Expression analysis of Escherichia coli MG1655 K-12 WT and M-bM-^HM-^FarcA mutant
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ABSTRACT: Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^FarcA mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the ArcA protein. The results are further described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli A six chip study using total RNA recovered from three separate cultures of Escherichia coli MG1655 K-12 WT and three separate cultures of the M-bM-^HM-^FarcA mutant strain. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding. A four chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA mutant strain under aerobic and anaerobic growth conditions. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 using a high-density tiling array consisting of ~385,000 60mer probes spaced every 12 bp.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions. A six chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT (aerobic and anaerobic) and two separate cultures of the ?fnr mutant strain (anaerobic). Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆arcA mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the ArcA protein. The results are further described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a M-bM-^HM-^FarcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli Mapping of occupancy of ArcA in the genome of Escherchia coli MG1655 K-12 during anaerobic fermentation and aerobic respiration. Immunoprecipitated DNA compared to INPUT for each sample.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Ffnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. A RNA-seq study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT and two separate cultures of the M-bM-^HM-^Ffnr mutant strain.The results are further described in the article "Genome-scale Analysis of E.coli FNR Revealse the Complexity of Bacterial Regulon Structure".
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 nsrR with AUG start codon compared to the wild type nsrR (with a GUG start codon) and to the control lacking the nsrR gene. Conversion of the nsrR start codon from the wild type GUG to AUG increased the efficiency of translation and had measurable effects on the expression patterns of some NsrR regulated genes. A nine chip study using total RNA recovered from three separate cultures of Escherichia coli MG1655 K-12 AUGnsrR, three separate cultures of the WT nsrR (GUGnsrR) and three separate cultures of nsrR deletion strain. Each chip measures the expression level of 4,254 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with 2-fold technical redundancy.
Project description:Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.
Project description:Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network. We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArcA and Fnr regulons experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring ArcA-8myc or Fnr-8myc under various conditions. The E. coli strains harboring Fnr-8myc and ArcA-8myc were generated as described previously [PMID 16454042]. A 12 chip study with two different strains under two different culture conditions.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein.