Microbial Metabolic Engineering and Bioproduction

Dynamic Kinetic Models Capture Cell-Free Metabolism for Improved Butanol Production

This paper develops a dynamic kinetic model of cell-free metabolism to optimize butanol production, identifying aldehyde/alcohol dehydrogenase as a key bottleneck.

Scalable Solar-Driven Chemical Production by Semiconductor Biohybrids Synthesized from Wastewater Pollutants

This paper develops a scalable method to produce semiconductor biohybrids from wastewater pollutants for solar-to-chemical conversion, achieving 13 g/L of 2,3-butanediol in a 5-L fermenter with lower cost and CO2 emissions.

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

Bactabolize generates strain-specific bacterial metabolic models and growth predictions, outperforming existing tools for Klebsiella pneumoniae.

Co-substrate pools can constrain and regulate pathway fluxes in cell metabolism

The paper develops a mathematical framework to show co-substrate cycling imposes flux limits in metabolic pathways and demonstrates this using simulations and existing metabolic data.

Paving the way for synthetic C1- metabolism in Pseudomonas putida through the reductive glycine pathway

This paper engineers Pseudomonas putida to assimilate C1 compounds like formate, methanol, and CO2 through the reductive glycine pathway, enabling growth on these substrates as sole feedstocks.

Complex waste stream valorisation through combined enzymatic hydrolysis and catabolic assimilation by Pseudomonas putida

This paper demonstrates the use of engineered Pseudomonas putida to efficiently co-utilize complex, heterogeneous waste streams for bio-product synthesis, showing climate and economic benefits over conventional waste treatment.

Integrated Constraint-Based Modeling of E. coli Cell-Free Protein Synthesis

The paper develops a dynamic constraint-based model of E. coli cell-free protein synthesis to analyze metabolic flux and protein production with and without electron transport chain inhibitors.

Parasites, infections and inoculation in synthetic minimal cells

This paper demonstrates a synthetic cell system that models host-parasite interactions, resistance to infection, and an inoculation system for immunity.

Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation

The paper develops a genome-scale model of Pseudomonas aeruginosa PA14 to study its metabolism, virulence, and drug interactions, revealing metabolic mechanisms and drug potentiation strategies.

Cell survival enabled by leakage of a labile metabolic intermediate

The paper shows that mutations in glutamine synthetase can rescue a proline biosynthesis block by leaking a phosphorylated intermediate, enabling a new pathway and organismal adaptation.

Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales

This study controls beta-carotene production in yeast using optogenetics across different lab-scale devices and finds that illumination, culture volume, and shaking affect performance differently.

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

The paper develops methods to generate context-specific genome-scale metabolic models from single-cell RNA-Seq data and shows that cell subtypes have unique metabolic profiles.

Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast

The paper presents a computational pipeline to predict gene engineering targets for increased production of 102 chemicals in yeast using enzyme-constrained models.

Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol

This study replaces the glycerate pathway with the β-hydroxyaspartate cycle in Pseudomonas putida, resulting in faster growth and higher biomass yield on ethylene glycol.

The pGinger family of expression plasmids

The paper introduces a family of 43 expression plasmids for precise gene expression in gram-negative bacteria, with constitutive and inducible systems tested in Escherichia coli and Pseudomonas putida.

Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by resting cells of E. coli RARE strains

The paper demonstrates that combinatorial gene inactivation of aldehyde dehydrogenases in E. coli reduces aldehyde oxidation in resting cells, improving aldehyde bioconversion.

A Novel Algorithm to Calculate Elementary Modes: Analysis of Campylobacter jejuni Metabolism

The paper introduces an algorithm, LPEM, to decompose metabolic flux vectors into elementary modes and applies it to analyze Campylobacter jejuni metabolism.

A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways

This paper demonstrates that increasing sugar phosphates using the XR/lactose system enhances cofactor generation in engineered metabolic pathways in E. coli, improving productivities by 2-4-fold.

A study of a diauxic growth experiment using an expanded dynamic flux balance framework

The paper develops decFBAecc, an extended dynamic flux balance analysis method that incorporates enzyme change constraints, and validates it using diauxic growth experiments in E. coli.

Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data

The paper evaluates the accuracy of E. coli genome-scale metabolic models using mutant fitness data and identifies improvements to enhance prediction accuracy.

An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

The paper introduces an automated system called Lila to design and optimize microbial strains for producing small molecules, achieving high titers for naringenin and creating strains for 242 molecules.

MitoMouse is a model reconstruction of murine mitochondrial metabolism

The paper develops a mouse-specific mitochondrial metabolic model called mitoMouse, validated to accurately model CoQ reduction in response to increased malate import.

A Bayesian model for genomic prediction using metabolic networks

The paper introduces a Bayesian model that integrates metabolic networks for genomic prediction, showing improved accuracy in simulated and real data.

Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data

The paper evaluates algorithms for generating context-specific metabolic models using gene expression data and identifies guidelines for selecting the best models.

Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica

This study shows that removing storage lipids in Yarrowia lipolytica causes protein misfolding and stress responses, and alters lipid composition under nitrogen limitation.

Elevated energy costs of biomass production in mitochondrial-respiration deficient Saccharomyces cerevisiae

This study uses a resource allocation model to compare metabolic strategies in Saccharomyces cerevisiae under different conditions, finding increased energy costs in respiratory-deficient strains.

RBAtools: a programming interface for Resource Balance Analysis modelling

RBAtools provides a programming API for Resource Balance Analysis, enabling custom workflows and model manipulation for non-expert users.

Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

The paper uses machine learning to optimize medium composition for improved production of foreign and native metabolites in Escherichia coli.

A Cellular Platform for Production of C4 Monomers

This study engineered microbial strains to produce three C4 chemicals with ~95% theoretical yield by altering gene loci that control carbon flow.

Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations

This study introduces FBAwEB, an extension of flux balance analysis that accounts for biomass equation variations across conditions by using ensemble representations of macromolecular compositions.