(3hj) Xenobiosynthesis of Metabolism and Genetic Codes

In its infinite complexity, life has been able to leverage a relatively limited set of building blocks in constructing biomolecules. Carbohydrates, lipids, proteins, and nucleic acids possess diverse chemical properties that emerge from just a few unique monomeric units. Our own ability to repurpose biomolecules has led to technology that forms the basis of a wide range of industries from biotech to food manufacturing to bio-renewable fuels and plastics. In contrast to living systems however, synthetic chemistry approaches diversity through the use tailorable functional groups and building blocks. However, synthesis is generally challenged in obtaining structural complexity: large chiral molecules, such as biomolecules, are difficult and many times prohibitively expensive to construct synthetically. A more elegant union of these two strategies for making molecules (one biological and one synthetic) would greatly expand the building blocks available to life to include a larger range of functional groups with a more varied set of chemical and electronic properties.

My research aims to utilize fundamental approaches in synthetic biology, chemical biology, biosynthesis, genetics, and biomolecular engineering to reprogram life. Following a xenobiological paradigm, the goal is to both extend the amino acid, nucleic acid, and carbohydrates building blocks available in living systems for biosynthesis and to use newly expanded metabolism for producing biomolecules with unique chemical and physical properties.

Graduate Research:

For my thesis project, I proposed original research to expand the amino acid genetic code through reverse engineering of a natural biosynthetic pathway for terminal alkyne amino acids. This project aimed to push the biosynthetic boundaries with an emphasis on amino acid R-groups that are immediately relevant and useful in a wide variety of application areas. Through this work, I discovered and characterized a previously unknown pathway to produce a terminal alkyne-containing amino acid, β-ethynylserine (βes), made by the soil microbe Streptomyces cattleya. For the fields of chemical and synthetic biology, this metabolic pathway was a major discovery in that it is the first to offer the potential to genetically encode the de novo biosynthesis of halo, alkene, and alkyne amino acids that can be incorporated into proteins and peptides without exogenous feeding of additional synthetic components.

Postdoctoral Research:

In my postdoctoral work, I am establishing the foundation for building a parallel genetic code based on orthogonal tRNAs. Unlike traditional approaches, the genetic code I seek to build will be established from the ground-up. The key innovation driving this work is the generation of >20 mutually orthogonal tRNAs that could, theoretically, be used to generate a genetic code that can translate up to 32 additional amino acids or non-standard building block. Additionally, this work is developing new technology to meet the challenges presented by leveraging translational-independent directed evolution. The proposed work would be a major contribution in synthetic and chemical biology, integrating advances in expanded genetic codes with recent efforts at engineering orthogonal ribosomes. This work will provide the first in vivo proof that o-tRNAs can offer a potential biosynthetic route to complex biomolecules. Some exciting example include o-tRNAs can one day form the basis to produce novel biomolecules composed of >20 non-amino acid units or even enzymes composed entirely of D-amino acids.

Selected Publications:

1. Marchand, J. A., Neugebauer, M. E., Ing, M. C., Lin, C.-I., Pelton, J. & Chang, M. C. Y. Discovery of a pathway for terminal-alkyne amino acid biosynthesis. 2019. 567, 420-424.
2. Neugebauer, M. E., Sumida, K. H., Pelton, J. G., Mcmurry, J. L., Marchand, J. A. & Chang, M. C. Y. (2019). A family of radical halogenases for the engineering of amino-acid-based products. Chem. Biol. 15, 1009-1016.

3. Marchand, J. A., Pierson Smela, M. D., Jordan, T. H. H., Narasimhan, K. & Church, G. M. (2020). TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs. bioRxiv.