Microbial Metabolic Engineering and Bioproduction

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes

This paper engineers a synthetic C2 auxotrophy in Pseudomonas putida to enable alternative sugar catabolism via the phosphoketolase shunt, improving growth through metabolic rewiring.

Designing a Minimal Artificial Glycolytic Pathway

This paper designs and tests a minimal artificial glycolytic pathway that efficiently converts various monosaccharides to acetyl-CoA with high yield.

From toxic waste to beneficial nutrient: acetate boosts Escherichia coli growth at low glycolytic flux

This study shows acetate enhances Escherichia coli growth by compensating for reduced glycolytic flux through co-utilization with glucose.

Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

This study uses resource balance analysis to evaluate proteome allocation and metabolic fluxes in yeast under different environmental conditions, identifying key limitations in biosynthetic pathways.

Optimizing a High Performing Multiplex-CRISPRi P. putida strain with Integrated Metabolomics and 13C-Metabolic Flux Analyses

The paper optimizes a P. putida strain for indigoidine production using 13C-MFA and metabolomics, identifying key metabolic bottlenecks and engineering improvements.

Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism

The paper integrates chlorophyll fluorescence data with genome-scale metabolic models to improve predictions of photosynthetic metabolism in diatoms.

Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters

This study demonstrates a modular design approach to selectively produce isoamyl acetate in microbes, achieving high titer, yield, and selectivity through proteome reallocation.

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

This paper introduces REKINDLE, a deep learning framework that generates kinetic models of metabolic networks with dynamic properties, demonstrating its efficiency and versatility through three studies.

Galaxy-SynBioCAD: Automated Pipeline for Synthetic Biology Design and Engineering

Galaxy-SynBioCAD provides an automated pipeline for synthetic biology design and engineering, achieving an 83% success rate in retrieving validated pathways.

Optimizing E. coli as a formatotrophic platform for bioproduction via the reductive glycine pathway

This paper optimizes an E. coli strain for formate-based bioproduction using the reductive glycine pathway, achieving improved growth and lactate production.

A genome-scale metabolic model of Drosophila melanogaster for integrative analysis of brain diseases

The paper develops a genome-scale metabolic model for Drosophila melanogaster to study metabolic disorders and Parkinson's disease.

Phenotypic response of yeast metabolic network to availability of proteinogenic aminoacids

The paper extends an enzyme-constrained GEM framework to include amino acid usage in yeast, showing how metabolic proteome demands affect amino acid availability and metabolic robustness.

A parallel glycolysis supports rapid adaptation in dynamic environments

The paper identifies that the Entner-Doudoroff pathway provides a metabolic advantage in dynamic nutrient environments by enabling faster response times during nutrient upshifts.

A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

The paper develops a computational model of fission yeast metabolism to explore resource allocation and metabolic strategies under different glucose conditions.

Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations

This study uses thermodynamically-constrained genome-scale models to simulate metabolic responses of a deep-sea bacterium to different temperatures, revealing changes in metabolic efficiency and pathway utilization.

From empirical to data-driven host selection: a broad-host-range expression platform to facilitate chassis screening

The paper introduces a modular expression platform for screening heterologous protein expression across diverse prokaryotic hosts, enabling data-driven host selection.

Exploring the adaptability and robustness of the central carbon metabolism of Mycoplasma pneumoniae

This study analyzes the adaptability and robustness of Mycoplasma pneumoniae's central carbon metabolism using metabolomics data and a dynamic model, identifying key control hubs.

Integration of external biomass reactions into existing metabolic models

This paper integrates external biomass reactions into metabolic models to improve prediction accuracy for gene essentiality and growth.

Comparative genome-scale constraint-based metabolic modeling reveals key lifestyle features of plant-associated Pseudomonas spp.

The paper uses metabolic modeling to compare plant-associated Pseudomonas strains and identifies metabolic differences between beneficial and pathogenic species.

On the flexibility of the cellular amination network in E. coli

The paper studies the flexibility of the amination network in E. coli by identifying key enzymes and amino acids involved in ammonium assimilation and glutamate production.

Metabolic network models of Gardnerella pangenome identify interactions in the vaginal environment

The paper uses metabolic network models to analyze the Gardnerella pangenome and identifies core metabolic functions in the vaginal environment.

An automated workflow for multi-omics screening of microbial model organisms

The paper describes an automated workflow for generating high-throughput microbial multi-omics datasets and evaluates its effectiveness with three model organisms.

Toward sustainable jet fuels: bioconversion of cellulose into isoprenoid biojet candidates using rumen bacteria and non-conventional yeast

This paper demonstrates the bioconversion of cellulose into bisabolene, a biojet fuel candidate, using rumen bacteria and non-conventional yeast in a sequential bioprocess.

Time-Optimal Adaptation in Metabolic Network Models

This paper introduces time-optimal adaptation (TOA), a constraint-based modeling approach that explains cellular metabolic responses to environmental changes and demonstrates its ability to explain experimental phenomena.

mergem: merging and comparing genome-scale metabolic models using universal identifiers

mergem merges and compares genome-scale metabolic models using universal identifiers to enable comparison across different pipelines and namespaces.

Using structurally fungible biosensors to evolve improved alkaloid biosyntheses

This paper evolves highly specific and sensitive biosensors for alkaloids using a combined screening and selection approach, enabling improved microbial production of therapeutic plant metabolites.

Decoupling growth and production by removing the origin of replication from a bacterial chromosome

This paper describes a method to decouple bacterial growth and production by permanently removing the origin of replication, enabling continued protein synthesis without growth.

A versatile active learning workflow for optimization of genetic and metabolic networks

The paper introduces METIS, an active learning workflow for optimizing genetic and metabolic networks, demonstrating significant improvements in efficiency with minimal experiments.

A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions

The paper develops a flux-based machine learning model to predict drug interactions in E. coli, accounting for metabolic heterogeneity and growth conditions, identifying 24 synergistic combinations.

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

The paper upgrades the GECKO method to create enzyme-constrained models for yeast and human, revealing common metabolic adaptations under stress.