Thomas Eng

Adaptive laboratory evolution rewires Pseudomonas putida for resource-efficient acetate assimilation

This study improves acetate tolerance in Pseudomonas putida through adaptive laboratory evolution and identifies gacA and fabB as key targets for efficient acetate assimilation.

Functional Genomics Reveals TNT Bioremediation Strategies in Pantoea sp. MT58 and Pseudomonas putida KT2440

This study identifies distinct TNT bioremediation strategies in Pantoea sp. MT58 and P. putida KT2440 using proteomics and RB-TnSeq, revealing nitrogen assimilation versus stress tolerance mechanisms.

Simultaneous optimization of lignocellulosic sugar catabolism via systematic laboratory evolution in dynamic conditions

This study evolves a microbial strain under dynamic conditions to optimize sugar catabolism, finding that mixed-sugar environments promote stable retention and coordinated optimization of multiple pathways.

RB-TnSeq analysis reveals alcohol and salt tolerance systems in a plant root colonizer Paraburkholderia graminis OAS925

This study identifies tolerance mechanisms in Paraburkholderia graminis OAS925 to alcohol and salt stress using RB-TnSeq, revealing key genes involved in membrane transport, efflux systems, signaling, and oxidative stress response.

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

The paper uses a biosensor-driven strategy to enhance isoprenol production in Pseudomonas putida through combinatorial strain engineering and omics analysis.

Differences in GenBank and RefSeq annotations may affect genomics data interpretation for Pseudomonas putida KT2440

This study compares GenBank and RefSeq annotations for Pseudomonas putida KT2440, showing 16% of ORFs differ in genomic position and highlighting potential impacts on RNA-seq analysis.

Evolution guided tolerance engineering of Pseudomonas putida KT2440 for production of the sustainable aviation fuel precursor isoprenol

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.

Novel origin of replication for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

The paper identifies and validates novel plasmid origins of replication from an environmental Pantoea strain, enabling expression of heterologous proteins and pathways in both model and non-model bacteria.

Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in Pseudomonas putida

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

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

This study identifies fumarate hydratase activity as a bottleneck in a genome-scale metabolic model design for bioproduction from para-coumarate, requiring optimization for growth and product formation.

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

This study demonstrates the use of EcoFABs to measure horizontal gene transfer frequency in the rhizosphere of Brachypodium distachyon, showing dependencies on plant stage, root exudates, donor cell numbers, and environmental stress.

Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum using statistical design of experiments

This paper engineers Corynebacterium glutamicum to produce 2,3,5,6-tetramethylpyrazine (TMP) at high titer using statistical design of experiments to optimize media composition.

Development of Modular Expression and Genome Editing Across Phylogenetically Distinct Diazotrophs

The paper develops modular genetic tools for manipulating diverse diazotrophic bacteria to enable synthetic biology and genome editing.

Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

The paper develops growth-coupled microbial strains for high-yield indigoidine production using iterative engineering and computational evaluation.

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.

Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation under Ionic Liquid Stress

The paper resequences and analyzes transcriptomic changes in an engineered C. glutamicum strain under bioreactor conditions with and without ionic liquid stress.

High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production In Pseudomonas putida

The paper identifies gene deletions that enhance indigoidine production in Pseudomonas putida using fitness profiling and bioreactor experiments.