Microbial Metabolic Engineering and Bioproduction

Competing constraints on protein availability and nutrient uptake reshape yeast genetic interactions

The paper shows that genetic interactions in yeast change with protein availability and nutrient uptake, revealing new insights into how metabolic constraints affect epistasis.

Machine-learning-guided enzyme discovery and redox-system engineering for efficient production of the nylon monomer methyl 12-aminododecanoate in Escherichia coli

This study uses machine learning to discover enzymes for producing ADAME in E. coli, achieving a 5.6-fold improvement over existing methods.

Glycerol alone effects 1,3-propanediol production via the aerobic propanediol utilization pathway in Salmonella enterica

This study shows Salmonella enterica can produce 1,3-propanediol from crude glycerol using the propanediol utilization pathway without high cofactor concentrations.

Adaptive laboratory evolution of a yeast co-culture chassis for modular bioproduction

This study uses adaptive laboratory evolution to optimize a yeast co-culture chassis for bioproduction, showing improved growth and production performance compared to monocultures.

Adaptive Laboratory Evolution (ALE) enables carbon-negative mixotrophic fermentation and enhanced chain elongation in Clostridium sp. JS66

This study evolves Clostridium sp. JS66 to enhance CO2 reassimilation and chain elongation, achieving carbon-negative fermentation of glucose to hexanoic acid.

Net conversion calculations of catabolic pathways

This paper introduces a computational framework to calculate net conversions in metabolic networks using elementary flux modes and thermodynamic parameters, with applications in microbial ecology and metabolic engineering.

Multi-Species, Genome-Wide Metabolic Network Reconstructions Reveal the Basis for Metabolic Versatility in Mycobacteria

The paper develops genome-scale metabolic models for five Mycobacterium species to test if metabolic versatility stems from nutrient uptake capabilities, finding that transporters and substrate availability are key.

Unbiased and scalable reduction of diverse bacterial genomes

This paper introduces SLIM, a method for unbiased genome reduction in diverse bacteria, and demonstrates its application in Escherichia coli and other species.

Beyond benchmark accuracy: machine-learning turnover-number predictors require system-level validation

The paper evaluates machine learning predictors of enzyme turnover numbers (kcat) by testing their impact on downstream metabolic models, finding that accuracy varies significantly and that validation must consider system-level effects.

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

PhysiCelldFBA links single-cell metabolism to multicellular spatial dynamics by integrating genome-scale metabolic models with agent-based simulations.

Conjugative serine recombinase engineering enables genome integration in transformation-resistant bacteria and bioproduction pathway prototyping

This paper introduces cSAGE, a conjugation-based genome engineering platform that enables site-specific integration in transformation-resistant bacteria, demonstrating its utility in bioproduction pathway prototyping.

Engineering Biosensors to Enhance Monoterpene Indole Alkaloid Production in Yeast

This study develops biosensors for MIAs and identifies metabolic engineering hits to enhance MIA production in yeast.

Improving acetate metabolism of Pseudomonas putida KT2440 by evolutionary and rational engineering

This paper improves acetate metabolism in P. putida KT2440 through rational and evolutionary engineering, enhancing growth rate and HAA production.

Combinatorial metabolic engineering of alkane biosynthesis in the osmotolerant yeast Debaryomyces hansenii CBS 767

This paper enables combinatorial metabolic engineering in Debaryomyces hansenii by developing genetic parts and integration loci, resulting in a high titer of heptadecane production.

Dynamic Control of Prokaryotic Chromosome Ploidy Rewires Metabolic Networks to Enhance Product Biosynthesis

This paper develops a dynamic polyploid engineering strategy that enhances L-threonine production by coupling chromosome ploidy to metabolic state during fermentation.

Alcohol dehydrogenase-mediated methanol dissimilation increases carbon efficiency in synthetic autotrophic yeast

This study improves carbon efficiency in autotrophic yeast by redirecting methanol dissimilation through alcohol dehydrogenase, increasing biomass yield and product titers.

Flux balance analysis of microbial communities from metabolic strategies: composition, cross-feeding and ecological service

The paper introduces a simplified cFBA method to predict microbial community composition, growth rates, and metabolic interactions by reducing species metabolism to macrochemical equations.

Decoding Tumour-Specific Rewiring and Synthetic Lethality Through Genome-Scale Metabolic Models

The paper builds genome-scale metabolic models for eight cancer types to identify tissue-specific metabolic rewiring and synthetic lethal gene pairs supported by computational validation.

Expression landscape of metabolic engineering enzymes in cyanobacteria

The paper quantifies protease-mediated degradation of heterologous enzymes in cyanobacteria and compares expression between E. coli and Synechocystis.

Growth costs of protein allocation in models of growing cells

The paper models growth costs of suboptimal protein allocation in microbial cells using growth balance analysis, showing how protein levels affect growth rates and fitness.

Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies

This paper develops a framework combining machine learning and metabolic modeling to predict synergistic cancer therapies influenced by microbiome composition in colorectal cancer.

Gas uptake stoichiometry governs carbon partitioning in syngas-fermenting Clostridium autoethanogenum

This study quantifies how syngas composition affects growth and metabolite production in Clostridium autoethanogenum during fermentation.

Engineering growth-coupled metabolic biosensors for disease prognosis and diagnosis using full growth trajectories

This paper develops growth-coupled metabolic biosensors for disease detection and prognosis using COVID-19 as a proof-of-concept, achieving high diagnostic and prognostic accuracy.

ContiDesigner: Bioprocess Intensification through System-Level Design of Continuous Fermentation Cascades

ContiDesigner is a tool for designing continuous fermentation cascades that identifies optimal operating conditions to maximize productivity.

Production of diverse retinal analogues in engineered Escherichia coli through promiscuous carotenoid cleavage by Blh

This paper demonstrates the biosynthesis of diverse retinal analogues in engineered E. coli using Blh, a carotenoid cleavage enzyme, through substrate promiscuity and structure-guided engineering.

Improved Metabolic Flux Estimations through Compositional Data Analysis

This paper improves metabolic flux estimation by applying compositional data analysis to isotopic metabolic flux analysis, reducing mean squared error and narrowing confidence intervals.

VariantFlux: A genotype-first modelling workflow for predicting the impact of genetic variations on human metabolism

VariantFlux integrates variant interpretation into genome-scale metabolic models to predict metabolic flux changes from genetic variation in kidney tissue.

Genetic and Biochemical Characterization Reveals PduU as a Modular Tool for Tuning Pdu Microcompartment Permeability

This study shows that modifying PduU, a shell protein in bacterial microcompartments, tunes permeability without disrupting structure, enhancing propionate production.

A benchmarking framework for single-cell genome-scale metabolic model construction

This study benchmarks strategies for constructing single-cell genome-scale metabolic models across nine scRNA-seq datasets, evaluating accuracy, sensitivity, and computational feasibility.

Combinatorial optimization of protein systems in synthetic cells

The paper optimizes synthetic protein systems in vitro by screening combinatorial DNA variants to identify optimal gene expression and functionality.