Transcriptomic data of CRP(T168P) and AC(S254R) mutant strain of E. coli W
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ABSTRACT:
PROVIDER: PRJNA682349 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13190159_1.fastq.gz | Fastqsanger.gz | |||
| SRR13190159_2.fastq.gz | Fastqsanger.gz | |||
| SRR13190160_1.fastq.gz | Fastqsanger.gz | |||
| SRR13190160_2.fastq.gz | Fastqsanger.gz | |||
| SRR13190161_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:CRP(T168P) and AC(S254R) mutant strain of E. coli W
| PRJNA682346 | ENA
Project description:Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene with a catabolite repression mutant (referred to as crp*) alleviates diauxic effects in E. coli and enables co-utilization of glucose and other sugars. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression. In this study, we compare the transcriptome of E. coli W3110 (expressing wild-type CRP) to that of mutant strain PC05 (expressing CRP*) in the presence and absence of glucose.
2009-08-12 | GSE17584 | GEO
Project description:Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene with a catabolite repression mutant (referred to as crp*) alleviates diauxic effects in E. coli and enables co-utilization of glucose and other sugars. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression. In this study, we compare the transcriptome of E. coli W3110 (expressing wild-type CRP) to that of mutant strain PC05 (expressing CRP*) in the presence and absence of glucose. Experiment Overall Design: Four different conditions were tested in this study: W3110 in LB medium (WT), W3110 in LB+glucose medium (WT G), PC05 in LB medium (CRP*), and PC05 in LB+glucose medium (CRP* G).
2009-08-21 | E-GEOD-17584 | biostudies-arrayexpress
Project description:Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. Our study provides a new perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
2021-08-23 | GSE162595 | GEO
Project description:As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation by the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutation in the gene encoding the cyclic AMP receptor protein, Crp*, has been shown to disable CCR and improve co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site specific crp* chromosomal mutant in E. coli BL21 starTM (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomic analysis further showed that cells link xylose consumption to energy production through the de novo nucleotide synthesis pathway, explaining the relatively slower growth of the crp* mutant strain. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.
| MSV000092810 | MassIVE
Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains
2016-12-13 | GSE92255 | GEO
Project description:We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ϕYS40. Keywords: time course, bacteriophage, infection, CRP, cAMP receptor protein, deletion mutant
2009-11-03 | GSE16955 | GEO
Project description:Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, DMSO, or Fe(III), whereas the deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III), and to a lesser extent with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and the cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways that include DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagella biosynthesis, and electron transport, were differentially expressed in the cyaC mutant, but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration, and may contribute to additional signaling pathways independent of CRP. To explore the roles of CyaC and CRP in the regulation of anaerobic respiration in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles of ÎcyaC and Îcrp mutants were compared to those of the wild type. Given the growth deficiencies displayed by Îcrp and ÎcyaC under anaerobic conditions, all strains were cultured in chemostats under O2 limitation. Since both Îcrp and ÎcyaC strains are not impaired in aerobic respiration, oxygen-limited conditions provided the means to maintain equal growth rates (0.06 h-1) among the mutant and wild-type strains thus eliminating the effect of growth on the overall transcriptome profiles. At the same time, while growing aerobically, the cells decreased dissolved O2 concentration in the medium below the detection threshold (DOTâ¤1%) allowing for the expression of anaerobic respiratory genes. The latter was confirmed by the reduction of fumarate by the wild-type culture which produced stoichiometric amounts of succinate under O2-limited conditions. The optical density (OD600) of the wild type, ÎcyaC, and Îcrp chemostat cultures used for transcriptome profiling was 0.50, 0.45 and 0.40, respectively. All the experiments were carried out in duplicate.
2010-06-19 | E-GEOD-15657 | biostudies-arrayexpress
Project description:The goal of this analysis is to define the anaerobic regulon for the global transcription factor CRP (catabolite repressor protein) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the CRP gene. Both strains were grown anaerobically.
2011-06-01 | GSE25459 | GEO
Project description:To understand the influence of global transcription regulators Fis and CRP on global gene expression in different growth phases of E. coli.
2017-10-03 | GSE104504 | GEO