Chemical Engineering. Renewable chemicals derived from plant biomass (stems, stocks, and leaves, mainly composed of cellulose and lignin) are attractive sustainable alternatives to petroleum-based products. In nature, enzymes often break down cellulose into simple sugars, which can be later fermented into value-added chemicals. However, known biomass-degrading enzymes offer a very limited range of activities because cellulose is trapped within a tightly bound network of crystalline fibers and interwoven lignin. With the advent of next‐generation genomic sequencing (NGS), we now have the tools to identify, screen, and characterize novel enzymes from previously unexplored microbes and communities. John's project explores diverse fungi to identify enzymes that solubilize, reorganize, or degrade lignin. The focus of his study is anaerobic fungi (Neocallimastigales) in the digestive tract of large herbivores and aerobic litter-decomposing fungi (Basidomycota and Ascomycota), which are powerful degraders of unpretreated crude biomass.
John's enzyme discovery platform relies on deciphering well-established regulatory patterns for cellulolytic genes to identify novel lignin-active enzymes and non-catalytic adaptor modules. This approach, called Metatranscriptomic Identification of Novel Enzymes (MINE), takes advantage of advanced RNA sequencing technology to find genes that show a pattern of regulation expected for fungal cellulases and accessory enzymes. Genes for fungal cellulases and lignin-reorganizing enzymes are fully induced during growth on lignocellulose (reed canary grass), but repressed when a preferred, less complex carbon source is available (glucose, fructose). To search for genes that exhibit this pattern of catabolite repression, regulated mRNA is extracted from fungi grown on carbon substrates of variable lignocellulolytic complexity, ranging from least complex (glucose) to most complex (reed canary grass).
John presented at the 2016 ACS Meeting in San Diego in March, 2016 and will have a poster at the Synthetic Biology Engineering Evolution and Design (SEED) meeting in Chicago in July 2016.