Anaerobic fungi (Neocallimastigomycota) are native to the digestive tracts of ruminant and hindgut fermenting animals where they are central to the digestion of crude lignocellulosic materials. Anaerobic fungi secrete the largest known diversity of lignocellulolytic carbohydrate active enzymes (CAZymes) in the fungal kingdom (&gt;300 CAZymes), which unaided can degrade up to 60% of the ingested plant material. By combining PacBio DNA sequencing and HiC chromatin conformation capture sequencing, we have generated chromosome resolved reference genomes for 3 isolates of anaerobic fungi representing two genera. These high quality assemblies enable insight to the genome structure, organization, and strategies (e.g. horizontal gene transfer and gene duplication) by which gut fungi have evolved to robustly degrade plant biomass. We have also examined the extent of epigenetic regulation in anaerobic fungal genomes, including a catalog of the most abundant histone post translational modifications. Additionally, RNAseq and differential gene expression analyses of fungal cultures treated with epigenetic antagonists such as butyrate, SAHA, and 5’ Azacytidine lead to significant transcriptome remodeling. These treatments enable control of global H3K4 and H3K27 trimethylation and are correlated with up to a 100% increase in xylanase activity. Our studies show for the first time that early diverging anaerobic fungi use epigenetic mechanisms for gene expression and establish their role in lignocellulose hydrolysis. These reference genomes and omics datasets provide a treasure trove of genetic parts and reveal key design rules for future genetic engineering efforts in anaerobic fungi. Our work provides insight into the mechanisms that control anaerobic fungal plant-degradation abilities and takes a step towards the development of facile tools to enhance CAZyme activity for efficient plant degradation.

Multiomics analyses elucidate lignocellulolytic regulatory strategies in anaerobic fungi

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.