6S RNA in <i>Rhodobacter sphaeroides</i>: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype

Elkina, Daria A.; Weber, Lennart; Lechner, Marcus; Burenina, Olga Y.; Weisert, Andrea; Кубарева, Е. А.; Hartmann, Roland K.; Klug, Gabriele

doi:10.1080/15476286.2017.1342933

Cited by 15 publications

(14 citation statements)

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“…Some 6S RNAs, notably from alpha-proteobacteria and A. aeolicus , have a shortened upstream stem and therefore are lacking the region critical for Ec 6S RNA interactions with σ 70 region 4.2 (25, 69, 72). However, pRNAs have been detected for A. aeolicus and R. sphaeroides 6S RNAs strongly supporting an RNA polymerase interaction, and the Aa 6S RNA has been demonstrated to bind B. subtilis Eσ A in vitro (48, 71). The H. pylori 6S RNA appears to bind RNA polymerase in either the “forward” or “reverse” orientation based on evidence of pRNAs templated from both strands of the central region (58), in contrast to Ec 6S RNA that binds quite specifically in one orientation and directs pRNA from one strand of the central region (64).…”

Section: The 6s Rna-rna Polymerase Complexmentioning

confidence: 93%

“…stationary phase). Rhodobacter sphaeroides and Caulobacter crescentus (free living alpha-proteobacteria) 6S RNA accumulation patterns change with cell growth, although the change between exponential and stationary phase levels is rather modest (~3 fold) (33, 48, 49). R. sphaeroides 6S RNA has been associated with high salt stress survival (48).…”

Section: S Rnas Are Widespread Throughout the Bacterial Kingdommentioning

confidence: 99%

“…For bacteria beyond E. coli and B. subtilis , the specific role of pRNA synthesis has not been investigated directly, but pRNAs have been detected in vivo for additional bacterial species (e.g. H. pylori (58), R. sphaeroides (48), A. aeolicus (71)) suggesting pRNA synthesis from 6S RNAs is widespread and potentially ubiquitous.…”

Section: S Rna – a Template For Prna Synthesismentioning

confidence: 99%

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6S RNA, a Global Regulator of Transcription

Wassarman

2018

Microbiol Spectr

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6S RNA is a small RNA regulator of RNA polymerase that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNA polymerase resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity including: 1. Addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; 2. The nature of the 6S RNA-RNA polymerase interaction through examination of variant proteins and mutant RNAs, crosslinking approaches, and ultimately a cryo-EM structure; 3. The physiological consequences of 6S RNA function through identification of the 6S RNA-regulon and promoter features that determine 6S RNA sensitivity; 4. The mechanism and cellular impact of 6S RNA-directed synthesis of pRNAs (i.e. pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action and how it is regulated; yet, much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.

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Section: The 6s Rna-rna Polymerase Complexmentioning

confidence: 93%

Section: S Rnas Are Widespread Throughout the Bacterial Kingdommentioning

confidence: 99%

Section: S Rna – a Template For Prna Synthesismentioning

confidence: 99%

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6S RNA, a Global Regulator of Transcription

Wassarman

2018

Microbiol Spectr

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“…Non-proteincoding genes also control gene expression during the transition to stationary phase (Mika and Hengge, 2013;Sedlyarova et al, 2016;Weiss et al, 2016). One example is the non-coding 6S RNA (Cavanagh et al, 2010;Elkina et al, 2017). 6S RNA shows growth phasedependent expression, interacts with the primary sigma factor (sigma-70) and regulates transcription of many sigma-70-dependent genes including the relA gene encoding a synthase of ppGpp, a secondary messenger molecule capable of triggering the stringent response (Cavanagh et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

McIntosh

Eisenhardt

Remes

et al. 2019

Environmental Microbiology

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Summary Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon‐limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS‐like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.

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“…However, interdependent expression of genes around the 6S RNA locus was noticed for other bacteria, e.g. R. sphaeroides (Proteobacteria), where a salt stress-induced membrane protein gene on the opposite strand immediately downstream of the 6S RNA locus is expressed at elevated levels in a 6S RNA knockout strain [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Insights into 6S RNA in lactic acid bacteria (LAB)

et al. 2021

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Background 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. Results We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. Conclusions Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.

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6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype

Cited by 15 publications

References 51 publications

6S RNA, a Global Regulator of Transcription

6S RNA, a Global Regulator of Transcription

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

Insights into 6S RNA in lactic acid bacteria (LAB)

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