Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis.

ABSTRACT: 6S RNAs function through interaction with housekeeping forms of RNA polymerase holoenzyme (Eσ(70) in Escherichia coli, Eσ(A) in Bacillus subtilis). Escherichia coli 6S RNA accumulates to high levels during stationary phase, and has been shown to be released from Eσ(70) during exit from stationary phase by a process in which 6S RNA serves as a template for Eσ(70) to generate product RNAs (pRNAs). Here, we demonstrate that not only does pRNA synthesis occur, but it is an important mechanism for regulation of 6S RNA function that is required for cells to exit stationary phase efficiently in both E. coli and B. subtilis. Bacillus subtilis has two 6S RNAs, 6S-1 and 6S-2. Intriguingly, 6S-2 RNA does not direct pRNA synthesis under physiological conditions and its non-release from Eσ(A) prevents efficient outgrowth in cells lacking 6S-1 RNA. The behavioral differences in the two B. subtilis RNAs clearly demonstrate that they act independently, revealing a higher than anticipated diversity in 6S RNA function globally. Overexpression of a pRNA-synthesis-defective 6S RNA in E. coli leads to decreased cell viability, suggesting pRNA synthesis-mediated regulation of 6S RNA function is important at other times of growth as well.

SUBMITTER: Cavanagh AT

PROVIDER: S-EPMC3299989 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Identification of a highly efficient stationary phase promoter in Bacillus subtilis.

Project description:A promoter that enabled high-level expression of the target gene during the stationary phase in the absence of an inducer would facilitate the efficient production of heterogeneous proteins at a low cost. In this study, a genome-scale microarray-based approach was employed to identify promoters that induced high-level expression of the target genes in Bacillus subtilis from the late log phase to the stationary phase without an inducer. Eleven candidate promoters were selected based on B. subtilis microarray data and the quantitative PCR analysis. Among the selected promoters, Pylb exhibited the highest activity with the reporter bgaB during the stationary phase. Compared with P43 (a commonly used constitutive promoter), promoter Pylb could express two reporter genes (egfp and mApple), and the expression levels of EGFP and RFP were 7.8- and 11.3-fold higher than that of P43, respectively. This finding was verified by overexpression of the genes encoding pullulanase and organophosphorus hydrolase, the activities of which were 7.4- and 2.3-fold higher, respectively, when driven by Pylb compared with P43. Therefore, our results suggest that the Pylb promoter could be used to overexpress target genes without an inducer; this method could facilitate the identification and evaluation of attractive promoters in the genome.

| S-EPMC4682092 | biostudies-literature

A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.

Project description:Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ(A)-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5'-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ(A)-RNAP. Among the pRNA length variants synthesized by σ(A)-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ(A)-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.

| S-EPMC3321203 | biostudies-literature

Environmental dependence of stationary-phase metabolism in Bacillus subtilis and Escherichia coli.

Project description:When microbes lack the nutrients necessary for growth, they enter stationary phase. In cases when energy sources are still present in the environment, they must decide whether to continue to use their metabolic program to harvest the available energy. Here we characterized the metabolic response to a variety of types of nutrient starvation in Escherichia coli and Bacillus subtilis. We found that E. coli exhibits a range of phenotypes, with the lowest metabolic rates under nitrogen starvation and highest rates under magnesium starvation. In contrast, the phenotype of B. subtilis was dominated by its decision to form metabolically inactive endospores. While its metabolic rates under most conditions were thus lower than those of E. coli, when sporulation was suppressed by a genetic perturbation or an unnatural starvation condition, the situation was reversed. To further probe stationary-phase metabolism, we used quantitative metabolomics to investigate possible small-molecule signals that may regulate the metabolic rate of E. coli and initiate sporulation in B. subtilis. We hypothesize a role for phosphoenolpyruvate (PEP) in regulating E. coli glucose uptake and for the redox cofactors NAD(H) and NADP(H) in initiation of sporulation. Our work is directly relevant to synthetic biology and metabolic engineering, where active metabolism during stationary phase, which uncouples production from growth, remains an elusive goal.

| S-EPMC3993301 | biostudies-literature

Stationary-phase regulation of RpoS translation in Escherichia coli.

Project description:In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonella enterica, SP induction of RpoS in rich medium is >30 fold and includes effects on both transcription and translation. Recently, we found that SP control of rpoS transcription in S. enterica involves repression of the major rpoS promoter during exponential phase by the global transcription factor Fis. Working primarily with E. coli, we now show that 24 nucleotides of the rpoS ribosome-binding site (RBS) are necessary and sufficient for a large part of the increase in rpoS translation as cells grow to SP. Genetic evidence points to an essential role for the leader nucleotides just upstream of the Shine-Dalgarno sequence but is conflicted on the question of whether sequence or structure is important. SP regulation of rpoS is conserved between E. coli and S. enterica. When combined with an fis mutation to block transcriptional effects, replacement of the rpoS RBS sequence by the lacZ RBS eliminates nearly all SP induction of RpoS.

| S-EPMC1272984 | biostudies-literature

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.

Project description:The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic ?-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ? 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ?ssrS strain when grown in the presence of 250 mM NaCl.

| S-EPMC5785217 | biostudies-literature

Recovery from stationary phase in LB + 0.2 % glucose

Project description:Responses of Escherichia coli as they recover from one stationary phase in rich media Keywords: time course

2006-03-08 | GSE4363 | GEO

Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase.

Project description:Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb_rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase.

| S-EPMC9931155 | biostudies-literature

Survival guide: Escherichia coli in the stationary phase.

Project description:This review centers on the stationary phase of bacterial culture. The basic processes specific to the stationary phase, as well as the regulatory mechanisms that allow the bacteria to survive in conditions of stress, are described.

| S-EPMC4717247 | biostudies-literature

Escherichia coli proteome during stationary phase

Project description:The aim of this study was to determine the fate of ribosomes and r-proteins. In this respect, SILAC (Stable Isotope Labeled Amino acids in cell Culture) based experimental approach was used. E.coli cells were grown in MOPS medium supplemented with “heavy” labeled arginine (Arg10) and lysine (Lys8). At the mid-log phase, the culture was further supplemented with a 20-fold molar excess of “light” unlabeled arginine (Arg0) and lysine (Lys0), divided into 8 aliquots, and grown for 14 days. Cell samples were collected at day one (24h), day two (48h), and subsequently in 48h intervals over the following 12 days. The quantities of r-proteins in the proteome were determined using SILAC based LC-MS/MS and normalized to the corresponding values of day one.

2023-10-10 | PXD035927 | Pride

Bacillus subtilis WN715 vs WN716 expression in early stationary phase.

Project description:Five batch cultures of Bacillus subtilis were subjected to laboratory evolution for 6,000 generations under conditions repressing sporulation in complex liquid medium containing glucose. Between 1,000 and 2,000 generations, variants with a distinct small-colony morphology arose and swept through four of the five populations. To understand the nature of adaptation in these variants, individual strains were isolated from one population before (WN715) and after (WN716) the sweep. In addition to colony morphology, strains WN715 and WN716 differed in their motility, aerotaxis, and cell morphology. Competition experiments of WN715 vs. WN716 showed that WN716 had gained a distinct fitness advantage during growth and the transition to stationary phase, which was more pronounced when WN715 was present in co-culture. Microarray analyses revealed candidate genes in which mutations may have produced some of the observed phenotypes.

2010-09-09 | GSE24018 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data