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From Biosynthesis to Functional Biomaterials

Microbes and plants synthesize a tremendous diversity of chemical compounds that is unmatched by chemical synthetic methods. These compounds are of a great interest for the discovery of new pharmaceuticals, as fine chemicals and chemical building blocks. The structural complexity of many of these molecules makes their production using synthetic approaches challenging. Biological systems use enzymes with different functions as catalysts to achieve biosynthesis of complex molecules at room temperature and in the absence of organic solvents. Advances in genetic methods makes and increasing knowledge of biosynthetic processes in a molecular level makes it possible to identify, isolate and combine enzyme function encoded by genes obtained from different organisms into new biosynthetic pathways in engineered cells for the bioproduction of desired compounds. Likewise, individual enzymes can be recombinantly produced and the purified proteins combined to carry out a series of biocatalytic reactions to synthesize target chemicals. We are interested in exploring and utilizing the metabolic manchineries of biological systems to enable the sustainable production of valuable chemicals in engineered microorganisms or by combining isolated enzymes in cell-free biocatalytic systems.

We are currently pursuing two major research focus areas: In one focus area, we are exploring and harnessing the unique biosynthetic and redox catalytic machineries of higher fungi. We are screening and characterizing the unique portfolios of bioactive compounds (natural products) made by mushrooms by building a field-to-lab biobank and identifying their biosynthetic pathways and oxidative enzymes. Another focus in our lab is the design of genetically programmable and self-assembling protein-based nanoarchitectures for applications in biocatalysis, biosynthesis, and for the fabrication of new types of self-assembling bio-nanomaterials for a variety of applications.

Natural Products and Enzymes from Fungi

Mushrooms (Basidiomycota) have been used for centuries in traditional medicine, and they are known to produce a range of unique chemicals, many of them with demonstrated antimicrobial, cytotoxic, immune-modulating and anti-inflammatory activities. Yet, the biosynthetic pathways that make these molecules in this group of fungi are largely unknown. We are identifying and characterizing the biosynthesis of novel compounds in this fascinating class of organisms. Over the past several years, we have investigated the biosynthesis of isoprenoid natural products in mushrooms. These compounds represent the largest class of natural products and are the major class of bioactive molecules made by mushrooms. We have identified and characterized the biosynthesis of one group of pharmaceutically important isoprenoids - the sesquiterpenes - in several mushroom species, which led to the development of a predictive, bioinformatic framework for this class of compounds.

Through this work, we have developed significant experience in the cultivation, screening, genome mining and sequencing, and heterologous expression and biochemical characterization of genes and pathways from Basidiomycota. In ongoing research, we are taking advantage of our expertise with this class of fungi by building a unique Field-to-Laboratory Biobank of Midwestern mushrooms that we are screening for the discovery of novel bioactive natural products. Mushrooms have also evolved the unique ability to degrade recalcitrant lignocellulose, ending the carboniferous period by allowing recycling of carbon bound in the lignin of dead plant material. They have become masters of oxidative biocatalysis performed by novel and expanded families of many different types of oxidoreductase enzymes. These types of enzymes are of great utility for the biomanufacturing of chemicals. We are therefore searching our mushroom strain collection for enzymes with new activities that we can use to synthesize desired chemicals. Our goal is the creation of a biocatalyst toolkit that will enhance our bioproduction capabilities.

Design of Self-assembling Protein Structures 

In biological systems, proteins, nucleic acids and lipids are precisely organized to form higher ordered structures. Principles underlying the assembly and organization of natural bionanomaterials can be harnessed for the design and fabrication of robust materials for biocatalysis and as functional biomaterials with emergent properties. Self-assembly provides a low-cost approach for bottom-up construction of supramolecular biomaterials from simple building blocks. Principles underlying these processes have inspired the design of self-assembling biomaterials across multiple scales for a different of applications. By varying building block composition, molecular structures and environmental conditions, assemblies can be controlled and altered by changing interaction types and strengths. Peptides and proteins offer the most versatility for the assembly of such designed structures due to the chemical diversity of their amino acid components. Unlike nucleic acid-based structures, protein materials are highly robust and can be readily modified and tailored for desired applications. Importantly, materials built from protein building blocks are genetically encoded. As such, they are programmable and can be produced recombinantly at low cost. By engineering a suitable recombinant production host, biofunctionalized, self-assembling protein materials may be produced in situ at the site of application.

We are designing and characterizing different types of self-organizing protein nanomaterials for biocatalysis and as biomaterials. We have designed a versatile platform of self-assembling protein scaffolds for the easy co-immobilization of biocatalysts. By modifying the stoichiometries of biocatalyst cargo proteins, scaffold building blocks with different peptide tags and scaffold building block variants, we can build different architectures with different surface properties and spatially organized enzyme cargo. We have used this platform to optimize the efficiency of an industrially relevant biocatalytic system. Because process efficiency is key for the cost-competitive use of enzyme-based processes in biomanufacturing, we are applying our programmable scaffolding system for the design of other multi-enzyme processes for the production of valuable molecules. For the design of different types of biomaterials, including self-healing, living materials for different applications, we are engineering our self-assembling protein building blocks with a range of different functionalities. Because the our building blocks are genetically encoded, our biomaterials platform is highly configurable.