Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase
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ABSTRACT: 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)
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.
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.
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 E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.
Project description:DNA microarrays were conducted on E. coli K12 cells stressed with 10 μM in N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Overall, 260 genes varied in expression, 114 up-regulated and 146 down-regulated by Zn deprivation Keywords: TPEN stress Array hybridizations were carried out for three RNA samples prepared from three independent cultures (control or TPEN-treated).
Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369 A 24 chip study using total RNA recovered from three separate wild-type cultures of Pectobacterium atrosepticum SCRI1043 and three separate cultures from three single mutant strains of SCRI1043 possessing deletions within relA (ECA3569), expI (ECA0105) or rpoS (ECA3530) when grown in Pel Minimal Broth (PMB) media to log-phase (6h) or early stationary phase (14h) growth. Each chip measures the expression level of 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
Project description:The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase. The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables. Experiment Overall Design: We used microarrays to investigate global bacterial gene expression in five genotypes of E. coli C600: WT (JO2057), hupA (JO2081), hupB (JO2083), hupAB (JO3020) and rpoS (MW30) at three growth growth phases: exponential, transition and stationary and in three growth media: LB, M9 minimal Glucose and M9 minimal Glycerol. The most relevant experiments were carried out in duplicate: the wild type (JO2057) and the hupAB (JO3020) strains were tested in the exponential and stationary phase, in LB. Wild type and hupAB strains were also tested in single experiments at the transition phase in LB. The single hupA (JO2081) and single hupB (JO2083) mutants were tested at the three growth phases in LB. Wild type and hupAB strains were compared in single experiments both in M9 Minimal Glucose and M9 Minimal Glycerol at the exponential and stationary phase. The last chips were used to test respectively the rpoS mutant at the at the exponential and stationary phase in LB.
Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition. A fourteen chip study using total RNA recovered from four separate culture conditions of E.coli K12 MG1655. E.coli strains were harvested at mid-exponential phase with exception of stationary phase experiments. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as three or more biological replicates (different cultures)