Microbial Metabolic Engineering and Bioproduction

The paper investigates whether microbial cells can reduce entropy production rate by shifting to less thermodynamically driven metabolism at faster growth rates, using yeast models and experimental data.

This paper engineers a biotin-independent Saccharomyces cerevisiae strain by bypassing acetyl-CoA carboxylase, enabling growth without biotin and improved malonate utilization.

This study evolves a unique Acinetobacter baylyi strain through a two-step adaptive laboratory evolution process to improve lignin valorization capabilities.

This study genetically engineers a probiotic yeast to produce abscisic acid (ABA) in the gut, but finds low serum ABA levels due to temperature-dependent production challenges.

This paper reports the de novo production of prenylnaringenin compounds in Escherichia coli using metabolic engineering and CRISPR-Cas12a to boost DMAPP availability.

This paper introduces SubNetX, a computational algorithm that extracts and assembles balanced reaction subnetworks for producing target biochemicals, and demonstrates its application to eight secondary metabolites and one non-natural chemical.

COSMOS compares microbial monocultures and communities to identify optimal systems for specific carbon sources and environments, finding Shewanella oneidensis-Klebsiella pneumoniae community most efficient for 1,3-propanediol production under anaerobic conditions.

This paper develops a genome-scale metabolic model of S. epidermidis that accurately predicts growth and carbon source utilization under in vitro conditions.

The paper uses genome-scale metabolic models to identify causal reactions influenced by SNP-SNP interactions affecting yeast sporulation efficiency.

This study uses adaptive laboratory evolution and rational engineering to improve Pseudomonas putida's tolerance to isoprenol, enhancing its production of a sustainable aviation fuel precursor.

This study improves D-lactic acid production from methanol in Komagataella phaffii using UV mutagenesis, achieving a 1.52-fold increase through transcriptome-guided metabolic engineering.

This study deletes AOR genes in C. ljungdahlii and shows changes in ethanol and acetic acid production with different carbon sources.

The paper describes a collaborative curation workshop to improve the metabolic reconstruction of Alteromonas macleodii ATCC 27126 using genomic and physiological data, identifying key metabolic pathways and gaps.

This paper improves isobutene production in Synechocystis sp. PCC 6803 by engineering the promiscuous RnKICD enzyme to enhance its selectivity for KIC over HPP, resulting in a 4-fold increase in isobutene yield.

This study evaluates the toxicity of methanol, formaldehyde, and formate on Yarrowia lipolytica growth, finding varying tolerance levels and demonstrating formate's utility in improving lipid production.

The paper introduces CHASING, a method for gain- or loss-of-function screening using chromosome-segment deletions, and applies it to identify metabolic engineering targets in B. subtilis.

This study investigates the role of signal sequences in bacterial microcompartment (MCP) assembly, showing that structural protein signal sequences are critical for MCP formation and that their deletion causes defects similar to full gene knockout.

The paper engineers Parageobacillus thermoglucosidasius to use methanol via the RuMP cycle for growth, achieving 17% biomass from methanol without heterologous enzyme expression.

This paper engineers a carbon-conserving cell-free system in E. coli to produce malate from formate and bicarbonate, achieving a 15-fold increase in titer and reducing background reactions by 6-fold.

This study evaluates the ability of Vibrio natriegens to produce nicotinamide mononucleotide (NMN) through metabolic engineering, finding that NAMPT from Chitinophaga pinensis yields the highest intracellular NMN concentration.

This paper develops a genome-scale metabolic model for Treponema pallidum, identifies glycerol-3-phosphate dehydrogenase as an alternative electron sink, and validates its predictive accuracy with proteomics data.

This paper demonstrates the de novo biosynthesis of cannabinoids and their analogs in Yarrowia lipolytica through metabolic engineering.

Seed2LP predicts nutritional requirements (seeds) for microorganisms using hybrid metabolic modeling, improving seed inference over graph-based methods in genome-scale metabolic networks.

The paper integrates RNA-seq-based genomic variants and gene expression data to reconstruct personalized metabolic models for Alzheimer's disease, showing improved detection of AD-associated metabolic pathways.

This paper develops acetate-tolerant Pseudomonas putida strains for isoprenol production using mixed carbon sources and identifies molecular mechanisms underlying tolerance and production.

The paper introduces SubtiToolKit, a cloning toolkit for Bacillus subtilis and Gram-positive bacteria, enabling efficient DNA construct design for various genetic applications.

The paper compares a reduced-genome Rhodopseudomonas strain to others, finding it retains core metabolic versatility but lacks genes for high-affinity transport and biodegradation.

This paper demonstrates the efficient conversion of formate into methyl groups in engineered Escherichia coli using SAM-dependent methyltransferases, achieving over 70% formate-derived methyl groups.

The paper shows that the Z. mobilis ndh promoter is strongly induced by oxygen, making it a strong candidate for metabolic engineering.

This study investigates why engineered E. coli strains for formate utilization do not reach theoretical biomass yields and identifies metabolic bottlenecks and evolutionary changes to improve them.