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Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)

ABSTRACT: Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)

PROVIDER: PRJNA487827 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7754372.fastq.gz	Fastqsanger.gz
	SRR7754373.fastq.gz	Fastqsanger.gz
	SRR7754374.fastq.gz	Fastqsanger.gz
	SRR7754375.fastq.gz	Fastqsanger.gz
	SRR7754376.fastq.gz	Fastqsanger.gz

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Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)

Project description:The goal of this study was to compare system level changes in gene-expression in naturally isolated alleles of stationary-phase sigma factor rpoS and two variants of it isolated during evolution under prolonged stationary-phase. We show that while rpoS819 was an attenuated form of wild type rpoS, rpoS92 partially reverses rpoS819 expression compensating rpoS819.

2018-08-25 | GSE119046 | GEO

RpdD and RpoS ChIP-exo in Klebsiella pneumoniae

Project description:With increasingly concerning strains of antimicrobial resistant strains of the commensal, gram-negative bacteria Klebsiella pneumoniae emerging, there is a pressing need to better understand the pathogen and mechanisms behind its pathogenicity. This study investigated the regulatory mechanisms in strain MGH 78578 of two major sigma factors, the house-keeping sigma factor RpoD, and the general stress response sigma factor RpoS, in mid-exponential and early stationary phase using chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) followed by deep sequencing. Combining ChIP-exo and transcriptome analysis allowed for the determination of sigma factor binding sites, binding motifs, and genes included in the phase-specific sigmulons. The number of genes included in the RpoS sigmulon was greater than in the RpoD sigmulon, with 1,833 and 1,690 genes included, respectively; however, a majority of sigmulon genes were found in all phase-specific sigmulons. Focussing on pathogenicity genes, 20 antimicrobial resistance genes (ARGs) and 155 virulence genes, only two ARGs were found exclusively in one phase-specific sigmulon, an oxacillin-hydrolysing class D beta-lactamase and chloramphenicol efflux MFS transporter CmlA5, which were found in the RpoD sigmulon in early stationary phase. Notably, six unnamed proteins that are or pertain to fimbrial proteins were found uniquely in the RpoS sigmulon in early stationary phase. From this, it can be hypothesised that early stationary phase might be an important phase for pathogenicity gene regulation. While there is little conservation in RpoS sigmulons from strain to strain, RpoS appears to have a consistent overarching role across strains, including a role as a regulator of pathogenicity genes.

2025-02-24 | GSE226119 | GEO

ChIP-seq of Escherichia coli RpoS during stationary phase

Project description:To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the Escherichia coli chromosome during stationary phase growth in minimal medium. To facilitate ChIP, RpoS was C-terminally SPA-tagged at its native locus.

2016-12-23 | E-MTAB-5339 | biostudies-arrayexpress

BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type

Project description:E. coli K-12 BW25113 persister cells generated via H202 pre-treatment and deletion of rpoS, relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2012-04-03 | GSE34028 | GEO

ChIP-seq of Escherichia coli RpoS during stationary phase

Project description:ChIP-seq of Escherichia coli RpoS during stationary phase

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Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

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Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose

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Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

Project description:RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli.RpoS also acts as a global regulator for stress control of gene expression, and actually dose so in log stage and stationary stage. To further understand the effect of environmental stresses on in ethanologenic strains, DNA microarrys was used to analyze the expression profiles of E. coli and its rpoS mutant strain. BW25113（rpoS-）and BW25113 were selected at log stages and stationary stage of early development for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected BW25113 and BW25113（rpoS-） according at different treatments: BW25113（rpoS-）at log stage (BW25113(rpoS-) log), BW25113 at log stage (BW25113 log),BW25113（rpoS-）atstationary stage ( BW25113(rpoS-) stationary), BW25113 at stationary stage ( BW25113 stationary)

2010-07-20 | E-GEOD-17526 | biostudies-arrayexpress

The timing of transcription of RpoS-dependent genes varies across multiple stresses

Project description:The alternative sigma factor RpoS regulates transcription of many genes in Escherichia coli in response to many different stresses. The rate of change of RpoS levels in response to stress, and the consequences of that change for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured the temporal pattern of RpoS levels in response to the entry to stationary phase, high osmolarity, or low temperature. We found that RpoS levels peaked 50 minutes after osmolarity increased, but took 240 minutes to peak in response to lowered temperature. We quantified the transcriptome across these stresses using RNA-seq. Stresses differed in the number of differentially expressed genes, with 1379 DE genes were identified in in stationary phase, 633 in high osmolarity, and 302 in cold shock. We attempted to fit sigmoid or double sigmoid models to each individual differentially expressed genes in each stress, and fit 47 to 62% of all DE genes, depending on the stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS.The timing of individual genes expression was not correlated across stresses. Taken together, our results demonstrate E. coli activates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response in each stress.

2023-08-23 | GSE224463 | GEO

Control of RpoS in global gene expression of Escherichia coli in minimal media

Project description:RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. coli grown in glucose minimal media using microarray analyses. The expression of over 200 genes was altered by loss of RpoS in exponential and stationary phases, with only 48 genes common to both conditions. The nature of the RpoS-controlled regulon in minimal media was substantially different from that expressed in rich media. Specifically, the expression of many genes encoding regulatory factors (e.g., hfq, csrA and rpoE) and genes in metabolic pathways (e.g., lysA, lysC and hisD) were regulated by RpoS in minimal media. In early exponential phase, protein levels of RpoS in minimal media were much higher than that in LB media, which may at least partly account for the observed difference in the expression of RpoS-controlled genes. Expression of genes required for flagellar function and chemotaxis was elevated in the rpoS mutant. Western blot analyses show that the flagella sigma factor FliA was expressed much higher in rpoS mutants than in WT in all phase of growth. Consistent with this, the motility of rpoS mutants was enhanced relative to WT. In conclusion, RpoS and its controlled regulators form a complex regulatory network that mediates the expression of a large regulon in minimal media.

2008-10-10 | GSE12797 | GEO

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