J. D. Keasling

Genetically refactored Agrobacterium-mediated transformation

This paper refactors the Agrobacterium tumor-inducing plasmid into a minimal set of genes for plant and fungal transformation, demonstrating a bottom-up engineering approach.

A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone

The paper identifies a Burkholderia polyketoacyl-CoA thiolase with significantly higher TAL production activity than 2-PS, achieving 2.8 g/L in E. coli fermentations.

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing

This study identifies genes and proteins involved in nitrogen metabolism in Pseudomonas putida using transposon sequencing and provides an interactive visualization tool for the data.

A synthetic RNA-mediated evolution system in yeast

This paper introduces CRAIDE, a method using RNA donors and CRISPR to evolve yeast genomes more efficiently than traditional methods.

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq

This study uses RB-TnSeq to functionally analyze fatty acid and alcohol metabolism in Pseudomonas putida, identifying gene roles and catabolic pathways for isoprenol and isopentanol.

REC protein family expansion by the emergence of a new signaling pathways

The paper identifies a mechanism of REC protein family expansion through gene recombination and positive selection, leading to functional divergence in bacterial response regulators.

Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida

This study identifies bottlenecks in T3PKS product production in Pseudomonas putida and shows that deleting a catabolic enzyme increases bisdemethoxycurcumin yield.

Chemoinformatic-guided engineering of polyketide synthases

This study uses chemoinformatics to engineer polyketide synthases for producing saturated β-carbon compounds, finding a correlation between chemical similarity and product titers.

Population dynamics analysis of Saccharomyces cerevisiae deletion library during fed-batch cultivation using Bar-seq

The paper uses Bar-seq to analyze population dynamics of a yeast deletion library during fed-batch cultivation, identifying genes associated with stress responses in industrial fermentation.

Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

This study engineers Pseudomonas putida to produce indigoidine with high titer, rate, and yield by coupling product formation with growth through metabolic rewiring and CRISPRi knockdowns.

Characterization of an ECF56-family sigma factor from Streptomyces venezuelae reveals a highly conserved regulome

This study characterizes the ECF56-family sigma factor from Streptomyces venezuelae, showing its C-terminal extension is conserved and regulates a highly conserved regulome across Actinobacteria.

Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

This study combines mechanistic and machine learning models to optimize tryptophan metabolism in yeast, achieving a 106% increase in tryptophan accumulation through predictive engineering.

Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase

This paper investigates the structural mechanism of regioselectivity in a bacterial acyl-CoA dehydrogenase, identifying key residues and structural features responsible for its unique substrate specificity.

Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis

This study investigates the role of hopanoid composition in the chemical tolerance of Zymomonas mobilis, showing that reduced hopanoid content and modified head group composition affect ethanol tolerance, while hopanoid amount influences low pH survival.

The response of Pseudomonas putida to a complex lignolysate

This paper shows that Pseudomonas putida can grow on lignolysate from sorghum, using aromatic monomers and other unknown factors like amino acids and ionic liquid.

The metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiency

This paper investigates the metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiencies, finding high metabolic flexibility that enables phenotypic stability but complicates metabolic engineering.

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

This paper uses RB-TnSeq to identify novel enzymes in Pseudomonas putida lysine metabolism, revealing new biochemical pathways and functions for DUF1338 proteins.

Engineered reversal of function in glycolytic yeast promoters

The paper reverses the regulatory function of glycolytic yeast promoters to enable induction under glucose-poor conditions and validates their use for vanillin biosynthesis.