Microbial Metabolic Engineering and Bioproduction

Genome-scale modeling reveals regulation of human metabolism by the histone deacetylase SIRT1

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

Petri Net-Based Framework for Oxygen-Sensitive Regulation of Pyruvate Metabolism in M. tuberculosis

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

Encapsulation of Select Violacein Pathway Enzymes in the 1,2-Propanediol Utilization Bacterial Microcompartment to Divert Pathway Flux

The paper shows that encapsulating specific enzymes in bacterial microcompartments shifts pathway flux toward the encapsulated pathway, providing quantitative evidence for their use in metabolic engineering.

Microbial photoproduction of heptane

This paper describes an E. coli strain engineered to produce heptane using FAP and a thioesterase, achieving a productivity of 22 mg.L-1.day-1 under blue light.

Contextualizing Models: Deriving a Kinetic Model of Cancer Metabolism including Growth via Stoichiometric Reduction

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

Efficient biosynthesis of 3-hydroxypropionic acid in recombinant Escherichia coli by metabolic engineering

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

Mixotrophy for carbon-conserving waste upcycling

This study explores carbon-conserving waste upcycling using Cupriavidus necator by evaluating mixotrophic scenarios with hydrogen and ethylene glycol as electron sources.

A recursive pathway for isoleucine biosynthesis arises from enzyme promiscuity

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: a Deep-learning-based Toolbox for Optimizing Enzyme-constrained Metabolic Modeling with Enhanced Proteome Abundance Prediction

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

Evaluation of Bacterial Microcompartment Cofactor Recycling and Permeability with a Model Guided In Vitro Assay

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.

Microbes use transporters to regulate the release of metabolites based on value

The paper shows that microbial metabolite release rates are negatively correlated with metabolite value, explaining variability better than other factors.

IsoPairFinder: A tool for biochemical pathway discovery using stable isotope tracing metabolomics

IsoPairFinder identifies metabolic pathway intermediates by analyzing isotope-labeled and unlabeled metabolomics data from gene-edited microbes.

Genomic Insights into Enhanced Medium-Chain Fatty Acid Production in Megasphaera elsdenii

This paper compares two Megasphaera elsdenii strains, finding that JCM 35779 produces 5.8 times more hexanoic acid than JCM 1772 due to genomic differences affecting carbon flux.

The growth benefits and toxicity of quinone synthesis are balanced by a dual regulatory mechanism and substrate limitations

This study identifies a dual regulatory mechanism and substrate limitations that balance quinone synthesis benefits and toxicity in Lactococcus lactis.

Evaluating plant growth-defence trade-offs by modelling the interaction between primary and secondary metabolism

The paper develops a genome-scale metabolic model for potato to study growth-defence trade-offs by integrating primary and secondary metabolism and applying transcriptomics data from stress experiments.

Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes

The paper demonstrates iterative SCRaMbLE to optimize synthetic genome modules and chromosomes in yeast by selecting for improved growth phenotypes.

novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection

novoSstoic2.0 streamlines pathway design by integrating stoichiometry, thermodynamics, and enzyme selection to identify efficient bioproduct synthesis routes.

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

This study characterizes the genomic and metabolic adaptations of Saccharomyces cerevisiae across diverse niches using pan-genome and metabolic modeling.

Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: Pseudomonas simiae as a case study

The paper develops a chemotaxis module for COMETS, a microbial ecosystem simulation tool, and applies it to Pseudomonas simiae to study chemotaxis and metabolism coupling.

HUMESS: Integrating Quantitative Transcriptomic Analysis and Metabolic Modeling to Unveil Condition-Specific Gene Signatures

HUMESS integrates transcriptomic data with metabolic modeling to identify condition-specific gene signatures by prioritizing genes based on metabolic significance.

Patient-specific metabolic fluxes reflect molecular subtype and heterogeneity in breast cancer

The paper infers patient-specific metabolic fluxes in breast cancer using metabolic models and machine learning, showing they reflect molecular subtypes and heterogeneity but not clinical features.

A Novel Phosphatase Reverses the Leloir Pathway to Promote Tagatose Synthesis from Glucose

This paper describes a novel biochemical pathway using a phosphatase to reverse the Leloir pathway in E. coli, enabling direct tagatose synthesis from glucose with high yield.

Entangled stoichiometric objectives shape microbial catabolism

The paper analyzes microbial catabolism using genome-scale stoichiometric models to show how energy and biosynthetic objectives shape metabolic pathways and precursor usage across species.

Activation-Free Upgrading of Carboxylic Acids to Aldehydes and Alcohols

This paper demonstrates an activation-free method to convert carboxylic acids to aldehydes and alcohols using aldehyde dehydrogenases, achieving high yields and carbon efficiency.

Genome-scale metabolic modelling of trimethoprim's mode of action reveals free ATP salvaged to restore purine pool

This study uses genome-scale metabolic modeling to show trimethoprim induces ATP salvage to repair DNA in E. coli when environmental purines are absent, validated by ATP bioluminescence screening.

Estimating flux dynamics from metabolite concentration time courses with dynafluxr

The paper introduces dynafluxr, a method to estimate metabolic flux dynamics from metabolite concentration time courses using constrained B-splines, showing it works well on both simulated and experimental data.

Metabolic engineering approach to boost γ-decalactone production in S. cerevisiae identifies a critical role for the peroxisomal Fatty Acyl-CoA Synthetase Faa2

This study enhances γ-decalactone production in S. cerevisiae by identifying Faa2 as critical for oleic acid-to-γ-decalactone conversion.

The FBA Solution Space Kernel -- Introduction and Illustrative Examples

This paper introduces the SSKernel tool to visualize and analyze the solution space of FBA-based metabolic models, enabling exploration of metabolic interventions and bioengineering strategies.

Sticky enzymes: increased metabolic efficiency via substrate-dependent enzyme clustering

This paper proposes a self-organization strategy for enzyme clustering based on substrate-dependent stickiness, showing significant increases in pathway flux and reductions in toxic metabolites.

Engineering Microbial R- and S- β-Hydroxybutyrate Production

This study engineers E. coli to produce high-yield, enantiomerically pure β-hydroxybutyrate (BHOB) for therapeutic applications in cancer and gut-brain disorders.