Abstract
BackgroundThe 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles.ResultsPhysiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation.ConclusionsThe combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria.
Highlights
The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla
When cells of Escherichia coli (E. coli) enter the stationary growth phase, this highly structured RNA regulates transcription by promoter mimicry, as the RNA polymerase (RNAP) holoenzyme carrying the housekeeping sigma factor σ70 binds to 6S RNA instead of the promoter regions of the household genes [19,20,21,22]
Upon nutrient-induced outgrowth from the stationary phase, which includes enhancement of NTP levels, 6S RNA acts as a template for the de novo synthesis of a ~20 nt product RNA [23, 24]. pRNA synthesis triggers the release of 6S RNA from RNAP reverting 6S RNAdependent inhibition [23, 25]. 6S RNA lacking mutants of E. coli and Bacillus subtilis (B. subtilis) show significant phenotypes under long-term nutrient deprivation [20], stress conditions, like alkaline stress [26, 27] and during outgrowth from stationary phase [28, 29]
Summary
The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. Cyanobacteria are photoautotrophic prokaryotes essentially relying on the availability of sunlight and CO2 as their major energy and carbon source, respectively. Due to their autotrophic lifestyle and versatile metabolism, cyanobacteria are suited as economical cellular chassis for diverse biotechnological applications like energy feedstock accumulation [1], third generation biofuel production [2,3,4,5] and commodity product biosynthesis [6,7,8]. Upon nutrient-induced outgrowth from the stationary phase, which includes enhancement of NTP levels, 6S RNA acts as a template for the de novo synthesis of a ~20 nt product RNA (pRNA) [23, 24]. The presence of 6S RNA leads to an upregulation of σ38-activity, while overexpression of 6S RNA in σ38-deficient cells results in reduced viability in late stationary phase [19]
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