Microbial Metabolic Engineering and Bioproduction

Itaconic acid production from acetate by Ustilago maydis: A step towards land-free biotechnology

This study demonstrates that Ustilago maydis can efficiently produce itaconic acid from acetate, achieving high titers and yields comparable to glucose-based processes, supporting acetate as a sustainable feedstock for land-free biotechnology.

in silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity

This paper introduces NIS, a method to simplify genome-scale metabolic models for comparing metabolic capabilities across organisms, revealing conserved and divergent patterns in metabolism.

METEOR: joint genome-scale reconstruction and enzyme prediction

METEOR integrates enzyme prediction with genome-scale metabolic model reconstruction to improve functional annotations and network viability.

Model-Driven Elucidation of Lactose and Galactose Metabolism via Oxidoreductive Pathway in Sungouiella intermedia for Cell Factory Applications

This paper investigates lactose and galactose metabolism in Sungouiella intermedia using a genome-scale metabolic model and experimental data to identify its potential as a cell factory for producing galactitol and tagatose from industrial side-streams.

Combining evolution and machine learning-guided pathway optimization to engineer a novel methylsuccinate module for synthetic C1 metabolism in vivo

This paper combines adaptive laboratory evolution and machine learning to engineer a methylsuccinate module for synthetic C1 metabolism in E. coli, achieving growth in three weeks versus six months with evolution alone.

Evaluating the Limitations of Bayesian Metabolic Control Analysis

This study evaluates Bayesian Metabolic Control Analysis (BMCA) using synthetic networks, finding it requires flux and enzyme data for accurate predictions and fails to reliably infer elasticity values and allosteric regulation.

Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants

The paper identifies an aerobicity stimulon in E. coli through computational analysis of evolved respiratory variants, showing gene groups co-regulated with aerobic capacity and proteome reallocation.

Fine modulation of carbon flow in the central carbon metabolism via ribosome-binding site modification in Escherichia coli

The paper constructs a combinatorial repression library in E. coli to optimize flux distribution for mevalonate production by modifying ribosome-binding sites of key genes.

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

The paper uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

Computational Approaches in Chemical Space Exploration for Carbon Fixation Pathways

The paper uses graph-based cheminformatics and ILP optimization to explore chemical space for carbon fixation pathways, identifying new enzymatic cascades and autocatalytic cycles.

MetaNetMap: automatic mapping of metabolomic data onto metabolic networks

MetaNetMap automates mapping of metabolomic annotations onto genome-scale metabolic networks through direct, conversion-table-bridged and partial identifier matching, reproducing 311 mappings from a Parkinson's disease study.

Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production

This paper builds a proteome-constrained metabolic model for Sus scrofa muscle stem cells to simulate their growth and metabolism under varying lactate and ammonium conditions, aiding in cultured meat production optimization.

Synthetic metabolic pathways for ethylene glycol assimilation outperform natural counterparts

This study compares synthetic and natural metabolic pathways for ethylene glycol assimilation, finding synthetic pathways offer higher thermodynamic driving forces and yields but natural pathways are more orthogonal to central metabolism.

Improved flux profiling in genome-scale modeling of human cell metabolism

The paper improves genome-scale flux profiling in human cell metabolism by introducing a new method for exo-metabolite exchange flux calculation, enhancing the biological relevance of metabolic models.

Going beyond size: Exploring the metabolic burden inPseudomonas putida during heterologous proteinproduction

This study investigates the metabolic burden in Pseudomonas putida during heterologous protein production, finding that transcript length, not protein size, is the main bottleneck.

Integration-coupled activation of promoterless combinatorial pathway libraries in Clostridium avoids burden during DNA assembly

The paper develops a method to enable combinatorial DNA assembly in Clostridium by preventing premature expression during library construction and activating it later through genomic integration.

MCC: Automated Mass and Charge Curation at Genome-Scale Applied to C. tuberculostearicum

The paper introduces MCC, a Python package for automating mass and charge balancing in genome-scale metabolic models, and applies it to create a high-quality model for Corynebacterium tuberculostearicum.

The geometry of cooperation: decoding microbial interactions

The paper introduces a geometric framework to analyze microbial community metabolism, linking interaction types to the structure of metabolic spaces and identifying isotypic and anisotypic mutualism.

Decoupling Central Metabolism from Catabolite Repression Enables Robust Cellulosic Sugar Co-consumption in E. coli

This paper introduces a Gluconate-Bypass in E. coli to decouple central metabolism from catabolite repression, enabling robust co-consumption of multiple lignocellulosic sugars.

Structural and Boolean Network Modeling of the Levan Biosynthetic Pathway in Bacillus subtilis.

The paper develops a structure-annotated genome-scale metabolic model for Bacillus subtilis to include levan biosynthesis, using AlphaFold2 for structural information.

Pseudomonas putida JM37 as a novel bacterial chassis for ethylene glycol upcycling

This study identifies Pseudomonas putida JM37 as a bacterial chassis capable of efficiently metabolizing ethylene glycol and producing polyhydroxyalkanoates, with potential for biotechnological applications.

Engineering Orthogonal Carbon Dissimilation: A Gluconate Bypass Platform for Robust Stationary-Phase Biomanufacturing

This paper introduces a gluconate-bypass platform to enhance stationary-phase biomanufacturing in E. coli by decoupling glucose uptake from pyruvate inhibition and co-generating NADPH, achieving high product titers.

Engineering Clostridium thermocellum for production of 2,3-butanediol from cellulose

This paper engineers Clostridium thermocellum to produce 2,3-butanediol from cellulose, achieving a titer of 19.7 mM with a metabolic yield of 24%.

A metabolic hierarchy directs cell cycle transition and morphogenesis

This study identifies a metabolic hierarchy in Caulobacter crescentus that coordinates cell cycle transitions and morphogenesis through redox dynamics.

From Light to Lipids: Constraint-Based Metabolic Modeling of Nannochloropsis oceanica Under Light Acclimation Conditions

This paper develops a genome-scale metabolic model for Nannochloropsis oceanica to study lipid production under light acclimation conditions.

Systems-level analysis identifies protein-RNA interactions contributing to autotrophy of Clostridium autoethanogenum

The paper identifies genome-wide protein-RNA interactions in Clostridium autoethanogenum that contribute to autotrophy using a combination of experimental and computational methods.

Steering fatty acid composition of yeast microbial oil via genetic modification and bioprocess adjustment

This study improves microbial oil fatty acid composition in yeast through genetic modification and cultivation parameter optimization.

Beyond synthetic lethality in large-scale metabolic and regulatory network models via genetic minimal intervention sets

The paper introduces genetic Minimal Intervention Sets (gMISs) to identify lethal genetic interactions beyond synthetic lethality in human cells and demonstrates their application in cancer research.

Thermo-Dynamic Flux Balance Analysis, a novel approach to simulate circadian metabolism

The paper introduces tdFBA, a novel method for simulating circadian metabolism across organs, and shows it can recapitulate metabolic oscillations and perturbations in mice and humans.

A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products