Microbial Metabolic Engineering and Bioproduction

The paper introduces a method to evolve complex bacterial phenotypes using inducible directed evolution, achieving faster growth on tagatose after two rounds of evolution.

MetAMDB provides an open-source database of atom mappings for 75,000 metabolic reactions and allows users to generate atom mapping models for metabolic networks.

The paper constructs an enzyme-constrained genome-scale metabolic model of Rhizophagus irregularis to predict its metabolic capabilities and physiological responses to environmental cues.

The paper introduces three new constraint classes for LK-DFBA to improve metabolic modeling accuracy and shows that a single wild-type dataset can identify optimal constraints for a system.

The paper reconstructs and validates a genome-scale metabolic model for Rhizobium leguminosarum, integrating it with multi-omics data to predict metabolic fluxes across different symbiotic stages.

This paper introduces a computational framework to identify metabolic engineering strategies for co-producing multiple metabolites, showing that anaerobic conditions support more co-productions in E. coli and S. cerevisiae.

This paper evolves a generalist biosensor for bicyclic monoterpenes using directed evolution and a novel screening method.

The paper investigates trade-offs in microbial central carbon metabolism, showing that glycolytic and gluconeogenic pathways cannot be optimized simultaneously due to regulatory limitations.

The paper uses machine learning to classify metabolic regulation by phosphorylation and acetylation across multiple organisms and conditions.

This study uses whole-body metabolic models to show that isoleucine availability limits SARS-CoV-2 virus shedding and identifies potential therapeutic strategies.

This study shows that yeast can adapt rapidly to non-native substrates with minimal metabolic engineering by integrating non-native genes with a native regulon system.

This paper predicts gene essentiality using machine learning on wild-type flux distributions, achieving near state-of-the-art accuracy for Escherichia coli.

This study identifies alternative glycolytic pathways in E. coli that bypass canonical EMP glycolysis, showing that the serine shunt is selected for in adaptive evolution.

The paper presents a framework for engineering microbial biosynthesis of butyryl-CoA-derived esters with controllable selectivity, achieving significant production increases in target compounds.

This paper uses multiobjective optimization to analyze trade-offs in biosensor design for dynamic pathway engineering, showing improved production in E. coli.

This study uses isotopically nonstationary 13C metabolic flux analysis to measure carbon fluxes in resting and thrombin-activated human platelets, revealing metabolic shifts during activation.

The paper addresses false positive enrichment in biosensor-guided biocatalyst engineering by desensitizing biosensors and using orthogonal pre-screens to reduce cheater cells during FACS.

This paper demonstrates a hybrid cellular-heterogeneous catalytic strategy to produce olefins from glucose using engineered microbial strains and catalysts.

The paper resequences and analyzes transcriptomic changes in an engineered C. glutamicum strain under bioreactor conditions with and without ionic liquid stress.

The paper introduces a modular cloning system for genetic engineering in Komagataeibacter bacteria to enable multigene construct assembly and programmed protein secretion.

COBREXA.jl is a Julia package for scalable constraint-based metabolic modeling, designed for high-performance computing environments and multi-organism community models.

DeltaFBA predicts metabolic flux changes between conditions using genome-scale models and gene expression data without requiring a specified cellular objective.

GPRuler automatically reconstructs gene-protein-reaction rules for metabolic networks using biological databases, achieving high accuracy in both small-scale and genome-scale models.

This paper describes a platform for de novo synthesis of nepetalactone in yeast, achieving 3.10 mg/L/OD600 from simple sugars by optimizing pathway genes and deleting competing enzymes.

This paper demonstrates that dynamic deregulation of central metabolism in E. coli improves process robustness and scalability for industrial chemical production.

The paper introduces a community-level gap-filling algorithm to resolve metabolic gaps and predict interactions in microbial communities.

This paper introduces SSA-FBA, a computational framework for simulating single-cell metabolism using genome-scale models and gene expression data, demonstrating its application to Mycoplasma pneumoniae.

The paper introduces a method to estimate in-vivo metabolic kinetic constants and metabolite concentrations from omics data by solving a convex optimization problem.

This paper quantifies how uncertainty in biomass coefficients and non-steady-state conditions affect flux balance analysis results.