show that the bulge does indeed bind in the active site of RNAP in a manner analogous to the open complex, which prevents RNAP binding to legitimate targets. In the presence of nucleotides, the RNAP can synthesize short product RNAs from the 6 S RNA template, which causes the RNAP to dissociate, freeing it to restart transcription during outgrowth from stationary phase and in response to nutrient availability. K. M. Wassarman, R. M. Saecker, Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 314 , 1601-1603 (2006). [Abstract] [Full Text]
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