E. coli 6S RNA: A universal transcriptional regulator within the centre of growth adaptation

Abstract

Bacterial 6S RNA has been shown to bind with high affinity to σ70-containing RNA polymerase, suppressing σ 70-dependent transcription during stationary phase, when 6S RNA concentrations are highest. We recently reported a genome-wide transcriptional comparison of wild-type and 6S RNA deficient E. coli strains. Contrary to the expected σ70- and stationary phase-specific regulatory effect of 6S RNA it turned out that mRNA levels derived from many alternative sigma factors, including σ38 or σ32, were affected during exponential and stationary growth. Among the most noticeably downregulated genes at stationary growth are ribosomal proteins and factors involved in translation. In addition, a striking number of mRNA levels coding for enzymes involved in the purine metabolism, for transporters and stress regulators are altered both during log- and stationary phase. During the study we discovered a link between 6S RNA and the general stress alarmone ppGpp, which has a higher basal level in cells deficient in 6S RNA. This finding points to a functional interrelation of 6S RNA and the global network of stress and growth adaptation. © 2010 Landes Bioscience.