6S RNA regulation of relA alters ppGpp levels in early stationary phase

Abstract

6S RNA is a small, non-coding RNA that interacts directly withσ70-RNA polymerase and regulates transcription at manyσ70-dependent promoters. Here, we demonstrate that 6S RNA regulates transcription ofrelA, which encodes a ppGpp synthase. The 6S RNA-dependent regulation ofrelAexpression results in increased ppGpp levels during early stationary phase in cells lacking 6S RNA. These changes in ppGpp levels, although modest, are sufficient to result in altered regulation of transcription fromσ70-dependent promoters sensitive to ppGpp, including those promoting expression of genes involved in amino acid biosynthesis and rRNA. These data place 6S RNA as another player in maintaining appropriate gene expression as cells transition into stationary phase. Independent of this ppGpp-mediated 6S RNA-dependent regulation, we also demonstrate that in later stationary phase, 6S RNA continues to downregulate transcription in general, and specifically at a subset of the amino acid promoters, but through a mechanism that is independent of ppGpp and which we hypothesize is through direct regulation. In addition, 6S RNA-dependent regulation ofσSactivity is not mediated through observed changes in ppGpp levels. We suggest a role for 6S RNA in modulating transcription of several global regulators directly, includingrelA, to downregulate expression of key pathways in response to changing environmental conditions.