Microbial Metabolic Engineering and Bioproduction

Leveraging engineered Pseudomonas putida minicells for bioconversion of organic acids into short-chain methyl ketones

This paper demonstrates the use of engineered Pseudomonas putida minicells to convert organic acids into short-chain methyl ketones through pathway optimization and whole-cell biocatalysis.

Design principles for engineering bacteria to maximise chemical production from batch cultures

This study identifies design principles for engineering bacteria to maximize chemical production in batch cultures by optimizing gene expression and metabolic resource allocation.

AraRoot - A Comprehensive Genome-Scale Metabolic Model for the Arabidopsis Root System.

The paper develops AraRoot, a genome-scale metabolic model for Arabidopsis root system, identifying key metabolic pathways and stress responses.

Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production

This study identifies oxygen's role in enabling renewable n-caprylate production from ethanol and acetate via intermediate metabolite synthesis in bioreactors.

Inferring Metabolic Objectives and Tradeoffs in Single Cells During Embryogenesis

The paper infers metabolic objectives and tradeoffs in single cells during embryogenesis using integrated omics data and a novel framework combining metabolic modeling and machine learning.

Insights into optimization of oleaginous fungi - genome-scale metabolic reconstruction and analysis of Umbelopsis sp. WA50703

This paper develops a genome-scale metabolic model for Umbelopsis sp. WA50703 to identify genes and reactions important for polyunsaturated fatty acid production.

The strength of selection for costly toxin production increases with growth rate.

The paper models how growth rate affects selection for costly toxin production in microbes, finding stronger selection at higher growth rates in spatially-structured environments.

MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING

This study introduces MINN, a metabolic-informed neural network that integrates multi-omics data to predict metabolic fluxes in E. coli, outperforming pure ML and pFBA methods.

Optimization of regulatory DNA with active learning

This paper demonstrates that active learning improves regulatory DNA sequence optimization for yeast promoters, outperforming one-shot methods in complex landscapes.

Engineering Artificial 5' Regulatory Sequences for Thermostable Protein Expression in the Extremophile Thermus thermophilus

This study develops and validates artificial 5' regulatory sequences for enhancing thermostable protein expression in Thermus thermophilus.

Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations

This paper develops a genome-scale metabolic model for Clostridium luticellarii to improve syngas fermentation, showing its potential for producing value-added biochemicals.

Probing Biomass Precursor Synthesis as a Key Factor in Microbial Adaptation to Unadapted Carbon Sources

This paper introduces a computational framework, AdaptUC, to predict metabolic engineering strategies for microbial adaptation to unadapted carbon sources, showing improved driving forces and reduced substrate requirements in case studies.

Production of Glycolic acid through Whole-Cell Bioconversion from PET Monomer Ethylene Glycol Using Engineered Corynebacterium glutamicum

This paper engineers Corynebacterium glutamicum to produce glycolic acid from ethylene glycol, achieving high titers through promoter engineering and a two-stage biotransformation strategy.

A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in Staphylococcus aureus

This study identifies a thermodynamic bottleneck in the TCA cycle of S. aureus that favors acetate overflow metabolism for bioenergetic efficiency.

H2-driven xylitol production in Cupriavidus necator H16

This study uses Cupriavidus necator H16 to convert D-xylose to xylitol using hydrogen as a reducing agent, achieving high conversion efficiency and productivity.

A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

The paper constructs a genome-scale metabolic model for Rhodothermus marinus and validates it using growth data and carotenoid production experiments.

Systematic Plasmid Engineering for Targeted Carotenoid Synthesis in Bacteria

This paper develops a plasmid engineering platform to systematically produce specific carotenoids in bacteria, constructing plasmids for 17 different carotenoids.

Modification and Analysis of Context-Specific Genome-Scale Metabolic Models: Methane-Utilizing Microbial Chassis as a Case Study

The paper develops a computational workflow for reconstructing and validating context-specific genome-scale metabolic models in non-model microbes using Methylotuvimicrobium alcaliphilum 20ZR as a case study.

Multi-omics analysis and genome-scale metabolic reconstruction of cattle Bos taurus for optimal production of cultured meat

This study performs multi-omics analysis and builds a genome-scale metabolic model for Bos taurus muscle cells to improve cultured meat production.

Dissecting Metabolic Landscape of Alveolar Macrophage

This study investigates metabolic shifts in alveolar macrophages during M1 and M2 activation phases, highlighting non-central carbon metabolism pathways and temperature's role in immune response.

Quantitative physiology and biomass composition of Cyberlindnera jadinii in ethanol-grown cultures

This study quantifies the physiology and biomass composition of C. jadinii grown on ethanol, identifying its high growth rate, energy efficiency, and protein content as promising traits for industrial applications.

A rapid CAT transformation protocol and nuclear transgene expression tools for metabolic engineering in Cyanidioschyzon merolae 10D

This paper introduces a rapid transformation protocol and tools for metabolic engineering in Cyanidioschyzon merolae, demonstrating isoprene production using a synthetic plasmid toolkit.

fluxTrAM: Integration of tracer-based metabolomics data into atomically resolved genome-scale metabolic networks for metabolic flux analysis

fluxTrAM automates processing of tracer-based metabolomics data and integrates it with genome-scale metabolic models for flux analysis.

In silico target discovery for aromatic amino acid production in Escherichia coli

This study uses a dynamic model of Escherichia coli to identify metabolic targets for increasing aromatic amino acid production through evolutionary algorithms.

Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by Chromochloris zofingiensis

The paper develops a genome-scale metabolic model for Chromochloris zofingiensis and demonstrates its ability to predict fermentation products and metabolic activity under different growth conditions.

Conserved moiety fluxomics

This paper introduces a new method for genome-scale metabolic flux inference using conserved moieties, demonstrating its computational efficiency and accuracy with isotopic labeling data.

Metabolic trade-offs in response to increased acetate metabolism in Escherichia coli

This study evolves Escherichia coli to improve acetate metabolism but finds that some mutations reduce growth on glucose, highlighting potential trade-offs in complex feedstocks.

A dual-inducible control system for multistep biosynthetic pathways

This paper develops a dual-inducible genetic control system for multistep biosynthetic pathways in microbial chassis, showing improved regulation and biosynthesis of target compounds.

Wild type domestication: loss of intrinsic metabolic traits concealed by culture in rich media

The paper identifies hidden metabolic mutations in Klebsiella pneumoniae cultures grown in rich media, showing how these mutations can persist undetected and affect auxotrophy.

Computer assisted multi-level optimization of malonyl-CoA availability in Pseudomonas putida

This study enhances malonyl-CoA availability in Pseudomonas putida through multi-level optimization, achieving a 5.8-fold increase in phloroglucinol production.