​Our Science

Teaching cells to create and harness non-standard amino acids

Proteins are incredible polymeric nano-machines and the molecular workhorses of cells. Despite their diversity of structure and function, their abilities are limited by the chemistry of the twenty standard amino acids used for protein synthesis. In my group, we program cells to create and utilize amino acids that can respond to a variety of stimuli, initiate various processes, and form chemical bonds with biologically orthogonal functional groups. By doing so, we endow living cells with the ability to autonomously access an expanded repertoire of protein biochemistry, which should be especially useful when creating live bacterial vaccines and therapeutics as well as for environmental applications.

Relevant publications:

Combined biosynthesis and site-specific incorporation of phenylalanine derivatives from aryl aldehydes or carboxylic acids in engineered bacteria​

A one-pot biocatalytic cascade to access diverse L-phenylalanine derivatives from aldehydes or carboxylic acids

Discovery of L-threonine transaldolases for enhanced biosynthesis of beta hydroxylated amino acids

A platform for distributed production of synthetic nitrated proteins in live bacteria

​(Review) Advances in engineering microbial biosynthesis of aromatic compounds and related compounds
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Advancing safeguards that control proliferation of engineered microbes

Living cells are capable of targeting regions of the body or influencing other organisms in the environment in unique ways. Synthetic biologists have created many tools to make engineered organisms more powerful and more useful in settings outside of traditional reactors, such as when administered to patients or released in the environment. To responsibly harness these new opportunities for engineered microbes, we need to better develop and characterize techniques for intrinsic biocontainment. Our lab focuses on synthetic auxotrophy, where an organism is engineered to depend on a synthetic nutrient for growth. By engineering a second organism to produce the synthetic nutrient, we have transitioned the system from a chemical dependence to a biological or ecological dependence. We are also interested in degradation of essential proteins or toxic proteins for further control of microbial survival.

Relevant publications:

Combinatorial mutagenesis of N-terminal sequences reveals unexpected and expanded stability determinants of the Escherichia coli N-degron pathway

Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid
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Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells

(Review) Deployment of engineered microbes: Contributions to the bioeconomy and considerations for biosecurity

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights​

​Engineering posttranslational proofreading to discriminate nonstandard amino acids​

Upgrading waste deconstruction products for polymer synthesis

The bulk of materials that we use in our daily lives are currently sourced from petroleum. Meanwhile, the majority of plastic that we use ends up in landfills, and the lignin that is leftover from products in forestry or agriculture is burned. These carbon-rich materials that are often discarded as waste can be broken down, but research is needed to identify efficient routes and end uses that justify the processing cost. At Delaware, we participate in two interdisciplinary projects where we collaborate with prominent researchers in catalysis and polymer science to create higher value materials from biomass and plastic wastes, starting with lignin and polyethylene terephthalate. We harness biocatalysis for selective introduction of chemical functional groups that add valuable properties to the resulting materials.

Relevant publications:
Robust cellular transformations of PET deconstruction products by import of glycol esters

Reductive enzyme cascades for valorization of polyethylene terephthalate deconstruction products

Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells

Genome engineering allows selective conversions of terephthalaldehyde to multiple valorized products in bacterial cells

Reductive amination cascades in cell-free and resting whole cell formats for valorization of lignin deconstruction products

​(Review) Innovations toward the valorization of plastic waste