Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity
Ontology highlight
ABSTRACT: We generated four strains of Escherichia coli K12 MG1655 with distinct proton motive force generation potential and performed the adaptive laboratory evolution of these strains to study how the system adapts to the loss of alternate electron transfer pathways of the Electron Transport System. RNA-Seq was performed to examine the underlying transcriptional rewiring.
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655
Project description:We performed evolution of Escherichia coli K12 MG1655 to study how the system adapts to loss of ubiC gene involved in ubiquinone biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.
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.
Project description:Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity
Project description:Geobacter sulfurreducens has a complex metabolism that adapts to use electron acceptors at a wide range of redox potentials. In this study, we used RNA-seq to identify genes associated with electron transfer pathways at different redox potentials. By correlating the RNA-seq data with cyclic voltammetry, we associated several multiheme cytochromes with specific electron transfer pathways.
Project description:The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. There is a detailed understanding of the structural and biochemical features of respiratory enzymes; however, a holistic examination of the system and its plasticity is lacking. Here we generate four strains of Escherichia coli harboring unbranched ETS that pump 1, 2, 3, or 4 proton(s) per electron and characterized them using a combination of synergistic methods (adaptive laboratory evolution, multi-omic analyses, and computation of proteome allocation). We report that: (a) all four ETS variants evolve to a similar optimized growth rate, and (b) the laboratory evolutions generate specific rewiring of major energy-generating pathways, coupled to the ETS, to optimize ATP production capability. We thus define an Aero-Type System (ATS), which is a generalization of the aerobic bioenergetics and is a metabolic systems biology description of respiration and its inherent plasticity.
Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains
Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.