Microbial Metabolic Engineering and Bioproduction

GBA Solver: a user-friendly web server for growth balance analysis

GBA Solver provides a web-based tool for constructing and solving GBA models with up to 20 reactions, integrating kinetic parameters and offering visualizations for cell metabolism and growth analysis.

A Comprehensive Genetic Toolkit for Rapid and High-Resolution Engineering of Metabolic Pathways in Zymomonas mobilis.

This paper develops a genetic toolkit for precise metabolic pathway engineering in Zymomonas mobilis, enabling high-resolution control of gene expression and pathway assembly.

A Computational Approach for Threonine Accumulation in Escherichia coli and Its Integraton as a Platform for Biosynthesis of High-Value Fine Chemicals

The paper develops an E. coli strain for enhanced threonine production using metabolic modeling and experiments, and explores its application for producing high-value chemicals like 2,5-dimethylpyrazine.

An Improved Systematic Method for Constructing ecGEMs using a Protein-Chemical Transformer

The paper introduces a transformer-based method to predict kcat values for E. coli enzymes, improving ecGEMs with fewer calibrations and better performance than existing models.

Enhancing Lipid Production in Yarrowia lipolytica through Continuous Fermentation and Adaptive Laboratory Evolution in Bioreactors

This study improves lipid production in Yarrowia lipolytica using continuous fermentation and adaptive laboratory evolution in bioreactors, achieving higher productivity and yield.

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

The paper uses a biosensor-driven strategy to enhance isoprenol production in Pseudomonas putida through combinatorial strain engineering and omics analysis.

Harnessing photosynthetic ATP for whole-cell biocatalysis in the cyanobacterium Synechocystis

This study demonstrates that ATP from photosynthesis in Synechocystis can power biocatalytic reactions, enabling sustainable chemical synthesis using whole-cell biocatalysis.

Enabling strong acetogenic growth on CO2 and H2: H2 solubility limits Clostridium ljungdahlii growth on CO2 and H2

This study shows that H2 solubility limits C. ljungdahlii growth on CO2 and H2, but high H2 mass transfer enables rapid growth using CO2 as the sole carbon source.

Engineering mutualism via nitrogen exchange in mixotrophic cocultures between Clostridium acetobutylicum and Clostridium ljungdahlii

This paper shows that engineering nitrogen exchange in a mixotrophic coculture of Clostridium acetobutylicum and Clostridium ljungdahlii enables mutualism, stabilizes population ratios, and improves product yields.

Feedstock-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in Escherichia coli

This paper engineers Escherichia coli to use hydrogen and formate as energy sources, improving mevalonate production by 57.6% through metabolic decoupling.

Evolution-assisted engineering of formate assimilation via the formyl phosphate route in Escherichia coli

This study establishes the formyl phosphate route for formate assimilation in E. coli through adaptive evolution and rational engineering, enabling formate-dependent growth.

Metabolic engineering of Acinetobacter baylyi ADP1 for efficient utilization of pentose sugars and production of glutamic acid

This paper engineers Acinetobacter baylyi ADP1 to efficiently utilize pentose sugars and produce L-glutamate, achieving high growth rates and carbon yields.

Cross-talk between engineered Clostridium acetobutylicum and Clostridium ljungdahlii in syntrophic cocultures enhances isopropanol and butanol production

This study enhances isopropanol and butanol production by engineering microbial syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, achieving high yields and efficiency.

Rapid discovery of antiviral targets through dimensionality reduction of genome-scale metabolic models

This paper develops a computational framework using dimensionality reduction of genome-scale metabolic models to identify host metabolic vulnerabilities for antiviral targets, validated across multiple coronaviruses.

Systematic data-driven genome-scale metabolic model reduction for dynamic bioprocess modeling: CHO cell culture case study

The paper develops a metabolomics-driven framework to systematically reduce genome-scale metabolic models, validated on CHO cell cultures to improve dynamic bioprocess simulation.

Microbial stem cells support productivity in dedicated factory cells in an asymmetrically dividing E. coli system

This paper describes a system in E. coli where asymmetric cell division separates reproductive stem cells from dedicated factory cells, enhancing protein productivity by reducing cytotoxicity.

AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits

The paper introduces a gene fusion strategy using machine learning to improve the evolutionary stability of synthetic gene circuits in yeast.

Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass

This paper presents an updated genome-scale metabolic model for Ruminiclostridium cellulolyticum to simulate lignocellulosic biomass fermentation.

Long-term homeostasis in microbial consortia via auxotrophic cross-feeding

This paper presents a method to control microbial consortium proportions using auxotrophic cross-feeding in continuous culture, demonstrating precise regulation through exogenous nutrient addition and mathematical modeling.

A universal law of thermodynamics-kinetics coupling shapes enzyme allocation and glycolytic efficiency across species

The paper derives and validates a universal law of thermodynamics-kinetics coupling that governs glycolytic enzyme allocation across species under optimal efficiency.

A rational approach for multicopy delta integration in Saccharomyces cerevisiae targeting a conserved Ty1 LTR sequence

The paper designs a conserved Ty1 LTR sequence for efficient multicopy gene integration in yeast, validated by integrating 15 xylose isomerase copies for ethanol production.

Accurate prediction of gene deletion phenotypes with Flux Cone Learning

This paper introduces Flux Cone Learning, a framework for predicting gene deletion phenotypes, showing improved accuracy over existing methods in various organisms.

Inferring the Metabolic Objectives of Mammalian Cells via Inverse Modeling of Fluxomics and Metabolomics

This paper introduces ObjFind-M, an inverse optimization framework that infers reaction-level metabolic objectives from fluxomic and metabolomic data in mammalian cells, finding mitochondrial ATP synthase as a central driver.

Engineering Spatial Control of Bacterial Organelles

This study shows that the McdAB system can be used to engineer spatial control of various bacterial organelles in E. coli, enabling programmable positioning for synthetic biology applications.

Epistatic mutations in ISC metabolism synergize with cell cycle regulation and the PPP to enhance xylose fermentation and acetic acid tolerance in industrial yeast

Thermodynamics shape the in vivo enzyme burden of glycolytic pathways

The paper quantifies enzyme burdens in glycolytic pathways of three bacteria, finding that thermodynamically favorable pathways require less enzymatic protein to sustain the same flux.

A novel expression system enabling scalable production of glycosylated flavonoids in Escherichia coli W using a plant-derived toxic gene

This paper develops a microbial platform in E. coli to produce glycosylated flavonoids using a phosphate-responsive promoter and optimized gene expression.

Integrative Thermodynamics Strategies in Microbial Metabolism

This study extends thermodynamic analysis of microbial metabolism to non-carbon nutrient limitations, showing more negative Gibbs free energy values for the Net Catabolic Reaction under anabolic limitations.

Calcium starvation leads to strain-specific gene regulation of lipid and carotenoid production in Mucor Circinelloides

The paper investigates strain-specific gene regulation of lipid and carotenoid production in Mucor circinelloides under calcium starvation using genomic and transcriptomic analyses.

In Vivo Pathway Optimization in Yeast via LoxPsym-Mediated Shuffling of Upstream Activating Sequences

The paper introduces PULSE, a method for in vivo promoter engineering in yeast to optimize biosynthetic pathways, achieving an eightfold increase in β-carotene production and improved growth on high xylose concentrations.