Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA.
Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.
Project description:Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0. This analysis suggests that C8 challenge causes intracellular acidification and membrane damage.
Project description:Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0. This analysis suggests that C8 challenge causes intracellular acidification and membrane damage. Escherichia coli MG1655 was grown to midlog (OD550 ~0.8) with or without 10 mM octanoic acid (pH=7.0) and the RNA was harvested and prepared for Affymetrix Microarray analysis.
Project description:Biosynthesis of carboxylic acids and fatty acids from renewable biomass is a key issue in biorefinery. However, their productivities are often limited due to various toxic effects of the products on the host organisms. Here, we have investigated the factors that influence tolerance of Escherichia coli to long chain carboxylic acid (e.g., n-heptanoic acid)-induced stress by using transcriptome analysis. The metabolic and genomic responses of E. coli BL21 and MG1655 strains with n-heptanoic acid indicated that acid stress is one of the major stresses, which might be generated by n-heptanoic acid in addition to the presumed solvent-like stress.
Project description:Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.
Project description:Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [ChIP-Seq]
Project description:Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]