6S RNA Regulates E. coli RNA Polymerase Activity

The E. coli 6S RNA was discovered more than three decades ago, yet its function has remained elusive. Here, we demonstrate that 6S RNA associates with RNA polymerase in a highly specific and efficient manner. UV crosslinking experiments revealed that 6S RNA directly contacts the σ70 and β/β′ subunits of RNA polymerase. 6S RNA accumulates as cells reach the stationary phase of growth and mediates growth phase–specific changes in RNA polymerase. Stable association between σ70 and core RNA polymerase in extracts is only observed in the presence of 6S RNA. We show 6S RNA represses expression from a σ70-dependent promoter during stationary phase. Our results suggest that the interaction of 6S RNA with RNA polymerase modulates σ70-holoenzyme activity.