Microbial Metabolic Engineering and Bioproduction

Optimal enzyme utilization suggests concentrations and thermodynamics favor condition-specific saturations and binding mechanisms

The paper develops a framework to analyze optimal enzyme operation modes under varying conditions, showing that enzyme efficiency depends on reactant concentrations and mechanism type.

OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production

OptDesign identifies optimal strain design strategies for biochemical production in E. coli by combining regulation and knockout interventions using a two-step approach.

Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum

This study quantifies the proteome of Clostridium autoethanogenum under different gas conditions, revealing proteome allocation priorities and enzyme dynamics.

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

ARBRE predicts biosynthetic pathways to industrially important aromatic compounds using a comprehensive reaction network and computational tools.

Harnessing cellular perception apparatus for smart metabolic reprogramming

The paper develops a platform for global metabolic reprogramming in Vibrio FA2 using CRISPRi-mediated dual-gene knockdown and metabolic interaction analysis to enhance glycine production and assess antibiotic resistance.

Computational design and construction of an Escherichia coli strain engineered to produce a non-standard amino acid

The paper optimizes the production of a non-standard amino acid in E. coli by combining computational modeling and experimental validation of metabolic interventions.

Dynamic Flux Balance Analysis Models in SBML

This paper introduces a method to encode dynamic FBA models in SBML, enabling exchange and simulation of hybrid models across tools.

Protein cost minimization promotes the emergence of coenzyme redundancy

The paper uses metabolic modeling and sequence analysis to show that coenzyme redundancy reduces protein costs and promotes coenzyme specificity in E. coli.

Network reconstruction and modelling made reproducible with moped

The paper introduces moped, a Python package for reproducible metabolic model construction, curation, and analysis, supporting both genome-based reconstruction and SBML import.

Reconstruction of a generic genome-scale metabolic network for chicken: investigating network connectivity and finding potential biomarkers

The paper reconstructs a genome-scale metabolic model for chicken and analyzes its connectivity and potential biomarkers using transcriptomics data.

Quantification of microbial robustness

The paper quantifies microbial robustness using a high-throughput strategy and finds that robustness is function-specific with trade-offs.

Bayesian multi-model-based 13C15N-metabolic flux analysis quantifies carbon-nitrogen metabolism in mycobacteria

This study quantifies carbon-nitrogen and nitrogen metabolism in mycobacteria using Bayesian multi-model-based 13C15N metabolic flux analysis, identifying glutamate as a central metabolic node.

All driven by energy demand? Integrative comparison of metabolism of Enterococcus faecalis wildtype and a glutamine synthase mutant

This study compares the metabolic and proteomic adaptations of E. faecalis wildtype and a glutamine synthase mutant under varying pH conditions, revealing energy demand as the key factor in adaptation.

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

The paper presents a comparative analysis of 192 protozoan parasite genomes using a metabolic network reconstruction pipeline to identify species-specific metabolic differences and improve experimental system selection.

Thermodynamic Constraints on Electromicrobial Protein Production

The paper establishes an upper limit on the energy efficiency of electromicrobial protein production using a molecular-scale model.

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

The paper develops a whole-cell metabolic model for yeast to predict compartment-specific proteome constraints that explain metabolic strategies under different growth conditions.

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation

INTEGRATE integrates metabolomics and transcriptomics data to identify metabolic flux regulation at the enzyme expression and metabolic levels in cancer cell lines.

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

The paper introduces a method to quantify genomic, biochemical, and phenotypic evidence for metabolic network reconstructions, improving accuracy by integrating continuous evidence.

Synthetic metabolic pathways for conversion of CO2 into secreted short- to medium-chain hydrocarbons using cyanobacteria

This study engineered cyanobacteria to convert CO2 into secreted short-to medium-chain hydrocarbons using synthetic metabolic pathways, achieving 230 mg/L of 1-alkene with 15% carbon partitioning.

Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define growth physiology

This study shows how deleting CRP in E. coli leads to metabolic and proteomic changes that allow growth recovery through mutations and pathway re-allocation.

Inducible Directed Evolution of Complex Phenotypes in Bacteria

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: METABOLIC ATOM MAPPING DATABASE

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.

Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis

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

Rhythm of The Night (and Day): Predictive metabolic modeling of circadian growth in Chlamydomonas

The paper develops a transient metabolic model for diurnal growth of Chlamydomonas using transcriptomic data, predicting phenotypes from genotypes under dynamic conditions.

Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework

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.

Dynamic control systems that mimic natural regulation of catabolic pathways enable rapid production of lignocellulose-derived bioproducts

The paper develops a biosensor to regulate a conditionally beneficial catabolic pathway, improving microbial bioproduction of cis,cis-muconic acid from xylose.

Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum

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.

A computational framework to identify metabolic engineering strategies for the co-production of metabolites

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.

Evolving a generalist biosensor for bicyclic monoterpenes

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

Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing

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