Fungi-inspired enzyme cocktails for fine-tuned deconstruction of plant biomass – FUNTUNE

The development of a bio-economy based on sustainable processes to transform renewable carbon sources as an alternative to fossil carbon chemistry is a major challenge. The lignocellulose contained in plant biomass is the most abundant biopolymer on earth and provides a renewable resource for bio-energy as well as for platform molecules aimed at new value-chains in bio-industry. However, cost-effective transformation of plant biomass is limited by the recalcitrance of lignocellulose and by its diversity in chemical composition. Plant biomass recalcitrance is mainly due to the crystalline structure of cellulose and to the presence of lignin, a polyphenolic polymer that restricts the accessibility of cellulosic enzymes to polysaccharides and strengthens the cell wall structure. Thermo-chemical pre-treatments are currently used to make the polysaccharide fractions amenable to enzymatic hydrolysis. In addition to their cost, these pre-treatments have negative environmental impacts. One promising alternative to thermo-chemical treatments is the development of eco-friendly enzymatic processes able to efficiently harness the recalcitrant lignocellulose. The second challenge is the chemical diversity of biomass feedstock. One response to this challenge is the development of enzymatic cocktails with high efficiency on a range of diverse biomasses.

In this project we propose to explore fungal enzymatic machineries in order to design new fungi-inspired enzyme cocktails able to mitigate recalcitrance of plant biomass from diverse sources. Plant-associated fungi have evolved enzymatic toolboxes to adapt to diverse host plants and lignocellulosic substrates. These enzymatic toolboxes are the key factors for finely tuned modification of plant cell walls during fungal growth. While fungal wood decayers use a large range of carbohydrate-acting enzymes (CAZymes) and oxidoreductases to degrade plant cell walls, symbiotic and biotrophic pathogenic fungi cause limited and targeted damage to plant cell walls leading to non - disruptive cell wall loosening. When switching from biotrophy to destructive necrotrophic growth, hemi-biotrophic plant pathogens secrete specific sets of enzymes that dramatically alter plant cell walls. Our purpose here is to identify and exploit the different sets of fungal enzymes associated with these different levels of plant cell wall deconstruction.

Using comparative analyses of available genomics and transcriptomics data, we will identify the sets of enzymes that are produced simultaneously by fungi when they alter plant cell wall structure or integrity. Fungal enzymes co-expressed upon growth on plant tissues will be used to develop optimised enzyme cocktails for the in vitro release of high value molecules from plant biomass. One original aspect of the project lies in the concomitant analysis of enzymes active on cellulose, hemicelluloses and lignin, as recent evidence has shown that synergistic effects arise from the combined action of enzymes on different cell wall components. As genetics tools are available for model plant pathogens and symbiotic fungi, the integration of these species into the study will allow further in planta functional analyses. The activity of the newly designed enzyme cocktails will be tested on model biomasses and on agriculture and forest co-products at the cell level as well as at the whole biomass level. Ultimately, we will identify high-value molecules released from each type of plant biomass after enzymatic treatment. Besides providing new enzymatic tools for green chemistry, the project will elucidate how wood decayers, symbiotic and pathogenic fungi modify plant cell walls to successfully establish within host tissues.