Project description:The mechanism of evolution in different conditions can be examined from various molecular aspects that constitute a cell, namely, transcript, protein or metabolite abundance. We have analyzed transcript and metabolite abundance changes in evolved and ancestor strains in three different evolutionary conditions, namely, excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift, in two different strains of Escherichia coli K-12 (MG1655 and DH10B).
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.
Project description:The RpoS sigma factor protein of Escherichia coli is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they are evolved in an osmotically stressful environment. We found that strains lacking RpoS adapt less variably, in terms of both fitness increase and changes in patterns of transcription, than strains with functional RpoS. This phenotypic uniformity was caused by the same adaptive mutation in every independent population: the insertion of IS10 into the promoter of otsBA. OtsA and OtsB are required to synthesize the osmoprotectant trehalose, and transcription of otsBA requires RpoS in the wild-type genetic background. The evolved IS10 insertion rewires expression of otsBA from RpoS-dependent to RpoS-independent, allowing for partial restoration of wild-type response to osmotic stress. Our results show that the regulatory networks of bacteria Keywords: evolution; expression This study started with wild-type and rpoS- strains, and evolved five lines from each, for a total of 12 strains. Expression was measured for each strain with two separate biological replicates of RNA
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.
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:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after chorismate synthase knockouts. Either isochorismate synthase (menF) or isochorismate synthase AND chorismate lyase (ubiC) was deleted from a strain of E. coli K-12 MG1655 that had already been previously adapted for growth on glucose minimal media. RNA-seq profiles of the original glucose-adapted strain, the 2 deletion strains, and 4 laboratory-evolved strains from each deletion are included in duplicate. ubiC catalyzes the first committed step of ubiquinone synthesis, an important molecule for the electron transport chain. Thus, these experiments allowed assessment of cellular adaptations to restore energy metabolism capability.
