Implication of the non-coding E. coli 6S RNA in central metabolism

Implication of the non-coding E. coli 6S RNA in central metabolism

Geißen R., Steuten B., Schneider S., Heilmann B., Shamungarajah K. and Wagner, R.

Molekularbiologie der Bakterien, Institut für Physikalische Biologie; Heinrich-Heine-Universität Düsseldorf

Non-coding bacterial 6S RNA structurally mimics an open DNA promoter, enabling efficient binding to RNA polymerase (RNAP). In stationary phase, when 6S RNA levels are highest, most of the RNAP is complexed by 6S RNA, resulting in preferential inhibition of the housekeeping genes. During nutritional upshift increasing intracellular NTP concentrations trigger a 6S RNA-directed transcription of short de novo RNAs. The exceptional synthesis of de novo RNA causes the rearrangement of the template 6S RNA, leading to the release of RNAP inhibition [1]. Structural details of this interesting self-regulatory reaction of a non-coding RNA will be reported.

Recent transcriptome studies revealed that 6S RNA affects the level of RNAs encoding translational compounds and the ppGpp level important for growth adaptation. Additionally, expression of genes involved in purine and fatty acid metabolism is altered in a 6S RNA mutant strain [2, 3]. We have performed experiments to unravel the link between 6S RNA and the central metabolic pathways.

We have shown that the RNA binding protein Hfq interacts with 6S RNA, supporting a more complex regulatory function of 6S RNA. Our preliminary analyses revealed that Hfq is involved in the recognition of the small de novo transcripts generated from 6S RNA. A potential function in regulation is discussed.