Structural and functional aspects of the small riboregulator 6S RNA

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Adaptation of the transcriptome to nutrient limitation and resupply is a fundamental process in bacteria, particularly in natural habitats. Bacterial 6S RNA, a ubiquitous and growth phase-dependent riboregulator of transcription, binds to RNA polymerase (RNAP) and inhibits transcription when nutrients are low. Upon nutrient resupply, when nucleoside triphosphate levels increase, RNAP acts as an RNA-dependent RNA polymerase by transcribing short RNAs (pRNAs) from 6S RNA as template, leading to dissociation of 6S RNA/RNAP complexes and degradation of 6S RNA. Whereas the majority of bacteria express a single 6S RNA species, Bacillus subtilis encodes two 6S RNAs (6S-1 and 6S-2) of similar secondary structure, but with different expression profiles. We have shown that B. subtilis 6S-1 RNA shares many functional hallmarks with the prototypic 6S RNA from E. coli, whereas 6S-2 RNA appears to function differently. Now, major efforts will be directed towards: (a) understanding the differential roles of the two B. subtilis 6S RNAs, (b) understanding the phenotypes of 6S RNA knockouts, (c) understanding the molecular basis of the individual steps of the 6S-1 RNA functional cycle, (d) understanding how 6S-1 pRNA synthesis is related to the GTP pool in B. subtilis and how the 6S RNA and RelA regulatory pathways are interdigitated, (e) analysis if pRNAs in B. subtilis have additional posttranscriptional functions.