Microbial Metabolic Engineering and Bioproduction

Yeast-MetaTwin for Systematically Exploring Yeast Metabolism through Retrobiosynthesis and Deep Learning

The paper develops Yeast-MetaTwin, a metabolic model for yeast that expands coverage of the metabolome using retrobiosynthesis and deep learning, revealing new insights into underground metabolism.

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

This paper introduces RENAISSANCE, a generative machine learning framework that accurately characterizes intracellular metabolic states by parameterizing kinetic models using omics data and experimental observations.

Genomically recoded Escherichia coli with optimized functional phenotypes

This study identifies and corrects fitness defects in genomically recoded E. coli, improving growth and functional capabilities.

Coenzyme A biosynthesis in Bacillus subtilis: Discovery of a novel precursor metabolite for salvage and its uptake system

This study identifies a novel salvage pathway for coenzyme A in Bacillus subtilis, involving the uptake of cysteinopantetheine via a cystine transporter.

Multi-omics data and model integration reveal the main mechanisms associated with respiro-fermentative metabolism and ethanol stress responses in Kluyveromyces marxianus

The paper uses multi-omics integration to identify mechanisms of ethanol stress response and respiro-fermentative metabolism in Kluyveromyces marxianus.

Expanding the biotechnological scope of metabolic sensors through computation-aided designs

This paper presents a computational workflow for designing and testing E. coli metabolic sensors that detect glyoxylate and glycolate across a wide concentration range, with applications in bioengineering and environmental monitoring.

A demand-based framework explains prioritization strategies upon transient limitations of different amino acids.

The paper shows cells prioritize restoring amino acids based on demand and biosynthetic cost, with arginine being the highest priority.

Genomically integrated orthogonal translation in Escherichia coli, a new synthetic auxotrophic chassis with altered genetic code, genetic firewall, and enhanced protein expression

This paper develops a genomically integrated orthogonal translation system in E. coli, enabling non-canonical amino acid incorporation and creating a biosafe synthetic chassis for enhanced protein production.

Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor

This paper introduces Nox Ortho, an enzyme that enables precise control of redox reactions using NMN+ as a cofactor, achieving high specificity and enabling chiral-pure product synthesis.

A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates

This study presents a cell-free biocatalytic system for converting one-carbon substrates into acetyl-CoA using a synthetic pathway called ReForm.

MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networks

MMINT provides an interactive tool for exploring and comparing metabolic networks derived from genome-scale models to identify metabolic drivers of phenotypes.

A quantitative description of light-limited cyanobacterial growth using flux balance analysis

This paper develops a novel flux balance analysis approach for light-limited cyanobacterial growth, incorporating photoinhibition and variable quantum yield to predict growth properties.

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes

PhysioFit quantifies cell growth parameters and extracellular fluxes using flexible growth models and provides a user-friendly software tool for non-computational biologists.

Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology

The paper measures the growth burden of 301 BioBricks in E. coli and finds that 19.6% reduce growth, with most burdens explained by gene expression resource diversion.

Systematic analysis of microorganisms' metabolism for selective targeting

The paper systematically analyzes genome-scale metabolic models of six microorganisms to identify multi-target drug candidates that selectively target specific organisms.

Efficient production of itaconic acid from the single carbon substrate methanol with engineered Komagataella phaffii

This study engineers Komagataella phaffii to produce itaconic acid from methanol, achieving titers of 55 g/L and a yield of 0.24 g/g.

Expanded Genome and Proteome Reallocation in a Novel, Robust Bacillus coagulans Capable of Utilizing Pentose and Hexose Sugars

This study characterizes a novel robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars, revealing proteome reallocation and metabolic strategies for biomass hydrolysate utilization.

Enhancing the accuracy of genome-scale metabolic models with kinetic information

This paper combines constraint-based and kinetic metabolic models to improve flux bounds in genome-scale models, enhancing predictive accuracy for E. coli growth and citramalate production.

Bioinformatic prediction and high throughput in vivo screening to identify cis-regulatory elements for the development of algal synthetic promoters

The paper identifies cis-regulatory elements in algae to create synthetic promoters, validated through in vivo testing and high-throughput screening.

Shikimate pathway-Dependent Catabolism:enabling near-to-maximum production yield of aromatics

This study redesigns bacterial catabolism by repurposing the shikimate pathway for aromatic compound production, achieving over 89% of theoretical yield.

Cybernetic control of a natural microbial co-culture

This paper demonstrates a cybernetic control method for microbial co-cultures using temperature adjustments to stabilize composition without genetic engineering.

Fast-track adaptive laboratory evolution of Cupriavidus necator H16 with divalent metal cations

This paper introduces an accelerated adaptive laboratory evolution (aALE) method using divalent metal cations to improve microbial tolerance to high glycerol concentrations in Cupriavidus necator H16.

Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

The paper uses machine learning and metabolic modeling to show phosphoglycerate mutase is critical for Chlamydia trachomatis persistence under nutrient starvation.

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

The paper reconstructs pangenomes of Lactobacillaceae to generate metabolic models for 26 species, enabling species-specific metabolic trait predictions.

Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models

The paper introduces MACAW, a workflow for detecting errors in genome-scale metabolic models, showing that error types vary with curation methods and that pathway-level errors are particularly challenging.

Comparative Approaches for Quantification of Product Yield in the Production of Recombinant Green Fluorescent Protein (GFPuv) Expressed in E. coli

The paper compares methods for quantifying GFPuv yield in E. coli bioreactors, identifying optimal harvest times and highlighting the strengths of imaging over other techniques.

Logistic PCA explains differences between genome-scalemetabolic models in terms of metabolic pathways

The paper introduces logistic PCA (LPCA) to compare genome-scale metabolic models by identifying mechanistic differences in metabolic pathways across diverse datasets.

Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models

Panera improves microbial community metabolic modeling by integrating 16S data with pan-genus models, reducing prediction error by 10%.

GENTANGLE: integrated computational design of gene entanglements

GENTANGLE is a computational tool for designing overlapping gene pairs in microbial genomes, enabling safer genetic engineering through gene entanglements.

Engineering Rhodosporidium toruloides for sustainable production of value-added punicic acid from glucose and wood residues

This study engineering Rhodosporidium toruloides to produce punicic acid from glucose and wood residues, achieving 12% lipid accumulation and 451.6 mg/L titer in shake flasks.