Microbial Metabolic Engineering and Bioproduction

This study identifies a new carbon fixation pathway in E. coli using only native enzymes and demonstrates its in vivo feasibility through genetic engineering.

This paper rationally engineers Kluyveromyces marxianus to produce 2-phenylethanol from minimal medium, demonstrating a platform for aromatic product synthesis.

This paper demonstrates the ability of Cupriavidus necator to produce sustainable chemicals from CO2 under lithotrophic conditions, including sucrose, PHAs, and LCOs.

This paper engineers Pseudomonas taiwanensis VLB120 to produce methyl ketones with a 4-fold higher titer than previous strains, achieving 9.8 g L-1.

This paper develops a high-yielding cell-free gene expression system from Clostridium autoethanogenum to enable in vitro prototyping of genetic parts and metabolic pathways.

MetaNetX/MNXref provides a unified namespace for metabolites and reactions, improving reconciliation between biochemistry databases and GSMNs with enhanced mapping tools.

This study uses a genome-scale metabolic model to design serum-free media for Mycoplasma pneumoniae, enabling growth and supporting vaccine production.

This study engineers yeast to produce phytosterols and reconstitutes downstream biosynthetic pathways, achieving measurable titers of several phytosterol derivatives.

This paper develops a multicriteria optimal control framework to predict enzyme activation and metabolite concentrations in complex metabolic pathways, demonstrating its application to yeast and Bacillus subtilis.

The paper modifies Escherichia coli MG1655 to create a more efficient host strain for chemical production by inactivating DNA defense systems, resulting in higher transformation efficiency and plasmid stability.

The paper updates a genome-scale metabolic model of CHO cells by adding new reactions and genes through gap-filling approaches, improving its predictive power.

The paper introduces mlLGPR, a multi-label logistic regression tool for metabolic pathway prediction using rich pathway features, and benchmarks its performance across diverse datasets.

The paper derives and validates a linear transform for correcting natural isotope abundance in metabolic flux analysis, showing it yields the same flux solution as observed data for noise-free cases.

This paper introduces a method to reduce computational cost in dynamic flux balance analysis by minimizing optimizations, achieving an 85% speed-up for microbial communities.

The paper introduces VFFVA, a C implementation of Flux Variability Analysis that achieves a threefold speedup and 14-fold memory reduction compared to fastFVA.

The paper introduces the ModelSEED biochemistry database, which integrates metabolic annotations and supports the reconstruction and analysis of metabolic models for plants, fungi, and microbes.

The paper performs 13C metabolic flux analysis on B. methanolicus to compare methylotrophic and non-methylotrophic metabolic states and better understand its metabolism.

This paper constructs a genome-scale metabolic model of Bdellovibrio bacteriovorus to analyze its growth-phase dependent metabolic states and provides insights into its biphasic lifestyle and metabolic robustness.

The paper uses an in silico model of yeast metabolism to identify modifier genes that buffer or potentiate the effects of mutations on growth, revealing pleiotropy, epistasis, and environmental dependencies.

The paper introduces a graph coloring method to generate atom identifiers for compounds, enabling compound harmonization across metabolic databases and improving metabolic network integration.

The paper compares metabolic differences between Streptomyces coelicolor strains M1152 and M145 using omics data and a genome-scale model to identify metabolic changes affecting heterologous compound production.

The paper introduces a cell-free method called iPROBE to rapidly prototype and optimize biosynthetic pathways for producing chemicals like limonene, increasing production from 0.2 to 4.5 mM in 24 hours.

The paper estimates in vivo enzyme turnover numbers (kcats) in E. coli using metabolic specialist strains and shows their stability and predictive power over in vitro kcats.

The paper designs a synthetic methanol utilization pathway in E. coli by combining methylotrophic enzymes from different sources and optimizing it for increased methanol assimilation.

This paper develops a cell-free system for styrene biosynthesis, achieving titers 10 times higher than cellular methods by optimizing reaction conditions.

K-FIT accelerates kinetic parameterization using steady-state fluxomic data, achieving a thousand-fold speed-up over meta-heuristic methods for E. coli metabolic models.

This study models microbial metabolic trade-offs in a chemostat to show how dynamic fitness landscapes enable ecological and evolutionary stable coexistence.

This study develops a genome-scale metabolic model for Clostridium thermocellum and applies it to integrate multi-omics data and design strains for biofuel and biochemical production.

This paper develops a computational framework to identify optimal growth and production phenotypes for two-stage microbial processes, showing that intermediate growth during production leads to better TRY metrics.

This study investigates how R. toruloides converts xylose into lipids and carotenoids, showing that oxidative stress improves lipid yields and adaptive evolution enhances carotenoid production.