Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA139341 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Housekeeping sigma factors in the Sigma70 family, as components of the RNA polymerase holoenzyme, are responsible for regulating transcription of genes related to vegetative growth. While these factors are well understood in model organisms such as Escherchia coli and Bacillus subtilis, little experimental work has focused on the sigma factors in members of the Lactobacillus genus such as Lactobacillus brevis and Lactobacillus plantarum. This study evaluates the ability of putative Sigma70 proteins from L. brevis (Sigma70-Lb) and L. plantarum (Sigma70-Lp) to complement a temperature sensitive mutation in E. coli 285c Sigma70. After finding that the heterologous sigma factors were capable of restoring the viability of E. coli 285c at 42 C through growth kinetics studies, the transcriptional responses of 285c to an extended heat shock in the presence of Sigma70-Lb and Sigma70-Lp were found to be similar to previous studies. These results indicate the Sigma70-Lb and Sigma70-Lp are capable of initiating transcription in a complex with the E. coli 285c RNA polymerase to a sufficient degree to restore viability at elevated temperatures without triggering unusual modifications to the native transcriptional program. These heterologous sigma factors may therefore be useful to improve biochemical knowledge of the sigma factor family or for use in transcriptional engineering.
2011-12-31 | GSE28320 | GEO
Project description:Housekeeping sigma factors in the Sigma70 family, as components of the RNA polymerase holoenzyme, are responsible for regulating transcription of genes related to vegetative growth. While these factors are well understood in model organisms such as Escherchia coli and Bacillus subtilis, little experimental work has focused on the sigma factors in members of the Lactobacillus genus such as Lactobacillus brevis and Lactobacillus plantarum. This study evaluates the ability of putative Sigma70 proteins from L. brevis (Sigma70-Lb) and L. plantarum (Sigma70-Lp) to complement a temperature sensitive mutation in E. coli 285c Sigma70. After finding that the heterologous sigma factors were capable of restoring the viability of E. coli 285c at 42 C through growth kinetics studies, the transcriptional responses of 285c to an extended heat shock in the presence of Sigma70-Lb and Sigma70-Lp were found to be similar to previous studies. These results indicate the Sigma70-Lb and Sigma70-Lp are capable of initiating transcription in a complex with the E. coli 285c RNA polymerase to a sufficient degree to restore viability at elevated temperatures without triggering unusual modifications to the native transcriptional program. These heterologous sigma factors may therefore be useful to improve biochemical knowledge of the sigma factor family or for use in transcriptional engineering. 3 biological replicates per sigma factor
2011-12-31 | E-GEOD-28320 | biostudies-arrayexpress
Project description:Time course experiment to analyze transcriptional changes to the E. coli transcriptome due to overexpressing the heterologous sigma70 factor (RpoD) of Lactobacillus plantarum. A plasmid control strain (pControl) and the sigma70 overexpression strain (pLPLσ) were cultivated in parallel and after induction of RpoD expression samples for transcriptional profiling were taken in exponential, transition and stationary phase.
2015-03-18 | GSE66995 | GEO
Project description:The E. coli temperature-sensitive mutant of the ygjD gene incubated at 37M-0C.
2011-09-01 | E-MEXP-3334 | biostudies-arrayexpress
Project description:The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30M-0C.
2011-09-01 | E-MEXP-3333 | biostudies-arrayexpress
Project description:Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma factors. Three (sigma M, sigma W and simga X) mediate responses to cell envelope active antibiotics. The functions of sigma Y, sigma Z, sigma V, and YlaC remain largely unknown, and strong inducers of these sigma factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under non-stress conditions between strains carrying deletions in all seven ECF sigma factor genes (Δ7ECF), a sigMWX triple mutant (∆MWX), and the parental 168 strain. Our results identify >80 genes as at least partially dependent on ECF sigma factors and, as expected, most of these are dependent on sigma M, sigma W or sigma X which are active at a significant basal level during growth. Several genes, including the eps operon encoding enzymes for exopolysaccharide (EPS) production, were decreased in expression in Δ7ECF but affected little if at all in ΔMWX. Consistent with this observation, Δ7ECF (but not ∆MWX) showed reduced biofilm formation. Extending previous observations, we also note that ∆MWX is sensitive to a variety of antibiotics and Δ7ECF is either as sensitive as, or slightly more sensitive than, the ΔMWX strain to these stressors. These findings emphasize the overlapping nature of the seven ECF s factor regulons in B. subtilis, confirm that three of these (sigma M, W or X) play the dominant role in conferring intrinsic resistance to antibiotics, and provide initial insights into the roles of the remaining ECF sigma factors.
2010-07-21 | GSE22930 | GEO
Project description:These data were used to infer the genome-wide localization of sigma70 and core RNAP beta subunit for the study "The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate-limiting" (Reppas et al. 2006). This study analyzes transfrags with respect to the ChIP profile of the sigma70 and the beta subunit of RNA polymerase. Keywords: ChIP-chip; tiled analysis of mRNA expression
2006-10-19 | GSE6061 | GEO
Project description:Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that sigB and sigD genes are both induced in bright light and high temperature stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (SigD is an only functional group 2 σ factor), and ΔsigCDE (SigD is an only functional group 2 σ factor) strains in standard, bright light and high temperature conditions revealed that the SigB and SigD factors regulate different set of genes, and that SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas in bright light the SigD regulon is bigger the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors do not lead to superior acclimation to bright light or high temperature conditions, indicating that all group 2 σ factors play roles in acclimation processes.
2022-01-19 | GSE192357 | GEO
Project description:Characterization of the activities of the transcription factors that AP3 and PI encode throughout flower development using perturbation assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development. The series contains two types of perturbation experiments, static permutations (null alleles pi-1 and ap3-3, respectively) and dynamic perturbations (temperature-sensitive ap3-1 allele).
2012-06-01 | GSE38362 | GEO
Project description:The in vivo trafficking patterns on DNA by the bacterial regulators of transcript elongation Sigma70, Rho, NusA, and NusG and the explanation for high promoter-proximal levels or peaks of RNA polymerase (RNAP) are unknown. Genome-wide ChIP-chip on E. coli revealed distinct association patterns of regulators as RNAP transcribes away from promoters (Rho first, then NusA, and then NusG). However, the interactions of elongating complexes with these regulators, including a weak interaction with Sigma70, did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from Sigma70 peaks in the direction of transcription and co-occurred with NusA and Rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of Rho did not increase RNAP levels within genes downstream of the RNAP peaks, suggesting the peaks are caused by a mechanism other than simple Rho-dependent attenuation. Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta' subunit), Sigma70, NusA, NusG, or Rho. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~24bp spacing across the entire genome. The series contains 17 total datasets.
2010-05-14 | E-GEOD-13938 | biostudies-arrayexpress