Skip to main content
Epigenetic regulation of anaerobic fungi for increased lignocellulose degradation
This project studies the impact of epigenetic regulation in anaerobic fungi to develop strategies that control lignocellulolytic enzyme expression and activity for increased lignocellulose breakdown. Anaerobic (gut) fungi are powerful digesters of fiber-rich plant materials within the digestive tracts of large herbivores, which possess one of the largest-known, and tightly-regulated fungal repertoires of lignocellulolytic enzymes (CAZymes; carbohydrate active enzymes). These CAZymes degrade a wide array of lignin-rich cellulosic biomass, including untreated agricultural residues, bioenergy crops, and woody biomass with high efficiency due to the precise combination of enzymes secreted. In so doing, anaerobic fungi create custom CAZyme cocktails with substrate to maintain sugar release efficiency, regardless of substrate composition. However, no tools currently exist to perturb this response, thereby enabling studies into the role of specific enzymes within the fungal cocktail, nor do means exist to induce CAZyme expression for production on simple substrates. Our recent work with epigenetic inhibitors demonstrates that anaerobic fungi possess defined global epigenetic states that may be altered, which are correlated with changes in CAZyme activity and expression. That is, supplementation with chemical inhibitors is a potent tool to induce anaerobic fungal CAZyme expression and tune functionality for precisely-defined CAZyme cocktails. In this proposal we seek to characterize the magnitude of epigenetic regulation globally on specific transcript and protein expression profiles in anaerobic fungi, and associate them with specific histone and DNA modifications at gene loci. We also aim to characterize local chromatin structure around these modifications to evaluate the mechanisms of regulation, and identify promising epigenetic targets for further engineering. Finally, we examine the significance of epigenetic mechanisms in natural substrate-specific regulation of fungal CAZyme activity. We propose to use the strengths of the EMSL and JGI to uncover the design principles of anaerobic fungal epigenetic regulation in 3 distinct species. Specifically, we request 250 Gbp of PacBio and Illumina HiSeq sequencing capacity at the JGI, and 156 h instrument time on the Orbitrap at EMSL for bottom-up proteomic analysis. This research addresses the FY19 FICUS Focused Topic Area of Biofuels and Bioproducts by investigating the biosystem design & dynamics of under-represented early-diverging anaerobic fungi with significant potential for biomass deconstruction. This study will characterize the regulation of anaerobic fungal CAZymes by epigenetic mechanisms, and develop strategies to precisely tune CAZyme activity and function in anaerobic fungi.