Project description:The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulation network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach. We determined the gene expression of four different strains of E. coli on three different media. The four strains corresponded to the wild-type E. coli (LJ110), a PdhR knockout mutant (LJ110deltapdhR), a strain carrying an empty plasmid (LJ110/pTM30) and a PdhR overexpression strain (LJ110/pTM30PdhRhis). These strains were cultivated on Luria-Bertani broth (LBo), standard phosphate minimal medium supplemented with acetate and standard phosphate minimal medium supplemented with pyruvate. We obtained an overall 24 microarray experiments from two replicates of each of these cultivations.
Project description:The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulation network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach.
Project description:We conducted whole genome sequencing on eight evolved E. coli strains (S1–S8) and the parental wild-type (WT) strain to identify mutations arising from ofloxacin treatments. These strains (S1-S8), generated through fluoroquinolone-mediated adaptive laboratory evolution (ALE), exhibited varying levels of tolerance and resistance. The ALE experiment involved intermittent antibiotic treatments of eight independent cultures over 22 days. The untreated WT strain served as a baseline to pinpoint mutations in the evolved strains.
Project description:We have performed adaptive laboratory evolution of E. coli pdhR gene deletion strain to examine the adaptive strategies of E. coli.
Project description:A strain of Acetivibrio thermocellus (colloquially, Clostridium thermocellum) DSM 1313 capable of growing in xylose was created by both rational engineering and adaptive laboratory evolution (ALE) approaches. This RNA-seq experiment compares the transcriptomes of the pre-ALE strain on native substrate with the pre-ALE and post-ALE strains growing in xylose (or xylose plus xylan). These data show the progression of the initially engineered strain from normal growth with a native substrate, to debilitated growth in the new engeered substrate, to improved growth on the engineered substrate after ALE. Genes of various biological functions are found to undergo coordinated changes at various stages of the engineering & ALE campaign. These correlations shed light on the state of the cell at each stage. All together, these data paint a picture of the strain initially undergoing a stress state, which is eventually overcome through ALE. Many of these changes dissipate in the fast growing strain, leaving only permanent changes that enable growth on xylose.