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

Geißen, René; Steuten, Benedikt; Polen, Tino; Wagner, Rolf

doi:10.4161/rna.7.5.12969

Cited by 16 publications

(20 citation statements)

References 22 publications

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“…The 6S RNA (also known as SsrS RNA) has been shown to negatively regulate the transcripts under the control of the major sigma factor σ 70 in E. coli and B. subtilis (where it is better known as σ A ) during the stationary phase of growth by interacting with the RNA polymerase holoenzyme [66]. 6S RNA has been found to be important in cell survival under stress in both E. coli and B. subtilis [67,68]. We have previously shown that the 6S RNA in C. acetobutylicum, which displays the conserved secondary structure (Figure 4A) of an asymmetric bubble [69], is expressed at high levels [40].…”

Section: Resultsmentioning

confidence: 99%

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

et al. 2013

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BackgroundSmall non-coding RNAs (sRNA) are emerging as major components of the cell’s regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metabolite stress, mostly in Gram- prokaryotes, but hardly any in Gram+ prokaryotes. Significantly, the role of sRNAs in the stress response remains poorly understood at the genome-scale level. It was previously shown that toxic-metabolite stress is one of the most comprehensive and encompassing stress responses in the cell, engaging both the general stress (or heat-shock protein, HSP) response as well as specialized metabolic programs.ResultsUsing RNA deep sequencing (RNA-seq) we examined the sRNome of C. acetobutylicum in response to the native but toxic metabolites, butanol and butyrate. 7.5% of the RNA-seq reads mapped to genome outside annotated ORFs, thus demonstrating the richness and importance of the small RNome. We used comparative expression analysis of 113 sRNAs we had previously computationally predicted, and of annotated mRNAs to set metrics for reliably identifying sRNAs from RNA-seq data, thus discovering 46 additional sRNAs. Under metabolite stress, these 159 sRNAs displayed distinct expression patterns, a select number of which was verified by Northern analysis. We identified stress-related expression of sRNAs affecting transcriptional (6S, S-box & solB) and translational (tmRNA & SRP-RNA) processes, and 65 likely targets of the RNA chaperone Hfq.ConclusionsOur results support an important role for sRNAs for understanding the complexity of the regulatory network that underlies the stress response in Clostridium organisms, whether related to normophysiology, pathogenesis or biotechnological applications.

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Section: Resultsmentioning

confidence: 99%

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

et al. 2013

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“…In addition, deletion of the gene for the riboregulator 6S RNA ( ssrS ) did not result in an altered rsd mRNA level. This is of special interest because 6S RNA itself is a regulator, considered to facilitate the switch in specificity between exponential and stationary growth transcription by interfering with the Eσ 70 holoenzyme [45], [46]. Hence, 6S RNA can be regarded as a functional homolog of Rsd [47].…”

Section: Resultsmentioning

confidence: 99%

The E. coli Anti-Sigma Factor Rsd: Studies on the Specificity and Regulation of Its Expression

2011

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BackgroundAmong the seven different sigma factors in E. coli σ70 has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting σ70-dependent transcription at the onset of stationary growth. Although binding of Rsd to σ70 has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown.Methodology/Principal FindingsWe have performed studies to unravel the function and regulation of Rsd expression in vitro and in vivo. Cross-linking and affinity binding revealed that Rsd is able to interact with σ70, with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with σ38, the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and σ38- or σ70-containing RNA polymerase in presence of Rsd. Under competitive in vitro transcription conditions, in presence of both sigma factors, a selective inhibition of σ70-dependent transcription was prevailing, however. Analysis of rsd expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the rsd promoters. Furthermore, the major promoter P2 was shown to be down-regulated in vivo by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced rsd promoter activity. Most notably, the dam-dependent methylation of a cluster of GATC sites turned out to be important for efficient rsd transcription.Conclusions/SignificanceThe results contribute to a better understanding of the intricate mechanism of Rsd-mediated sigma factor specificity changes during stationary phase.

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“…In E. coli the ppGpp concentration is adjusted by two different enzymes, the ribosome‐associated RelA, responsible for the rapid synthesis to high concentrations (stringent response), and the bi‐functional SpoT regulating the basal ppGpp concentration by a balanced synthesis and hydrolysis activity (Potrykus and Cashel, ; Wagner, ). The 6S RNA‐dependent change in the ppGpp level could be demonstrated in both relA + and relA − strains indicating that SpoT‐dependent ppGpp synthesis is likely responsible for the enhanced ppGpp pool (Geißen et al ., ; Neußer et al ., ). An independent study demonstrated that transcription of relA is inhibited by 6S RNA during early stationary phase, thus also leading to elevated ppGpp levels in a 6S RNA deletion strain.…”

Section: Role Of 6s Rna As ‘Resource Sentinel’ During Stressmentioning

confidence: 97%

“…Consistent with a role of 6S RNA in general metabolism many 6S RNA‐dependent genes in E. coli are differentially expressed also during exponential growth (Trotochaud and Wassarman, ; Neußer et al ., ; Cavanagh et al ., ; Geißen et al ., ). Next to transporters and stress regulators several important enzymes of the purine metabolism are affected.…”

Section: Role Of 6s Rna As ‘Resource Sentinel’ During Stressmentioning

confidence: 97%

6S RNA: recent answers – future questions

Steuten

Schneider

Wagner

2014

Molecular Microbiology

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Summary6S RNA is a non-coding RNA, found in almost all phylogenetic branches of bacteria. Through its conserved secondary structure, resembling open DNA promoters, it binds to RNA polymerase and interferes with transcription at many promoters. That way, it functions as transcriptional regulator facilitating adaptation to stationary phase conditions. Strikingly, 6S RNA acts as template for the synthesis of small RNAs (pRNA), which trigger the disintegration of the inhibitory RNA polymerase-6S RNA complex releasing 6S RNA-dependent repression. The regulatory implications of 6S RNAs vary among different bacterial species depending on the lifestyle and specific growth conditions that they have to face. The influence of 6S RNA can be seen on many different processes including stationary growth, sporulation, light adaptation or intracellular growth of pathogenic bacteria. Recent structural and functional studies have yielded details of the interaction between E. coli 6S RNA and RNA polymerase. Genome-wide transcriptome analyses provided insight into the functional diversity of 6S RNAs. Moreover, the mechanism and physiological consequences of pRNA synthesis have been explored in several systems. A major function of 6S RNA as a guardian regulating the economic use of cellular resources under limiting conditions and stress emerges as a common perception from numerous recent studies.

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E. coli6S RNA: A universal transcriptional regulator within the centre of growth adaptation

Cited by 16 publications

References 22 publications

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

The E. coli Anti-Sigma Factor Rsd: Studies on the Specificity and Regulation of Its Expression

6S RNA: recent answers – future questions

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