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Expression data from control and colicin M treated E. coli MG1655 culture

ABSTRACT: Among colicin producing E. coli, colicin M producing strains are the most frequently present in natural populations. Bacteria must be able to sense and respond to unfavourable conditions, resulting in adaptive responses. To gain insight into colicin M ecological role and the purposes related to antimicrobial therapy, the effects of subinhibitory concentrations of colicin M on E. coli whole genome transcription was investigated. We used microarray analysis to follow differential gene expression in E. coli upon colicin M exposure. Colicin M inhibits peptidoglycan synthesis altering expression of genes involved in envelope stress, osmotic and other stresses, exopolysaccharide prodoction, biofilm formation, and cell motility. A sub-lethal concentration of colicin M was used to treat E. coli MG1655 cultures at an early logarithmic phase. The experiments were performed in parallel with untreated control E. coli MG1655 cultures. Total RNA was extracted after 30 min and 60 min treatment with colicin M and used for hybridization on Affymetrix microarrays.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: simona kamensek

PROVIDER: E-GEOD-37026 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from control and colicin M treated E. coli MG1655 culture

Project description:Among colicin producing E. coli, colicin M producing strains are the most frequently present in natural populations. Bacteria must be able to sense and respond to unfavourable conditions, resulting in adaptive responses. To gain insight into colicin M ecological role and the purposes related to antimicrobial therapy, the effects of subinhibitory concentrations of colicin M on E. coli whole genome transcription was investigated. We used microarray analysis to follow differential gene expression in E. coli upon colicin M exposure. Colicin M inhibits peptidoglycan synthesis altering expression of genes involved in envelope stress, osmotic and other stresses, exopolysaccharide prodoction, biofilm formation, and cell motility.

2012-11-26 | GSE37026 | GEO

Expression analysis of Escherichia coli CC72 before and after osmotic stress

Project description:Expression level of whole genome genes in Escherichia coli CC72 at early-exponential phase, and 10 min, 20 min and 45 min after osmotic stress. Venus was fused to the 3' end of rpoC in E. coli MG1655 to localize RNA polymerase as reported previously (C. Cagliero and D. J. Jin, 2013).

2018-04-11 | GSE110730 | GEO

Expression analysis of Escherichia coli MG1655 K-12 WT and M-bM-^HM-^Ffnr mutant

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.

2013-06-20 | E-GEOD-41189 | biostudies-arrayexpress

Expression analysis of Escherichia coli MG1655 K-12 WT and M-bM-^HM-^FarcA mutant

Project description: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.

2013-10-17 | E-GEOD-46412 | biostudies-arrayexpress

Transcriptional profiling of E. coli K-12 and E. coli O157 (Sakai) following heat shock at 45 degree celsius

Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more resistant to heat stress than MG1655. A microarray study of these strains subjected to sub-lethal heat-stress at 45M-BM-0C was carried out. In E. coli O157 (Sakai), 380 genes responded significantly to the treatment compared to 410 genes in MG1655. Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37M-BM-0C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask flask was transferred to a shaking water bath and incubated at 45M-BM-0C for 10 min; the other flask was incubated at 37M-BM-0C for 10 min. After incubation, the cultures were transferred to 50 mL centrifuge tubes and treated with RNAprotectM-bM-^DM-" to stabilise the mRNA. The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from untreated and heated E. coli O157 (Sakai) or MG1655.

2018-03-20 | E-MTAB-5912 | biostudies-arrayexpress

Expression analysis of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA from aerobic and anaerobic growth conditions

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.

2013-06-20 | E-GEOD-46144 | biostudies-arrayexpress

RNA-seq data of Escheirchia coli K12 MG1655 of overexpression of GcvB, MicA, ArcZ, RyhB or CyaR sRNAs

Project description:To study the regulatory outcome of Hfq-mediated sRNA-target interactions, we measured the change in gene expression following overexpression of each of five well-established sRNAs: GcvB, MicA, ArcZ, RyhB and CyaR. For each of the studied sRNAs we applied RNA-seq to two E. coli K-12 MG1655 strains: (1) a WT strain or a strain deleted of the sRNA gene; (2) a strain overexpressing the sRNA, either artificially from a plasmid or from the endogenous sRNA gene by changing the growth condition. For GcvB induction, the E. coli K-12 MG1655 Z1 gcvB::Cm, pZA12-gcvB and the E. coli K-12 MG1655 Z1 gcvB::Cm, pTP-011 strains were used. For MicA overexpression the E. coli K-12 MG1655lacIq pBRplac, pEF21-Hfq and the E. coli K-12 MG1655lacIq pMicA, pEF21-Hfq strains were used. For ArcZ induction the E. coli K-12 MG1655 Z1 arcZ::Cm, pZE12-ArcZ and the E. coli K-12 MG1655 Z1 arcZ::Cm, pJV300 strains were used. For RyhB overexpression the E. coli K-12 MG1655 ryhB::Cm and the E. coli K-12 MG1655 were used. For CyaR induction the E. coli K-12 MG1655 Z1 cyaR::Cm, pZE12-CyaR and the E. coli K-12 MG1655 Z1 cyaR::Cm, pJV300 strains were used. All E. coli strains used in this study were grown overnight in Luria Bertani (LB) medium at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB medium, and re-grown with shaking at 37 °C to exponential phase, for GcvB (OD600 = 0.3) and for RyhB (OD600 = 0.5), or to stationary phase, for ArcZ WT, ArcZ M1, ArcZ M2 and CyaR (OD600 = 1.0) and for MicA (grown for 6 hr). For induction of ArcZ and GcvB, IPTG was added (1mM, 20 min). MicA was constitutively expressed and further induced at the end of growth with IPTG (1mM, 20 min). For induction of RyhB, the iron chelator 2,2'-Dipyridyl was added (200 μM, 30 min).

2020-03-03 | E-MTAB-8229 | biostudies-arrayexpress

High-throughput Solexa sequencing of total RNA from Escherichia coli wild type and M-bM-^HM-^Ffnr strain (PK4854)

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".

2013-06-20 | E-GEOD-41190 | biostudies-arrayexpress

Sphingomonas elodea

Project description:Exopolysaccharide-producing bacterium

| PRJNA15728 | ENA

ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and M-bM-^HM-^FarcA strains

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.

2013-10-17 | E-GEOD-46413 | biostudies-arrayexpress

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