Microbial Metabolic Engineering and Bioproduction

Benzylisoquinoline alkaloid production in yeast via norlaudanosoline improves selectivity and yield

This paper improves the microbial synthesis of benzylisoquinoline alkaloids in yeast by using human monoamine oxidase A to increase selectivity and yield of (S)-reticuline and its derivatives.

Identifying Essential Genes in Genome-Scale Metabolic Models of Consensus Molecular Subtypes of Colorectal Cancer

This paper identifies essential genes in colorectal cancer subtypes using a fuzzy optimization framework and validates them against experimental data.

Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida

This study uses D-fluxomics to reveal the dynamic and hierarchical metabolism of glucose in Pseudomonas putida through the periplasmic gluconate shunt.

Host-aware RNA-based control of synthetic microbial consortia

This paper develops an RNA-based feedback control system to stabilize microbial consortia composition without using toxins or syntrophy.

Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum

This study investigates the effects of deleting two genes linked to the C1-fixing gene cluster in Clostridium autoethanogenum, revealing growth defects and altered by-product profiles.

Pichia pastoris growth - coupled heme biosynthesis analysis using metabolic modelling

The paper uses metabolic modeling to optimize heme production in Pichia pastoris by analyzing growth conditions and suggesting gene regulation strategies.

Improving xylose consumption in Rhodotorula toruloides through heterologous expression of xylose reductase and xylulokinase

This study improves xylose consumption in Rhodotorula toruloides by overexpressing xylose reductase and xylulokinase from different organisms, showing significant increases in consumption rate and growth.

Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation

The paper uses dynamic flux balance analysis to identify conserved and strain-specific metabolic mechanisms in Saccharomyces cerevisiae that influence ester formation during alcoholic fermentation.

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides

This study investigates lipid remodeling in Rhodotorula toruloides under nitrogen starvation, identifying phospholipid-to-storage lipid conversion and regulatory mechanisms for lipid accumulation.

A digital twin of bacterial metabolism during cheese production

This paper models the metabolism of a three-species bacterial community during cheese production using genome-scale models and omics data integration, accurately predicting community dynamics and interactions.

A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)

This paper introduces a tRNA modification-based strategy to identify amino acid overproducers in microbial hosts.

Mycobacterial Metabolic Model Development for Drug Target Identification

The paper develops metabolic models for M. leprae and M. abscessus to identify potential drug targets, highlighting unique pathways for precision medicine.

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

This paper describes an end-to-end pipeline for cost-effective succinic acid production using Issatchenkia orientalis, achieving high titers and financial viability with reduced greenhouse gas emissions.

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

This paper engineers Pseudomonas putida for isoprenol production using computational modeling and strain optimization, achieving a titer of 3.5 g/L.

Screening non-conventional yeasts for organic acid tolerance and engineering Pichia occidentalis for production of cis,cis-muconic acid

The paper screens non-conventional yeasts for organic acid tolerance and engineers Pichia occidentalis to produce cis,cis-muconic acid with improved metrics compared to Saccharomyces cerevisiae.

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

BayFlux quantifies metabolic fluxes and their uncertainty using Bayesian inference, showing genome-scale models reduce flux uncertainty compared to core models and improve knockout predictions.

Growth balance analysis models of cyanobacteria for understanding resource allocation strategies

The paper develops two simplified growth balance analysis models for Synechocystis sp. PCC 6803 to predict cellular resource allocation under different environmental conditions and photodamage effects.

Parameter inference for enzyme and temperature constrained genome-scale models

The paper develops an evolutionary algorithm to improve parameter inference for enzyme and temperature constrained genome-scale models, showing that the Bayesian approach is unstable and that more data is needed to narrow predictions.

A benchmark of optimization solvers for genome-scale metabolic modeling

This study benchmarks six optimization solvers for genome-scale metabolic modeling, showing open-source solvers can match commercial ones in performance.

Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling

The paper improves metabolic flux predictions in Arabidopsis by integrating tissue-specific gene expression data into Flux Balance Analysis, significantly reducing prediction errors compared to standard methods.

The unraveling of balanced complexes in metabolic networks

The paper presents factorizations to categorize balanced complexes in metabolic networks and shows their presence across all kingdoms of life.

Transcriptional Biomarker Discovery Towards Building A Load Stress Reporting System for Engineered Escherichia coli Strains

The paper identifies gene biomarkers to detect load stress in engineered E. coli strains using machine learning.

Sensitivity analysis of genome-scale metabolic flux prediction

The paper develops a sensitivity analysis strategy for genome-scale metabolic flux prediction using TRIMER, showing its utility in guiding optimal experimental design for metabolic engineering.

Standard-GEM supports reproducible development of genome-scale metabolic models

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

Engineering Escherichia coli to utilize erythritol as sole carbon source

This paper engineers Escherichia coli to utilize erythritol as a sole carbon source, enhancing growth and enabling detection of erythritol-containing beverages.

Data integration across conditions improves turnover number estimates and metabolic predictions

The paper shows that integrating data improves turnover number estimates and metabolic predictions for E. coli and S. cerevisiae.

Standard Intein Gene Expression Ramps (SIGER) for protein-independent expression control

The paper introduces the SIGER system to control protein expression by decoupling translation initiation features from target genes using inteins, improving protein yield and quality.

Engineering the biological conversion of formate into crotonate in Cupriavidus necator

This paper engineers the bacterium C. necator to convert formate into crotonate, achieving higher titer, productivity, and yield through metabolic pathway optimization.

Constraint-based modelling predicts metabolic signatures of low- and high-grade serous ovarian cancer

This study uses constraint-based modeling to predict metabolic differences between low- and high-grade serous ovarian cancer subtypes, supported by CRISPR-Cas9 and literature data.

Preventing production escape during scale-up using an engineered glucose-inducible genetic circuit

The paper engineers a glucose-inducible genetic circuit in Bacillus subtilis to maintain production capacity during scale-up by switching metabolic states, improving industrial production efficiency.