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Iterative genome engineering of E. coli for fed-batch production of L-tyrosine.

ABSTRACT: In this project we aim to construct a tyrosine-producing E. coli strain through iterative steps of genome engineering. High PEP availability through knockout of the PTS was combined with the precise, in-place genomic integration of several engineering interventions, known to increase L-tyrosine production yields, to create a tyrosine-overproducing E. coli strain that can function as a platform for further engineering and optimization. Utilizing a design-build-test-learn (DBTL) cycle, an evolved pts-knockout E. coli strain was equipped with optimizations of the aroG, aroB and tyrA genes and cultivated under batch and fed-batch conditions. Subsequently, metabolomics, transcriptomics and proteomics samples from the fed-batch experiments were analyzed to inform the design of new genomic interventions.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE264483 | GEO | 2025/07/01

REPOSITORIES: GEO

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Project description:Nishio2008 - Design of the phosphotransferase system for enhanced glucose uptake in E. coli. This model is described in the article: Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Nishio Y, Usuda Y, Matsui K, Kurata H. Mol. Syst. Biol. 2008; 4: 160 Abstract: The phosphotransferase system (PTS) is the sugar transportation machinery that is widely distributed in prokaryotes and is critical for enhanced production of useful metabolites. To increase the glucose uptake rate, we propose a rational strategy for designing the molecular architecture of the Escherichia coli glucose PTS by using a computer-aided design (CAD) system and verified the simulated results with biological experiments. CAD supports construction of a biochemical map, mathematical modeling, simulation, and system analysis. Assuming that the PTS aims at controlling the glucose uptake rate, the PTS was decomposed into hierarchical modules, functional and flux modules, and the effect of changes in gene expression on the glucose uptake rate was simulated to make a rational strategy of how the gene regulatory network is engineered. Such design and analysis predicted that the mlc knockout mutant with ptsI gene overexpression would greatly increase the specific glucose uptake rate. By using biological experiments, we validated the prediction and the presented strategy, thereby enhancing the specific glucose uptake rate. This model is hosted on BioModels Database and identified by: BIOMD0000000571. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Iterative genome engineering of E. coli for fed-batch production of L-tyrosine.

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