Microbial Metabolic Engineering and Bioproduction

This paper identifies novel carbon fixation pathways using bioretrosynthetic analysis and expert knowledge, finding several that could outperform the Calvin cycle in biomass yield and do not require vitamin B12.

The paper develops and characterises a promoter library for Sulfolobus acidocaldarius, showing a 5-fold range of expression levels in the organism.

The paper introduces BiosInt, a genetic circuit for dynamic pathway regulation in biomanufacturing, validated through synthetic datasets and applied to flavonoid production.

The paper presents a genome-scale metabolic model of Escherichia coli Nissle 1917 that includes cryptic plasmids, improving predictive accuracy and revealing its unique probiotic metabolic traits.

This paper designs and tests synthetic CO2 fixation pathways in E. coli, demonstrating their potential to outperform natural pathways.

The paper repurposes the yeast Ehrlich pathway to synthesize pharmaceutical alkaloids using retrobiosynthetic analysis and enzyme screening.

The paper engineering Pseudomonas putida KT2440 to produce 3-hydroxy fatty acids (3-HFAs) with controlled chain lengths, achieving titers up to 0.73 g/L using a direct route and demonstrating scalability.

The paper predicts neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases using a systems biology approach and integrates metabolic networks with single nucleus RNA sequencing data.

StrainOptimizer improves microbial cell factory design by integrating multi-scale metabolic models with expression and proteome constraints, achieving higher bioproduction in yeast.

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

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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

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.

The paper integrates SIRT1 transcriptional regulation into a genome-scale metabolic model to simulate host-microbiome interactions and metabolic responses to diet.

The paper develops a Petri net model of pyruvate metabolism in M. tuberculosis to simulate oxygen-dependent metabolic transitions and their regulatory mechanisms.

The paper develops a kinetic model of cancer metabolism that incorporates cellular growth, showing differences in control properties compared to models without growth.

This paper improves 3-hydroxypropionic acid production in E. coli through metabolic engineering strategies including gene knockout, overexpression, and adaptive evolution.

The paper identifies a recursive isoleucine biosynthesis pathway in E. coli driven by the promiscuous activity of acetohydroxyacid synthase II, using glyoxylate and pyruvate directly instead of threonine.

EnzymeTuning optimizes enzyme kinetic parameters in metabolic models using a GAN framework, improving proteome predictions and model performance across yeast species.

The paper evaluates cofactor recycling and permeability in bacterial microcompartments using an in vitro assay and kinetic model of the Pdu system, showing benefits for pathway flux.