6S RNA Regulation of Transcription

Abstract

The 6S RNA forms a specific, stable complex with the σ70 containing form of RNA polymerase, resulting in down‐regulation of transcription at many promoters. We have shown that the 6S RNA is near the active site of RNA polymerase, and surprisingly can be used as a template for RNA synthesis analogous to transcription from a DNA promoter template. Studies of 6S RNA complexes revealed that 6S RNA remains stably bound to RNA polymerase when nutrients are limiting, but when nutrients become available, 6S RNA is released from RNA polymerase as a result of its use as a template for pRNA synthesis.A phylogenetically conserved structure of 6S RNA is critical for function. This structure bears a striking resemblance to the DNA conformation in open complexes during transcription initiation, which suggested 6S RNA might contact RNA polymerase in a manner similar to DNA binding. Indeed, similar to DNA binding at most promoters, region 4.2 of σ70 is required for 6S RNA binding. However, analysis of the contribution of individual residues within region 4.2 of σ70 for 6S RNA binding revealed that RNA binding is distinct from promoter DNA binding. The nature of this 6S RNA‐RNA polymerase interaction as well as its impact on promoter specificity for 6S RNA regulation of transcription will be discussed.