Projects and Publications

Bacterial catabolism of acetovanillone

Bacteria are uniquely capable of catabolizing the aromatic compounds generated during lignin depolymerization, however, many of these catabolic pathways have not yet been elucidated. Acetovanillone, a key component in various industrial lignin streams, including black liquor from the Kraft pulping process and oxidative catalytic fractionation of softwood biomass, has been a focus of our research. 

Objectives

We set out to characterize a novel metabolic pathway using a multifaceted approach including enrichment cultures, whole genome sequencing, transcriptomics, and enzymatic studies. 

Results

This study identified two Rhodococcus rhodochrous strains, GD01 and GD02, capable of metabolizing acetovanillone as the sole carbon source. Transcriptomic analyses highlighted a unique hydroxyphenylethanone (Hpe) pathway, involving phosphorylation, carboxylation, and β-elimination, facilitating degradation of hydroxyphenylethanones including 4-hydroxyacetophenone and acetovanillone. 

High-throughput genetic engineering via iterative site-specific genome integration

Objectives

The application of synthetic biology is often limited by the lack of effective genetic tools for high-throughput genome engineering, particularly in environments where antibiotic selection is impractical. These issues are especially problematic for microbes used in industrial reactors, agriculture, and bioremediation. We developed a high-throughput method for genetic engineering of nonmodel bacteria using a serine integrase system for iterative site-specific genome integration.

Results

We developed a serine integrase-based method that enables multiple rounds of precise genetic insertions, demonstrating high-throughput capabilities for generating and screening large libraries of genetic variants. This system was effective across diverse bacterial species, including nonmodel and undomesticated bacteria, showcasing its broad applicability. The study highlighted the method's ability to perform complex genetic modifications, advancing research in gene function and metabolic pathways, and facilitating new biotechnological applications. Overall, the results indicate that this serine integrase system overcomes significant limitations of traditional genetic manipulation methods, providing a powerful tool for high-throughput genetic engineering.